Contacts of the helix formed by residues 86 - 125 (chain A) in PDB entry 1H7I
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 ALA 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 1.3 76.2 - - - +
87A GLU* 1.3 68.0 + - - +
88A GLU* 3.3 29.6 - - + +
89A THR* 2.9 23.5 + - - +
90A ARG* 3.1 9.2 + - - +
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Residues in contact with GLU 87 (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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85A VAL 3.2 4.9 + - - -
86A ALA* 1.3 71.8 - - - +
88A GLU* 1.3 70.1 + - - +
90A ARG* 3.2 30.0 + - - +
91A ALA* 3.2 34.1 + - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 3.3 24.3 - - + +
87A GLU* 1.3 86.1 + - - +
89A THR* 1.3 61.5 + - - +
91A ALA* 4.2 4.0 - - - +
92A ARG* 3.3 23.0 + - - +
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Residues in contact with THR 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.3 27.6 - - + -
86A ALA* 2.9 24.4 + - - +
88A GLU* 1.3 73.9 - - - +
90A ARG* 1.3 58.3 + - - -
92A ARG* 3.3 22.5 + - - +
93A LEU* 2.9 43.7 + - + +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 6.2 1.8 - - - -
82A LEU* 5.1 14.9 - - + +
85A VAL* 3.5 18.8 - - + +
86A ALA 3.1 5.9 + - - +
87A GLU* 3.5 27.5 + - - +
89A THR* 1.3 75.4 - - - +
91A ALA* 1.3 76.9 + - - +
93A LEU* 2.9 9.2 + - - +
94A SER* 2.8 46.1 + - - -
162A TYR* 4.8 8.9 + - + +
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Residues in contact with ALA 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.2 27.2 + - - +
88A GLU* 4.2 4.3 - - - +
90A ARG* 1.3 90.9 - - - +
92A ARG* 1.3 62.5 + - - +
94A SER* 3.4 5.2 + - - -
95A LYS* 3.1 23.0 + - - +
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Residues in contact with ARG 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU 3.3 16.6 + - - +
89A THR* 3.3 23.1 + - - +
90A ARG 3.1 0.8 - - - -
91A ALA* 1.3 79.0 - - - +
93A LEU* 1.3 85.6 + - - +
95A LYS* 2.9 9.0 + - - +
96A GLU* 2.9 58.5 + - + +
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Residues in contact with LEU 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 5.7 3.1 - - + -
89A THR* 2.9 34.2 + - + +
90A ARG* 2.9 7.4 + - - +
92A ARG* 1.3 110.0 - - - +
94A SER* 1.3 56.5 + - - +
96A GLU* 3.3 14.2 + - - +
97A LEU* 2.8 30.5 + - - +
161A VAL* 4.5 24.9 - - + -
162A TYR* 3.9 22.6 - - + -
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Residues in contact with SER 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 5.4 3.3 - - - +
79A GLU* 4.5 6.4 + - - -
90A ARG* 2.8 29.0 + - - -
91A ALA* 3.7 8.5 - - - -
93A LEU* 1.3 78.7 - - - +
95A LYS* 1.3 56.7 + - - +
97A LEU* 3.5 6.4 + - - +
98A GLN* 2.9 39.7 + - - +
162A TYR* 3.6 21.7 + - - -
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Residues in contact with LYS 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 3.1 11.9 + - - +
92A ARG* 2.9 9.5 + - - +
94A SER* 1.3 74.9 - - - +
96A GLU* 1.3 66.6 + - - +
97A LEU 3.2 0.2 - - - -
98A GLN* 3.8 8.4 - - + +
99A ALA* 2.9 23.4 + - - +
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Residues in contact with GLU 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ARG* 2.9 58.6 + - + +
93A LEU* 3.6 16.7 - - - +
95A LYS* 1.3 78.9 - - + +
97A LEU* 1.3 61.4 + - - +
99A ALA* 3.4 5.6 + - - +
100A ALA* 3.1 23.2 + - - +
158A ARG* 3.7 33.3 + - - +
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Residues in contact with LEU 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.9 26.5 - - + -
93A LEU 2.8 18.1 + - - +
94A SER 3.6 7.2 - - - +
96A GLU* 1.3 73.4 - - - +
98A GLN* 1.3 64.6 + - - +
