Contacts of the helix formed by residues 107 - 142 (chain A) in PDB entry 2C3E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLY 4.2 3.5 - - - +
102A VAL* 3.3 31.0 - - + +
103A ASP* 3.1 13.9 + - - +
104A ARG 4.0 3.4 - - - -
105A HIS 3.5 0.2 - - - -
106A LYS* 1.3 94.5 - - + +
108A PHE* 1.3 66.3 + - - +
109A TRP 3.5 2.0 - - - -
110A ARG* 3.5 25.4 + - + +
111A TYR* 3.1 22.9 + - - +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 3.8 17.1 + - + +
105A HIS 5.0 1.7 + - - +
106A LYS 4.1 0.2 - - - -
107A GLN* 1.3 74.5 - - - +
109A TRP* 1.3 110.0 + + + +
111A TYR* 3.3 4.7 + - - +
112A PHE* 2.9 37.1 + + - +
192A GLY* 6.3 0.4 - - - -
195A ASP* 4.0 37.7 - - + -
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Residues in contact with TRP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN 3.5 0.4 - - - -
108A PHE* 1.3 103.8 - + + +
110A ARG* 1.3 60.5 + - - +
111A TYR 3.1 1.8 - - - -
112A PHE* 3.2 27.0 + + + +
113A ALA* 3.0 30.1 + - - +
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE 5.1 2.6 + - - -
98A PHE* 2.8 32.1 + - - +
99A LEU* 4.6 0.2 - - - +
100A GLY 4.6 4.2 + - - -
102A VAL* 3.6 35.3 - - + +
107A GLN* 3.5 27.6 + - + +
108A PHE 3.4 0.6 - - - -
109A TRP* 1.3 78.8 - - - +
111A TYR* 1.3 55.2 + - - +
113A ALA* 4.7 5.6 - - - +
114A GLY* 3.2 21.3 + - - +
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Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.5 37.6 - - + +
102A VAL* 3.3 28.9 - - + +
104A ARG* 3.6 62.9 + - + -
107A GLN 3.1 18.0 + - - +
108A PHE* 3.4 6.1 - - - +
109A TRP 3.1 0.6 - - - -
110A ARG* 1.3 77.7 - - - +
112A PHE* 1.3 66.1 + - - +
115A ASN* 3.0 36.7 + - + +
191A PHE* 6.2 0.4 - + - -
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 2.9 31.5 + + + +
109A TRP* 3.4 34.1 - + + +
111A TYR* 1.3 80.4 - - - +
113A ALA* 1.3 64.2 + - - +
115A ASN* 3.6 5.6 + - - +
116A LEU* 3.0 48.3 + - + +
188A ALA* 3.5 31.6 - - + -
191A PHE* 4.3 11.4 - - + -
192A GLY* 3.9 25.4 - - - -
195A ASP* 4.5 4.7 - - - -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TRP 3.0 15.9 + - - +
110A ARG* 4.3 7.9 - - - +
112A PHE* 1.3 78.5 - - + +
114A GLY* 1.3 66.7 + - - +
116A LEU* 2.9 21.9 + - - +
117A ALA* 3.0 15.2 + - - +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.4 15.9 - - - +
99A LEU* 3.6 10.3 - - - -
110A ARG* 3.2 31.8 + - - +
113A ALA* 1.3 77.9 - - - +
115A ASN* 1.3 56.7 + - - +
117A ALA* 4.6 2.0 - - - -
118A SER* 2.8 29.6 + - - -
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.4 21.8 - - + +
111A TYR* 3.0 31.6 + - + +
112A PHE* 3.6 6.2 + - - +
114A GLY* 1.3 74.0 - - - +
116A LEU* 1.3 67.4 + - - +
118A SER* 3.5 5.7 - - - -
119A GLY 3.0 10.0 + - - -
187A ARG* 3.0 43.8 + - - +
191A PHE* 3.3 43.4 - - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.0 39.5 + - + +
113A ALA* 2.9 11.9 + - - +
115A ASN* 1.3 75.9 - - - +
117A ALA* 1.3 55.1 + - - +
119A GLY* 2.9 3.1 + - - -
120A GLY* 2.5 35.7 + - - -
184A ILE* 3.8 31.8 - - + +
187A ARG* 4.1 15.2 - - + +
188A ALA* 3.7 37.7 - - + +
191A PHE* 6.3 0.2 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.7 28.9 - - + -
