Contacts of the helix formed by residues 97 - 132 (chain A) in PDB entry 4MBS
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 GLY 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TRP* 2.8 27.8 + - - +
95A ASP* 3.6 2.2 - - - +
96A PHE* 1.3 79.4 - - - +
98A ASN* 1.4 63.9 + - - -
99A THR 3.6 1.8 - - - -
100A MET 3.6 0.2 + - - -
101A CYS 3.2 7.6 + - - -
169A SER* 4.0 7.2 - - - -
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Residues in contact with ASN 98 (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 GLY* 1.4 68.4 - - - -
99A THR* 1.4 68.0 + - - +
101A CYS* 3.2 3.3 + - - +
102A GLN* 3.2 44.2 + - - +
168A ARG* 3.4 14.2 - - - +
169A SER* 3.0 41.2 + - - +
1106A OLC 4.1 4.9 + - - -
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Residues in contact with THR 99 (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 GLY 3.6 0.2 - - - -
98A ASN* 1.4 76.6 + - - +
100A MET* 1.3 58.8 + - - +
102A GLN* 3.2 5.3 + - - +
103A LEU* 2.9 39.2 + - + +
1106A OLC 3.7 47.5 + - - +
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Residues in contact with MET 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.1 25.1 - - + -
94A TRP* 4.0 2.5 - - - -
96A PHE* 3.2 44.8 + - + +
97A GLY 3.6 2.2 - - - +
99A THR* 1.3 80.6 - - - +
101A CYS* 1.3 55.4 + - - +
103A LEU* 3.3 28.0 + - + -
104A LEU* 2.9 47.8 + - + +
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Residues in contact with CYS 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TRP* 3.6 20.3 - - - +
97A GLY 3.2 5.2 + - - +
98A ASN 3.2 10.3 + - - +
100A MET* 1.3 77.2 - - - +
102A GLN* 1.3 54.8 + - - +
104A LEU* 4.2 0.9 - - - +
105A THR* 2.7 35.9 + - - -
167A THR* 3.6 13.0 - - - -
168A ARG* 3.6 17.0 - - - -
169A SER* 4.2 5.8 - - - +
178A CYS* 2.0 55.3 - - - -
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Residues in contact with GLN 102 (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 ASN* 3.2 29.9 + - - +
99A THR 3.8 3.8 - - - +
101A CYS* 1.3 74.3 - - - +
103A LEU* 1.3 60.7 + - - +
105A THR* 3.9 4.1 - - - -
106A GLY* 2.9 26.2 + - - -
164A ILE* 3.0 37.4 - - + +
165A ILE* 4.1 7.1 - - - +
167A THR* 3.3 25.4 - - - +
168A ARG* 4.8 0.2 - - - -
1106A OLC 2.8 50.3 + - - +
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Residues in contact with LEU 103 (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 THR* 2.9 26.3 + - + +
100A MET* 3.6 31.9 - - + +
102A GLN* 1.3 77.4 - - - +
104A LEU* 1.4 56.6 + - + +
106A GLY* 3.3 3.0 + - - -
107A LEU* 2.9 57.6 + - + +
1106A OLC 4.0 32.1 + - + +
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Residues in contact with LEU 104 (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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81A LEU* 4.5 2.0 - - + +
82A THR* 3.4 30.4 - - + +
85A PHE* 3.6 52.0 - - + -
86A TRP* 4.1 15.4 - - + -
94A TRP* 3.6 21.1 - - + -
100A MET* 2.9 32.0 + - + +
101A CYS 4.4 0.7 - - - +
103A LEU* 1.4 79.7 - - + +
105A THR* 1.4 60.4 + - - +
106A GLY 3.2 0.2 - - - -