100A ALA* 3.4 2.6 + - - +
101A GLN* 3.0 23.6 + - + +
155A LEU* 4.1 10.8 - - + -
158A ARG* 3.9 29.6 - - + +
159A LEU* 3.6 39.7 - - + +
162A TYR* 3.9 29.2 - - + -
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Residues in contact with GLN 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.5 32.3 + - + +
94A SER* 2.9 32.0 + - - +
95A LYS* 3.2 10.3 + - + +
97A LEU* 1.3 79.2 - - - +
99A ALA* 1.3 62.8 + - - +
101A GLN* 3.3 15.7 + - - +
102A ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LYS 2.9 16.9 + - - +
96A GLU* 3.4 6.0 + - - +
98A GLN* 1.3 78.1 - - - +
100A ALA* 1.3 58.0 + - - +
102A ALA* 3.2 8.5 + - - +
103A ARG* 2.9 33.4 + - - +
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Residues in contact with ALA 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU 3.1 16.1 + - - +
97A LEU 3.9 3.8 - - - +
98A GLN 3.4 0.2 - - - -
99A ALA* 1.3 76.9 - - - +
101A GLN* 1.3 63.6 + - - +
103A ARG* 3.2 13.9 + - - +
104A LEU* 3.2 18.9 + - - +
151A ASP 5.2 1.9 - - - +
154A ASP* 4.4 4.5 - - - +
155A LEU* 4.0 29.1 - - + +
158A ARG* 3.9 25.1 - - - +
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Residues in contact with GLN 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 3.5 16.5 - - + +
71A LEU* 3.4 39.5 - - + +
72A LYS* 3.5 33.3 + - - +
75A LYS* 3.2 33.9 - - - +
97A LEU* 3.0 19.4 + - + +
98A GLN* 3.8 15.2 + - - +
99A ALA 3.2 0.2 - - - -
100A ALA* 1.3 75.1 - - - +
102A ALA* 1.3 64.2 + - - +
104A LEU* 3.2 14.4 + - - +
105A GLY 3.2 9.4 + - - -
155A LEU* 4.3 9.1 - - + +
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Residues in contact with ALA 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 5.1 3.1 - - - -
98A GLN 3.0 13.9 + - - +
99A ALA* 3.4 11.2 - - - +
101A GLN* 1.3 77.4 + - - +
103A ARG* 1.3 62.0 + - - +
105A GLY* 3.1 1.8 + - - -
106A ALA* 2.9 24.4 + - - +
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Residues in contact with ARG 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 2.9 19.1 + - - +
100A ALA* 3.2 15.9 + - - +
101A GLN 3.2 0.2 + - - -
102A ALA* 1.3 73.9 - - - +
104A LEU* 1.3 65.7 + - - +
106A ALA* 3.2 5.6 + - - +
107A ASP* 2.9 30.3 + - - +
150A ARG* 5.2 6.8 - - - +
151A ASP* 3.9 33.4 + - + +
154A ASP* 5.0 10.6 + - - +
158A ARG* 5.7 3.4 - - - +
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Residues in contact with LEU 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 4.4 11.0 - - + -
30A LEU* 4.4 10.1 - - + -
67A THR* 4.5 4.5 - - + -
68A MET* 4.6 1.6 - - - -
71A LEU* 4.1 12.6 - - + -
100A ALA 3.2 7.4 + - - +
101A GLN 3.2 10.2 + - - +
103A ARG* 1.3 80.2 - - - +
105A GLY* 1.3 62.7 + - - +
107A ASP* 3.2 6.2 + - - +
108A MET* 3.0 48.8 + - + +
148A LEU* 3.5 25.4 - - + +
151A ASP* 4.5 4.6 - - + +
152A ALA* 4.0 30.7 - - + +
155A LEU* 3.7 22.9 - - + -
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Residues in contact with GLY 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 4.2 4.0 - - - +
68A MET* 4.1 22.8 - - - -
101A GLN 3.2 5.4 + - - -
102A ALA* 3.1 6.7 + - - -
104A LEU* 1.3 75.1 - - - +
106A ALA* 1.3 61.0 + - - +
108A MET* 3.2 9.2 + - - +
109A GLU* 2.9 33.5 + - - +
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Residues in contact with ALA 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA 2.9 16.9 + - - +
103A ARG* 3.8 5.4 - - - +
105A GLY* 1.3 77.4 - - - +
107A ASP* 1.3 64.0 + - - +
109A GLU* 3.4 7.5 + - - +
110A ASP* 2.9 33.0 + - - +
147A ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 2.9 19.1 + - - +
104A LEU* 3.5 6.0 - - - +
106A ALA* 1.3 76.9 - - - +
108A MET* 1.3 65.3 + - - +
