Contacts of the helix formed by residues 83 - 109 (chain B) in PDB entry 10GS
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 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 4.5 6.6 + - + -
74A ARG* 3.4 42.4 + - + +
75A THR* 3.3 31.9 - - + +
82B ASP* 1.3 72.9 - - - +
84B GLN* 1.3 65.5 + - - +
86B ALA* 3.2 8.8 + - - +
87B ALA* 2.9 23.7 + - - +
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 5.1 5.6 - - - +
60A LEU* 4.0 34.9 - - + +
71A HIS* 5.5 0.7 - - - -
82B ASP* 3.2 11.9 + - - +
83B GLN* 1.3 77.3 - - - +
85B GLU* 1.3 64.9 + - + +
87B ALA* 3.2 9.2 + - - +
88B LEU* 3.2 36.6 + - + +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 3.5 13.8 - - - -
81B LYS* 2.9 51.7 + - + +
82B ASP* 3.0 23.0 + - - +
84B GLN* 1.3 75.3 - - + +
86B ALA* 1.3 60.8 + - - +
88B LEU* 3.0 9.6 + - + +
89B VAL* 2.8 35.5 + - - +
144B VAL* 3.8 13.0 - - + +
145B GLY* 3.5 29.8 - - - -
146B ASP* 4.8 2.0 + - - +
147B GLN* 4.8 5.4 - - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.7 26.7 - - - +
79B TYR* 3.6 30.9 + - + +
82B ASP 2.9 14.6 + - - +
83B GLN* 3.4 11.7 - - - +
85B GLU* 1.3 76.2 - - - +
87B ALA* 1.3 60.4 + - - +
89B VAL* 3.4 3.8 + - - +
90B ASP* 3.1 27.0 + - - +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.4 3.4 - - + -
62A LEU* 4.1 22.9 - - + -
67A THR* 3.2 15.7 - - + +
71A HIS* 3.8 23.6 - - + +
74A ARG* 3.7 10.7 - - - +
83B GLN 2.9 12.4 + - - +
84B GLN 3.4 9.6 - - - +
85B GLU 3.2 0.2 - - - -
86B ALA* 1.3 78.4 - - - +
88B LEU* 1.3 57.6 + - - +
90B ASP* 3.4 0.7 + - - -
91B MET* 3.0 23.7 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.1 11.4 - - + -
61A THR 4.7 2.0 - - - +
62A LEU* 4.0 17.3 - - + -
84B GLN* 3.2 28.7 + - + +
85B GLU* 3.0 12.4 + - + +
87B ALA* 1.3 75.2 - - - +
89B VAL* 1.3 59.0 + - - +
91B MET* 3.2 29.4 + - + +
92B VAL* 3.0 33.3 + - + +
144B VAL* 3.9 25.4 - - + -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 4.3 4.5 - - + -
80B GLY* 4.3 13.9 - - - +
85B GLU 2.8 23.6 + - - +
86B ALA 3.6 5.6 - - - +
87B ALA 3.3 0.2 - - - -
88B LEU* 1.3 73.7 - - - +
90B ASP* 1.3 58.3 + - - +
92B VAL* 3.3 5.0 + - - +
93B ASN* 2.9 27.0 + - - +
144B VAL* 3.9 21.8 - - + +
149B SER* 3.8 23.3 - - - +
150B PHE* 3.5 34.3 - - + -
151B ALA* 3.7 17.6 - - + +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 3.2 17.9 - - + +
70A ARG* 3.7 12.5 - - - +
74A ARG* 3.1 34.5 + - - -
70B ARG* 2.8 26.3 + - - +
79B TYR* 2.7 24.8 + - - -
86B ALA 3.1 8.9 + - - +
87B ALA 3.5 8.5 - - - +
88B LEU 3.3 0.2 - - - -
89B VAL* 1.3 74.2 - - - +
91B MET* 1.3 59.7 + - - +
93B ASN* 3.2 1.6 + - - +
94B ASP* 2.8 35.3 + - - +
150B PHE* 3.9 2.1 - - - -
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Residues in contact with MET 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 24.0 - - + -
49A TYR* 2.8 31.7 + - + -
61A THR 4.6 3.6 - - - +
62A LEU* 4.3 7.2 - - + -
63A TYR* 3.6 41.1 - - + +
64A GLN* 4.1 2.2 - - + +
67A THR* 3.1 15.4 + - + -
87B ALA 3.0 14.4 + - - +