107A LEU* 3.3 13.7 + - + +
108A TYR* 3.0 26.5 + - - +
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Residues in contact with THR 105 (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 TRP* 3.9 15.7 - - - -
101A CYS 2.7 23.4 + - - -
102A GLN* 4.0 3.1 - - - -
104A LEU* 1.4 73.7 - - - +
106A GLY* 1.3 62.4 + - - +
108A TYR* 3.3 6.3 + - - +
109A PHE* 3.1 53.3 + - + -
163A ASN 4.4 5.4 - - - +
164A ILE* 4.9 1.8 - - - -
167A THR* 3.5 37.3 - - + +
178A CYS* 4.2 2.6 - - - -
1101A MRV 4.6 10.9 - - + +
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Residues in contact with GLY 106 (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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102A GLN 2.9 16.3 + - - -
103A LEU* 3.4 5.6 - - - -
104A LEU 3.2 0.4 - - - -
105A THR* 1.3 75.0 - - - +
107A LEU* 1.4 56.0 + - - +
108A TYR 3.3 0.3 + - - -
109A PHE* 3.3 3.6 + - - +
110A ILE* 3.0 40.8 + - - +
164A ILE* 3.6 26.0 - - - +
1106A OLC 5.6 3.6 - - - -
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Residues in contact with LEU 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.9 45.5 - - + +
79A PHE 4.3 0.2 + - - -
81A LEU* 5.0 13.7 - - + -
82A THR* 3.8 16.4 - - + -
103A LEU* 2.9 44.3 + - + +
104A LEU* 3.3 14.1 + - + -
106A GLY* 1.4 71.4 - - - +
108A TYR* 1.3 56.9 + - - +
110A ILE* 4.5 4.5 - - + -
111A GLY* 2.9 27.2 + - - -
1106A OLC 4.3 23.8 - - + -
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Residues in contact with TYR 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.3 43.2 - + - +
82A THR* 3.7 11.6 - - + +
83A VAL* 5.9 0.2 - - + -
86A TRP* 3.7 20.2 - + + -
104A LEU 3.0 13.7 + - - +
105A THR* 3.4 12.6 - - - +
106A GLY 3.2 0.2 - - - -
107A LEU* 1.3 73.8 - - - +
109A PHE* 1.3 62.2 + + + +
112A PHE* 3.1 27.7 + - - +
248A TRP* 4.2 2.4 - - - -
283A GLU* 2.8 36.1 + - - +
287A MET* 4.0 6.6 - - + +
1101A MRV 3.6 75.4 - + + +
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Residues in contact with PHE 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR* 3.1 49.0 + - + +
106A GLY* 4.0 1.3 - - - +
108A TYR* 1.3 75.9 - + - +
110A ILE* 1.4 59.8 + - - +
112A PHE* 3.2 6.0 + - - +
113A PHE* 2.9 49.1 + + - -
160A SER* 3.3 21.5 - - - +
163A ASN* 3.4 46.0 - - + -
164A ILE 5.6 0.2 - - - -
194A GLN* 5.3 0.2 - - - -
198A ILE* 4.4 11.2 - - + -
1101A MRV 3.5 57.4 - + + -
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Residues in contact with ILE 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.5 8.1 - - + -
106A GLY* 3.0 29.2 + - - +
107A LEU* 4.3 5.2 - - - +
109A PHE* 1.4 72.8 - - - +
111A GLY* 1.3 53.4 + - - +
114A SER* 2.6 38.6 + - - -
153A TRP* 3.9 28.3 - - + -
156A ALA* 4.1 8.1 - - + +
157A VAL* 3.9 32.3 - - + -
160A SER* 3.6 19.3 - - - +
164A ILE* 4.6 6.5 - - + -
1106A OLC 4.0 33.7 - - + -
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Residues in contact with GLY 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 3.5 28.4 - - - +
78A PHE* 4.4 7.2 - - - -
79A PHE* 4.1 8.0 - - - -