113A ALA 3.0 11.7 + - - +
114A GLY* 3.7 5.2 - - - +
116A LEU* 1.3 79.2 - - - +
118A SER* 1.3 57.7 + - - +
120A GLY* 4.2 2.7 - - - +
121A ALA* 2.7 36.4 + - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 4.6 0.3 + - - +
94A TYR* 3.8 14.2 - - - +
95A LYS* 3.4 35.0 + - - +
98A PHE* 3.7 13.2 - - - -
99A LEU* 4.5 4.6 - - - +
114A GLY 2.8 20.7 + - - -
115A ASN* 3.5 14.7 + - - -
116A LEU 3.1 0.2 - - - -
117A ALA* 1.3 79.0 - - - +
119A GLY* 1.3 61.3 + - - +
122A ALA* 3.3 21.1 + - - +
187A ARG* 5.6 0.9 + - - -
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN 3.0 7.5 + - - -
116A LEU 2.9 6.2 + - - -
118A SER* 1.3 74.6 - - - +
120A GLY* 1.3 65.6 + - - +
122A ALA* 4.1 4.6 - - - +
123A GLY* 3.0 21.7 + - - -
183A ILE* 4.3 7.8 - - - +
187A ARG* 3.6 30.0 - - - +
401A CXT 5.1 1.7 - - - +
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Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU 2.5 21.7 + - - -
117A ALA* 3.5 2.2 - - - -
119A GLY* 1.3 73.5 - - - +
121A ALA* 1.3 62.3 + - - +
123A GLY* 3.9 0.5 - - - -
124A ALA* 3.0 24.8 + - - +
180A VAL* 5.3 5.6 - - - +
183A ILE* 4.7 6.9 - - - +
184A ILE* 4.4 23.5 - - - +
187A ARG* 4.7 0.2 - - - +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 3.7 33.8 - - + +
98A PHE* 3.9 12.1 - - + -
117A ALA* 2.7 20.3 + - - +
118A SER 4.2 0.2 - - - +
120A GLY* 1.3 72.7 - - - +
122A ALA* 1.3 63.0 + - - +
124A ALA* 3.3 6.9 + - - +
125A THR* 3.0 25.5 + - - -
802A CDL 4.5 8.5 - - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASN* 5.1 8.5 - - - +
90A PHE* 5.5 0.7 - - + -
91A LYS* 4.5 23.6 - - + +
94A TYR* 3.5 21.5 - - + -
118A SER 3.3 16.4 + - - +
119A GLY* 4.1 4.9 - - - +
121A ALA* 1.3 77.1 - - - +
123A GLY* 1.3 64.2 + - - +
125A THR* 3.0 5.2 + - - -
126A SER* 3.0 23.8 + - - -
401A CXT 5.0 2.2 - - - +
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLY 3.0 16.5 + - - -
120A GLY 3.9 0.7 - - - -
122A ALA* 1.3 76.6 - - - +
124A ALA* 1.3 55.3 + - - +
126A SER* 2.6 20.7 + - - -
127A LEU* 2.9 21.0 + - - +
183A ILE* 4.3 12.8 - - - -
401A CXT 3.4 25.0 + - - -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY 3.0 17.3 + - - +
121A ALA* 3.6 7.4 - - - +
123A GLY* 1.3 73.9 - - - +
125A THR* 1.3 57.4 + - - +
127A LEU* 3.7 2.7 - - - +
128A CYS* 3.0 28.1 + - - +
176A PHE* 3.9 9.9 - - + -
180A VAL* 3.9 31.1 - - + +
183A ILE* 5.1 0.4 - - - +
802A CDL 4.7 17.8 - - + +
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 5.3 7.4 - - + -
90A PHE* 4.1 29.6 - - + -
94A TYR* 2.9 28.6 + - - -
121A ALA 3.0 11.1 + - - -
122A ALA* 3.0 9.4 + - - -
124A ALA* 1.3 74.1 - - - +
126A SER* 1.3 63.2 + - - +
128A CYS* 2.9 26.1 - - - +
129A PHE* 3.5 9.4 - - + -
802A CDL 3.6 32.3 - - + +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 4.5 16.8 - - - -
86A LEU* 4.1 21.1 - - - -
87A ASN* 5.1 7.2 - - - -
122A ALA 3.0 6.8 + - - -
123A GLY* 2.6 23.4 + - - -
125A THR* 1.3 74.4 - - - +
127A LEU* 1.3 71.8 + - - +
129A PHE* 2.8 14.9 + - - +
130A VAL* 3.1 15.6 + - - +
401A CXT 3.3 26.0 + - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLY 2.9 14.0 + - - +
124A ALA 3.7 4.0 - - - +