110A ASP* 3.0 4.0 + - - +
111A VAL* 3.0 28.4 + - - +
144A LEU 5.4 1.6 - - - +
147A ARG* 2.7 47.9 + - - +
148A LEU* 3.6 27.0 - - + +
151A ASP* 2.5 35.6 - - - +
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Residues in contact with MET 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.7 6.7 - - - -
33A PHE* 3.6 39.8 - - + -
64A MET* 3.1 63.7 - - + +
67A THR* 4.2 8.5 - - + -
68A MET* 3.9 26.7 - - - -
104A LEU* 3.0 34.3 + - + +
105A GLY* 3.2 4.7 + - - +
107A ASP* 1.3 76.8 - - - +
109A GLU* 1.3 61.7 + - - +
111A VAL* 3.2 7.0 + - - +
112A CYS* 3.0 19.1 + - - -
148A LEU* 4.0 9.2 - - + -
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Residues in contact with GLU 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 2.7 39.6 + - - -
64A MET* 3.8 13.2 - - - +
105A GLY 2.9 18.7 + - - +
106A ALA* 3.8 7.6 - - - +
107A ASP 3.2 0.2 - - - -
108A MET* 1.3 79.6 - - - +
110A ASP* 1.3 56.8 + - - +
112A CYS* 3.3 1.1 + - - +
113A GLY* 2.8 26.7 + - - -
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Residues in contact with ASP 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA* 2.9 19.8 + - - +
107A ASP 3.0 7.8 + - - +
109A GLU* 1.3 73.9 - - - +
111A VAL* 1.3 67.8 + - - +
113A GLY* 3.5 2.3 + - - +
114A ARG* 3.1 22.2 + - - +
144A LEU* 4.1 14.6 - - + +
147A ARG* 2.7 36.5 + - - +
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Residues in contact with VAL 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 5.0 2.9 - - + -
37A LEU* 3.5 44.2 - - + -
60A LEU* 4.4 5.8 - - + -
107A ASP 3.0 20.5 + - - +
108A MET* 3.5 9.4 - - - +
110A ASP* 1.3 78.0 - - - +
112A CYS* 1.3 65.1 + - - +
114A ARG* 3.0 14.8 + - - +
115A LEU* 3.1 21.2 + - + +
141A LEU* 4.0 10.3 - - + -
144A LEU* 4.1 35.7 - - + +
145A ARG 5.2 0.2 - - - +
148A LEU* 5.1 4.9 - - + -
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Residues in contact with CYS 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 5.1 0.9 - - - -
57A THR* 3.6 18.5 - - + +
60A LEU* 3.8 30.5 - - - -
61A ARG* 3.5 29.4 - - - +
64A MET* 3.4 29.6 - - - -
108A MET 3.0 9.8 + - - +
109A GLU 3.9 5.2 - - - +
111A VAL* 1.3 74.9 - - - +
113A GLY* 1.3 61.4 + - - +
115A LEU* 3.3 8.9 + - - +
116A VAL* 3.2 26.1 + - - +
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Residues in contact with GLY 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 5.3 0.8 - - - +
109A GLU* 2.8 20.9 + - - -
110A ASP* 3.7 3.6 - - - -
112A CYS* 1.3 69.9 - - - +
114A ARG* 1.3 59.8 + - - +
116A VAL* 3.4 10.3 - - - +
117A GLN* 3.0 27.0 + - - +
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Residues in contact with ARG 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP 3.1 11.9 + - - +
111A VAL 3.0 10.9 + - - +
113A GLY* 1.3 73.7 - - - -
115A LEU* 1.3 64.5 + - + +
117A GLN* 3.4 30.1 + - - +
118A TYR* 3.1 23.5 + - - +
121A GLU* 3.4 17.6 + - - -
133A LEU 5.0 0.6 + - - -
136A ARG* 3.8 27.3 + - - +
137A LEU* 3.6 46.6 - - + +
140A HIS* 2.8 39.9 + - + +
141A LEU* 5.4 2.7 - - + +
144A LEU* 3.9 17.3 - - + -
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Residues in contact with LEU 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.9 1.1 - - + -
40A VAL* 4.1 9.9 - - + -
51A LEU* 3.8 24.0 - - + +
56A VAL* 4.0 14.4 - - + -
57A THR* 3.8 14.4 - - + -
60A LEU* 3.5 32.3 - - + -
111A VAL* 3.1 21.1 + - + +
112A CYS 3.6 7.4 - - - +
113A GLY 3.2 0.4 - - - -
114A ARG* 1.3 74.5 - - - +
116A VAL* 1.3 63.3 + - - +
118A TYR* 3.3 7.9 + - + +
119A ARG* 3.1 20.7 + - - +
137A LEU* 4.1 26.9 - - + -
141A LEU* 4.1 16.8 - - + -