107A LEU 2.9 20.5 + - - -
108A TYR 4.0 0.7 - - - -
110A ILE* 1.3 75.6 - - - +
112A PHE* 1.3 59.5 + - - +
114A SER* 3.5 5.4 + - - -
115A GLY* 3.3 17.7 + - - -
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Residues in contact with PHE 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.8 11.4 - + + -
108A TYR 3.1 18.4 + - - +
109A PHE 3.2 4.4 + - - +
111A GLY* 1.3 72.6 - - - +
113A PHE* 1.3 94.3 + + - +
115A GLY* 3.3 3.3 + - - -
116A ILE* 3.3 21.7 + - + +
198A ILE* 4.2 17.9 - - + -
202A GLY* 4.2 16.2 - - - -
244A TYR* 3.5 28.0 - + - -
248A TRP* 3.8 38.1 - + - -
251A TYR* 6.3 0.2 - + - -
252A ASN* 5.3 3.8 - - - -
1101A MRV 3.7 34.8 - + + -
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Residues in contact with PHE 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 2.9 42.4 + + - +
110A ILE 4.2 1.3 - - - +
112A PHE* 1.3 93.0 - + - +
114A SER* 1.3 62.3 + - - +
116A ILE* 3.3 7.3 - - + +
117A PHE* 3.0 45.2 + + + -
156A ALA* 4.2 7.6 - - + +
159A ALA* 3.8 25.8 - - + -
160A SER* 3.4 14.8 - - - -
197A LYS* 4.3 16.6 - - + -
198A ILE* 4.4 17.0 - - + -
201A LEU* 3.6 43.5 - - + -
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Residues in contact with SER 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 3.2 17.0 - - - -
110A ILE 2.6 24.8 + - - -
113A PHE* 1.3 74.6 - - - +
115A GLY* 1.3 57.7 + - - +
117A PHE* 3.1 12.6 + - - +
118A PHE* 2.8 48.4 + - - -
152A THR* 5.0 2.0 - - - -
153A TRP* 3.3 28.8 - - - -
156A ALA* 3.9 9.1 - - - +
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Residues in contact with GLY 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.4 20.2 - - - +
75A SER* 3.5 16.6 - - - -
76A ASP* 6.1 0.4 - - - -
111A GLY 3.3 9.9 + - - -
112A PHE 3.3 4.5 + - - -
113A PHE 3.2 0.8 - - - -
114A SER* 1.3 81.3 + - - +
116A ILE* 1.3 61.2 + - - +
119A ILE* 3.2 22.9 + - - +
244A TYR* 5.5 0.9 - - - -
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Residues in contact with ILE 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.3 13.9 + - + +
113A PHE* 3.3 20.6 - - + +
115A GLY* 1.3 74.9 - - - +
117A PHE* 1.4 62.5 + - + +
119A ILE* 3.3 17.0 + - + -
120A ILE* 3.0 31.1 + - + +
201A LEU 3.8 18.4 - - - +
202A GLY* 4.5 3.4 - - - -
206A PRO* 3.6 35.4 - - + -
241A MET* 5.0 1.8 - - + -
244A TYR* 3.5 52.8 - - + +
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Residues in contact with PHE 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.0 43.9 + + + -
114A SER* 3.1 8.5 + - - +
116A ILE* 1.4 86.7 - - + +
118A PHE* 1.4 57.1 + - - +
120A ILE* 3.4 14.7 + - + +
121A LEU* 3.0 32.0 + - + +
152A THR* 3.5 31.0 - - + -
155A VAL* 3.9 17.9 - - + -
156A ALA* 3.9 27.6 - - + -
159A ALA* 5.0 2.0 - - + -
201A LEU* 4.5 20.4 - - + -
205A LEU* 4.6 10.3 - - + -
1103A OLC 4.5 11.9 - - + -
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Residues in contact with PHE 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 4.1 23.0 - + - +
71A ASN* 3.5 42.0 - - + -
72A LEU* 4.2 10.8 - - + -
75A SER* 4.5 1.1 - - - -