126A SER* 1.3 80.2 + - - +
128A CYS* 1.3 55.5 + - - +
129A PHE 2.4 15.1 + - - -
130A VAL* 4.6 2.0 - - + -
131A TYR* 2.7 49.9 + - + +
134A ASP* 3.9 16.6 - - - +
176A PHE* 3.8 10.5 - - + -
179A SER* 3.3 26.9 - - - +
180A VAL* 4.1 18.8 - - + -
183A ILE* 4.2 13.5 - - + -
234A ARG* 4.2 5.8 - - - +
401A CXT 3.6 23.1 - - + -
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Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ALA 3.0 12.4 + - - +
125A THR* 2.9 20.2 - - - +
127A LEU* 1.3 77.2 - - - +
129A PHE* 1.3 58.7 + - + +
173A TYR* 2.7 34.0 + - - -
176A PHE* 3.9 10.9 - - + -
802A CDL 3.6 74.6 - - + +
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.8 30.5 - - + -
125A THR* 3.5 12.6 - - + -
126A SER 2.8 6.3 + - - +
127A LEU 2.4 11.2 + - - -
128A CYS* 1.3 86.7 - - + +
130A VAL* 1.3 60.4 + - + +
131A TYR 3.3 0.7 - - - -
132A PRO* 3.4 16.5 - - - +
173A TYR* 4.2 2.5 + - - -
802A CDL 3.8 40.2 - - + -
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Residues in contact with VAL 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 3.3 25.6 - - + -
82A PRO* 4.2 15.9 - - + -
83A THR* 3.6 34.1 - - - +
86A LEU* 4.6 2.2 - - + -
126A SER 3.1 12.7 + - - +
127A LEU* 3.0 5.6 + - - +
129A PHE* 1.3 77.2 - - + +
131A TYR* 1.3 69.4 + - - +
132A PRO* 3.1 4.3 - - - -
133A LEU* 2.7 39.6 + - + +
134A ASP* 3.6 7.1 + - - +
401A CXT 4.3 10.5 - - + -
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 2.7 41.5 + - + +
130A VAL* 1.3 69.4 - - - +
132A PRO* 1.3 69.9 - - + +
134A ASP* 2.8 24.5 + - - +
135A PHE 3.0 8.5 + - - -
172A LEU 3.6 15.9 - - - -
173A TYR* 3.7 30.5 - + + -
174A GLN 2.7 26.6 + - - -
175A GLY* 3.1 14.2 - - - -
176A PHE* 3.6 19.7 - + + -
179A SER* 3.6 15.5 - - - -
234A ARG* 3.2 23.0 + - - +
238A MET* 3.2 27.2 - - + +
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Residues in contact with PRO 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE 3.4 11.9 - - - +
130A VAL 3.2 4.5 - - - -
131A TYR* 1.3 95.6 - - + +
133A LEU* 1.3 58.3 + - + +
135A PHE* 3.0 13.4 - - + +
136A ALA* 2.8 30.4 + - - +
160A ILE* 5.0 15.5 - - + +
169A LEU* 5.9 0.7 - - + -
172A LEU* 4.2 22.0 - - + +
173A TYR* 3.7 31.9 - - + +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ALA* 3.6 15.1 - - + +
78A ILE* 4.3 17.0 - - + -
79A ARG* 3.5 41.7 - - + +
82A PRO* 4.4 5.2 - - + -
130A VAL* 2.7 37.2 + - + +
132A PRO* 1.3 70.5 - - + +
134A ASP* 1.3 59.9 + - - +
136A ALA* 3.7 4.0 - - - -
137A ARG* 2.8 33.9 + - - +
156A LEU* 4.7 15.3 - - + -
160A ILE* 5.0 4.0 - - + -
800A CDL 4.2 26.0 - - + -
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Residues in contact with ASP 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASN* 5.7 0.3 - - - +
79A ARG* 2.8 43.8 + - - -
127A LEU* 3.9 15.9 - - - +
130A VAL* 4.2 0.7 - - - +
131A TYR* 2.8 16.7 + - - +
133A LEU* 1.3 73.2 - - - +
135A PHE* 1.3 54.6 + - - +
137A ARG* 3.3 7.3 + - - +
138A THR* 2.8 39.6 + - - +
234A ARG* 3.8 33.0 + - - +
235A ARG* 5.8 0.7 - - - +
238A MET* 3.9 4.5 - - + -
401A CXT 4.8 3.5 + - - +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR 3.0 7.0 + - - +