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Residues in contact with VAL 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 4.3 12.1 - - + -
61A ARG* 5.8 3.8 - - - +
112A CYS 3.2 16.6 + - - +
113A GLY* 3.4 11.0 - - - +
115A LEU* 1.3 72.8 - - - +
117A GLN* 1.3 70.1 + - - +
119A ARG* 3.0 36.5 + - - +
120A GLY* 3.0 10.6 + - - -
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Residues in contact with GLN 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 3.0 12.6 + - - +
114A ARG* 3.4 38.2 + - - +
116A VAL* 1.3 85.4 - - - +
118A TYR* 1.3 61.9 + - - +
120A GLY* 3.2 2.1 + - - +
121A GLU* 2.9 52.0 + - + +
136A ARG* 4.8 1.8 - - - +
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Residues in contact with TYR 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 5.8 0.4 - - + -
48A GLN* 4.5 8.9 + - + +
51A LEU* 3.8 34.1 - - + -
52A LEU* 4.2 12.5 - - + +
114A ARG* 3.1 20.4 + - - +
115A LEU* 3.6 9.0 - - - +
116A VAL 3.1 0.4 - - - -
117A GLN* 1.3 76.9 - - - +
119A ARG* 1.3 68.6 + - - +
121A GLU* 3.4 17.2 + - - +
122A VAL* 3.0 47.5 + - + +
130A THR* 4.0 7.1 + - - -
133A LEU* 3.9 28.3 - - + -
134A ARG* 3.3 27.0 - - + +
137A LEU* 3.8 25.4 - - + -
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Residues in contact with ARG 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU 3.6 12.2 + - - +
52A LEU* 3.9 30.8 - - + +
53A SER 3.0 25.5 + - - -
54A SER* 3.6 12.0 - - - +
57A THR* 3.1 37.2 + - - +
115A LEU 3.1 10.7 + - - +
116A VAL* 3.0 35.1 + - - +
118A TYR* 1.3 79.0 - - - +
120A GLY* 1.3 65.2 + - - +
122A VAL* 3.5 4.3 + - - +
123A GLN* 3.2 27.9 + - + +
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Residues in contact with GLY 120 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL 3.0 12.0 + - - -
117A GLN* 3.7 3.4 - - - -
119A ARG* 1.3 77.3 - - - +
121A GLU* 1.3 60.2 + - - +
123A GLN* 3.1 9.7 + - - +
124A ALA* 2.8 28.6 + - - +
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Residues in contact with GLU 121 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.4 22.2 + - - -
117A GLN* 2.9 46.3 + - + +
118A TYR* 3.2 14.0 + - - +
120A GLY* 1.3 72.0 - - - +
122A VAL* 1.3 68.5 + - - +
124A ALA* 2.9 19.0 + - - +
125A MET* 3.0 18.7 + - + +
133A LEU* 3.7 26.0 - - + +
136A ARG* 3.1 27.6 + - - -
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Residues in contact with VAL 122 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.7 31.6 - - + -
118A TYR* 3.0 55.8 + - + +
119A ARG 3.6 7.9 - - - +
121A GLU* 1.3 78.3 - - - +
123A GLN* 1.3 67.3 + - - +
125A MET* 3.1 19.7 + - - +
126A LEU 3.8 2.3 + - - -
127A GLY 4.9 1.7 + - - -
130A THR* 3.9 21.7 - - + +
133A LEU* 4.1 6.3 - - + -
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Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 5.4 17.2 + - - +
119A ARG* 3.2 20.5 + - + +
120A GLY* 3.1 11.2 + - - +
122A VAL* 1.3 80.7 - - - +
124A ALA* 1.3 64.3 + - - +
125A MET 3.1 1.2 + - - -
126A LEU* 3.1 22.3 + - - +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY 2.8 13.2 + - - +
121A GLU* 2.9 13.2 + - - +
123A GLN* 1.3 76.7 - - - +
125A MET* 1.3 66.3 + - + +
126A LEU* 3.4 13.9 + - - +
128A GLN* 5.3 0.9 + - - -
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Residues in contact with MET 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.1 16.2 - - + +
122A VAL* 3.2 12.3 - - - +
123A GLN 3.1 0.4 + - - -
124A ALA* 1.3 80.0 - - + +
126A LEU* 1.3 69.5 + - - +
127A GLY 3.2 1.4 + - - +
128A GLN* 3.1 55.8 + - - +
129A SER 4.5 12.1 - - - +
130A THR* 4.9 4.0 - - + -
133A LEU* 3.7 26.9 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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