114A SER* 2.8 34.9 + - - +
115A GLY 4.0 3.6 - - - +
116A ILE 3.4 0.2 - - - -
117A PHE* 1.4 72.5 - - - +
119A ILE* 1.4 61.2 + - - +
121A LEU* 3.7 24.4 - - + +
122A LEU* 3.1 34.9 + - - +
149A SER* 3.7 18.6 - - - -
152A THR* 3.6 19.1 - - + -
153A TRP* 3.5 35.0 - + - -
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Residues in contact with ILE 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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72A LEU* 3.8 17.9 - - + -
115A GLY 3.2 17.6 + - - +
116A ILE* 3.3 12.1 + - + +
118A PHE* 1.4 76.6 - - - +
120A ILE* 1.4 59.3 + - - +
122A LEU* 3.4 8.5 + - + +
123A THR* 3.0 27.6 + - - +
237A ILE* 4.9 2.6 - - + +
240A ILE* 3.8 25.6 - - + -
241A MET* 3.8 42.8 - - + +
244A TYR* 3.9 34.3 - - + -
289A HIS* 4.9 7.9 - - + -
293A ASN* 5.0 0.7 - - - +
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Residues in contact with ILE 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.0 27.7 + - + +
117A PHE* 3.6 11.9 - - + +
118A PHE 3.4 0.2 - - - -
119A ILE* 1.4 72.7 - - - +
121A LEU* 1.4 56.4 + - + +
123A THR* 3.1 6.1 + - - -
124A ILE* 2.9 52.4 + - + +
205A LEU* 3.8 34.8 - - + -
206A PRO* 4.0 20.6 - - + -
209A VAL* 4.0 15.9 - - + -
241A MET* 4.0 20.4 - - + -
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Residues in contact with LEU 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 5.3 0.2 - - - +
68A TYR* 3.8 35.9 - - + +
117A PHE* 3.0 21.8 + - + +
118A PHE* 3.7 27.1 - - + +
120A ILE* 1.4 76.2 - - + +
122A LEU* 1.4 52.4 + - - +
124A ILE* 3.7 12.7 - - + +
125A ASP* 2.8 35.3 + - - +
148A THR* 4.5 10.8 - - + +
152A THR* 3.2 29.8 - - + +
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Residues in contact with LEU 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 3.7 34.5 - - + +
68A TYR* 3.6 27.4 - - + -
69A LEU* 4.0 22.9 - - + -
72A LEU* 4.0 20.6 - - + -
118A PHE 3.1 24.1 + - - +
119A ILE* 3.7 9.0 - - + +
120A ILE 3.3 0.2 - - - -
121A LEU* 1.4 71.9 - - - +
123A THR* 1.3 59.4 + - - +
125A ASP* 3.5 9.2 + - - +
126A ARG* 3.1 27.5 + - - +
237A ILE* 3.7 25.5 - - + +
240A ILE* 5.0 5.6 - - + -
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Residues in contact with THR 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 3.0 13.8 + - - +
120A ILE 3.1 9.3 + - - -
122A LEU* 1.3 73.7 - - - +
124A ILE* 1.4 58.9 + - - +
126A ARG* 3.3 5.0 + - - +
127A TYR* 3.0 26.0 + - - +
209A VAL* 4.0 13.5 - - + +
213A CYS* 3.7 21.1 - - + -
214A TYR* 3.6 36.7 + - + -
217A ILE* 4.4 2.0 - - + +
237A ILE* 3.9 9.5 - - - +
241A MET* 3.4 20.2 - - + +
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Residues in contact with ILE 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 2.9 39.0 + - + +
121A LEU* 4.1 12.3 - - + +
123A THR* 1.4 72.0 - - - +
125A ASP* 1.4 65.7 + - - +
127A TYR* 3.1 15.4 + - + +
128A LEU* 3.0 38.2 + - + +
209A VAL* 4.4 9.2 - - + -
213A CYS* 4.2 15.0 - - - -
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Residues in contact with ASP 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 3.4 34.5 - - + +