132A PRO 3.0 12.1 - - - +
134A ASP* 1.3 77.0 - - - +
136A ALA* 1.3 56.6 + - + +
138A THR* 3.1 4.2 + - - -
139A ARG* 2.8 62.8 + - + +
159A CYS* 4.4 5.4 - - - -
160A ILE* 6.0 0.4 - - - -
163A ILE* 3.7 23.1 - - + -
171A GLY 3.7 3.4 - - - -
172A LEU* 3.5 39.5 - - + +
174A GLN 4.8 1.8 - - - -
238A MET* 3.1 53.3 - - + +
241A SER* 3.5 31.4 - - - -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO 2.8 16.4 + - - +
133A LEU 3.8 1.6 - - - +
135A PHE* 1.3 73.3 - - + +
137A ARG* 1.3 64.4 + - - +
139A ARG* 2.9 1.7 + - - +
140A LEU* 2.8 31.6 + - + +
156A LEU* 3.1 36.8 - - + -
159A CYS* 3.5 28.7 - - + -
160A ILE* 4.4 5.2 - - + -
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 4.2 17.0 + - - +
29A GLU* 2.8 38.2 + - - +
30A ARG* 4.7 3.8 - - - +
33A LEU* 3.9 17.7 - - - +
69A PHE 5.4 1.0 + - - -
70A TRP 5.8 0.2 - - - -
71A ARG 3.2 23.8 + - - -
72A GLY* 3.3 27.1 - - - +
73A ASN* 4.4 6.1 - - - +
75A ALA* 3.8 11.3 - - + +
76A ASN* 3.5 28.2 - - - +
133A LEU 2.8 22.0 + - - +
134A ASP* 3.4 9.0 - - - +
136A ALA* 1.3 72.1 - - - +
138A THR* 1.3 61.8 + - - +
140A LEU* 4.1 0.9 - - - +
141A ALA* 3.2 21.6 + - - +
235A ARG* 5.3 2.5 - - - +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.9 13.8 - - + +
37A VAL* 5.0 6.5 - - + +
134A ASP 2.8 22.2 + - - -
135A PHE 3.6 2.9 - - - -
137A ARG* 1.3 75.8 - - - +
139A ARG* 1.3 69.9 + - - +
141A ALA* 3.6 4.6 + - - +
142A ALA* 3.3 19.6 + - - +
235A ARG* 2.7 53.1 + - + +
238A MET* 3.7 18.0 - - + -
239A MET* 5.3 3.1 - - - -
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 2.8 48.5 + - + +
136A ALA 2.9 3.5 + - - +
138A THR* 1.3 77.0 - - - +
140A LEU* 1.3 63.2 + - - +
142A ALA* 3.1 14.2 + - - +
143A ASP* 3.3 9.7 + - - +
152A GLU* 3.6 32.5 + - - +
153A PHE* 3.8 29.4 - - + -
159A CYS* 4.0 7.9 - - - -
163A ILE* 4.3 0.4 - - - +
238A MET* 3.2 32.6 + - - -
239A MET* 3.0 36.7 + - - +
241A SER 3.2 22.4 + - - -
243A ARG* 3.7 13.5 - - - +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.0 20.7 - - + +
72A GLY* 3.6 29.4 - - - +
75A ALA* 6.2 0.4 - - + -
136A ALA* 2.8 26.4 + - + +
137A ARG 4.7 0.4 - - - +
139A ARG* 1.3 70.3 - - - +
141A ALA* 1.3 66.2 + - - +
143A ASP* 2.8 18.4 + - - +
151A ARG* 4.4 10.1 - - - +
153A PHE* 4.0 28.3 - - + +
155A GLY* 3.9 22.4 - - - +
156A LEU* 3.8 28.9 - - + +
159A CYS* 4.6 4.0 - - + -
800A CDL 4.0 11.4 - - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 2.9 39.5 + - + +
33A LEU* 3.5 34.3 - - + -
34A LEU* 3.2 9.8 - - - +
71A ARG 3.4 11.4 + - - +
137A ARG* 3.2 25.3 + - - +
138A THR 3.9 3.4 - - - +
139A ARG 3.3 0.2 - - - -
140A LEU* 1.3 77.1 - - - +
142A ALA* 1.3 58.5 + - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.6 0.6 - - + +
34A LEU* 3.7 12.7 - - + +
37A VAL* 3.8 16.2 - - + -
41A SER* 4.6 6.8 + - - +
43A GLN* 3.5 8.5 + - - -
44A ILE* 5.6 2.3 - - - +
138A THR 3.3 10.3 + - - +
139A ARG 3.1 10.4 + - - +
140A LEU 3.1 1.0 - - - -
141A ALA* 1.3 77.2 - - - +
143A ASP* 1.3 59.3 + - - +
144A VAL* 2.8 13.5 + - - +
152A GLU* 4.8 4.0 - - - +
239A MET* 3.7 30.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il