65A THR* 2.9 31.1 + - - +
68A TYR* 4.1 4.3 - - + -
121A LEU 2.8 22.6 + - - +
122A LEU* 3.5 12.3 - - - +
124A ILE* 1.4 72.1 - - - +
126A ARG* 1.3 69.9 + - - +
128A LEU* 3.5 3.3 + - - +
129A ALA* 3.3 16.5 + - - +
140A ARG* 2.7 39.2 + - - -
237A ILE* 4.9 0.2 - - - +
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Residues in contact with ARG 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 3.6 6.8 + - - +
122A LEU 3.1 15.2 + - - +
123A THR* 3.7 6.7 - - - +
124A ILE 3.3 0.2 - - - -
125A ASP* 1.3 84.9 + - - +
127A TYR* 1.3 65.2 + - - +
129A ALA* 3.3 11.1 + - - +
130A VAL* 3.0 30.1 + - + +
140A ARG* 3.5 31.9 - - - +
214A TYR* 5.6 0.9 - - - +
217A ILE* 4.3 9.9 - - + -
230A ARG* 2.9 35.2 + - - +
233A ASP* 3.6 33.7 + - - +
234A VAL* 3.6 26.0 - - + +
237A ILE* 3.7 30.8 - - + +
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Residues in contact with TYR 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A THR 3.0 14.1 + - - +
124A ILE* 3.1 15.5 + - + +
126A ARG* 1.3 74.4 - - - +
128A LEU* 1.3 62.1 + - + +
131A VAL* 2.8 60.9 + - + +
132A HIS* 3.5 32.0 + + - -
212A ILE* 4.3 9.8 + - + +
213A CYS* 3.3 52.0 - - + -
216A GLY* 4.0 11.0 - - - -
217A ILE* 3.9 9.3 - - + +
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Residues in contact with LEU 128 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 4.7 11.4 - - + -
124A ILE* 3.0 31.9 + - + +
125A ASP 3.7 4.9 - - - +
127A TYR* 1.3 77.3 - - + +
129A ALA* 1.3 59.4 + - - +
132A HIS* 2.9 51.6 + - + +
135A PHE* 3.7 35.2 - - + -
136A ALA* 3.7 12.1 - - + -
139A ALA* 5.2 7.2 - - + -
140A ARG* 4.4 13.5 - - + -
144A PHE* 6.0 4.7 - - + -
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Residues in contact with ALA 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP 3.3 10.7 + - - +
126A ARG* 3.3 31.4 + - - +
128A LEU* 1.3 76.2 - - - +
130A VAL* 1.3 57.3 + - + +
133A ALA* 3.4 17.5 - - - -
136A ALA* 3.8 12.0 - - - +
140A ARG* 3.8 17.5 - - - +
230A ARG* 3.3 26.6 + - + -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.0 18.5 + - + +
127A TYR 4.3 0.4 - - - +
129A ALA* 1.3 80.5 - - + +
131A VAL* 1.4 62.2 + - - +
133A ALA* 4.5 3.9 + - - +
217A ILE* 4.1 16.8 - - + +
220A THR* 3.3 34.8 - - + +
221A LEU* 3.6 25.8 - - + -
230A ARG* 3.8 36.5 + - + +
231A HIS* 4.1 10.3 - - + -
234A VAL* 3.8 17.9 - - + -
1001A MET* 5.4 0.3 - - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 2.8 44.5 + - + +
130A VAL* 1.4 73.3 - - - +
132A HIS* 1.3 82.8 + - + +
133A ALA 3.6 1.4 + - - -
216A GLY* 3.5 35.7 - - - +
217A ILE* 3.7 9.2 - - + +
220A THR* 3.7 14.6 - - - +
223A ARG* 5.6 5.3 + - - +
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 3.5 39.6 + + - -
128A LEU* 2.9 27.5 + - + +
131A VAL* 1.3 89.1 + - + +
133A ALA* 1.3 53.9 + - - +
134A VAL* 3.5 3.4 - - - -
135A PHE* 3.1 26.5 + + + -
136A ALA* 2.8 30.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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