88B LEU* 3.2 35.6 + - + +
90B ASP* 1.3 75.6 - - - +
92B VAL* 1.3 61.8 + - + +
94B ASP* 4.0 1.7 - - - +
95B GLY 3.2 10.9 + - - -
132B LEU* 4.4 13.2 - - + -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.6 6.8 + - - -
88B LEU* 3.0 19.2 + - + +
89B VAL 3.5 7.2 - - - +
91B MET* 1.3 77.7 - - + +
93B ASN* 1.3 58.3 + - - +
95B GLY* 3.0 4.3 + - - -
96B VAL* 2.9 37.2 + - + +
129B PHE* 4.0 9.7 - - + -
132B LEU* 3.9 24.0 - - + -
143B ILE* 3.8 22.4 - - + -
144B VAL* 3.7 20.6 - - + -
151B ALA* 4.0 17.5 - - + +
155B LEU* 4.7 4.3 - - + -
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 2.9 32.3 + - - +
69B LEU* 4.3 1.3 - - - +
70B ARG* 4.0 15.0 - - - +
89B VAL 2.9 16.9 + - - +
90B ASP 3.7 3.6 - - - +
92B VAL* 1.3 77.2 - - - +
94B ASP* 1.3 57.5 + - - +
96B VAL* 3.1 6.4 + - - +
97B GLU* 2.8 29.5 + - - +
150B PHE* 3.7 31.5 - - + -
151B ALA* 4.0 5.6 - - + +
154B ASN* 2.9 30.9 + - - +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 3.6 29.2 - - + +
66A ASN* 3.7 14.0 - - - +
67A THR* 2.8 31.8 + - - -
70A ARG* 4.6 2.8 + - - -
70B ARG* 3.1 24.7 + - - -
90B ASP 2.8 20.5 + - - +
93B ASN* 1.3 72.2 + - - +
95B GLY* 1.3 62.5 + - - +
97B GLU* 3.4 8.6 + - - +
98B ASP* 3.0 28.6 + - - +
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.5 29.0 - - - -
64A GLN* 3.7 7.8 - - - +
91B MET 3.2 6.9 + - - -
92B VAL 3.0 8.8 + - - -
94B ASP* 1.3 75.3 - - - +
96B VAL* 1.3 63.8 + - - +
98B ASP* 3.3 5.5 + - - +
99B LEU* 3.2 19.2 + - - +
129B PHE* 3.8 11.2 - - - -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 2.9 23.3 + - + +
93B ASN* 3.1 9.8 + - - +
95B GLY* 1.3 75.8 - - - +
97B GLU* 1.3 57.4 + - - +
99B LEU* 3.2 4.3 + - - +
100B ARG* 2.8 32.2 + - - +
129B PHE* 3.8 15.7 - - + -
151B ALA 4.8 1.6 - - - +
154B ASN* 3.6 39.9 - - + +
155B LEU* 4.0 27.4 - - + +
158B LEU* 3.7 22.6 - - + +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 6.6 0.4 - - + -
13B ARG* 3.0 36.4 + - - -
66B ASN* 2.9 34.6 + - - +
93B ASN* 2.8 17.0 + - - +
94B ASP* 3.6 10.1 - - - +
96B VAL* 1.3 76.6 - - - +
98B ASP* 1.3 65.2 + - - +
100B ARG* 3.3 9.9 + - - +
101B CYS* 3.0 39.0 + - - -
154B ASN* 5.4 2.4 + - - +
210B VWW 5.8 0.3 + - - -
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 6.0 0.3 - - - +
51A GLN* 5.0 4.9 + - - -
64A GLN* 3.1 15.5 + - - -
210A VWW 2.9 31.5 + - - +
94B ASP 3.0 14.4 + - - +
95B GLY* 3.3 9.4 + - - +
97B GLU* 1.3 80.8 - - - +
99B LEU* 1.3 61.7 + - - +
101B CYS* 3.3 15.9 + - - +
102B LYS* 3.3 25.0 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLY 3.2 8.1 + - - +
96B VAL 3.2 7.7 + - - +
98B ASP* 1.3 76.4 - - - +
100B ARG* 1.3 65.6 + - - +
102B LYS* 3.2 13.2 + - + -
103B TYR* 3.0 20.1 + - - +
118B TYR* 3.5 19.5 - - + +
122B LEU* 4.8 2.5 - - + -
125B GLN* 4.0 49.4 - - + +
126B LEU* 4.2 20.0 - - + -
129B PHE* 4.5 5.6 - - + -
158B LEU* 3.8 22.0 - - + -
162B HIS* 4.2 13.0 - - + +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 4.3 13.1 + - - -
13B ARG* 3.9 34.1 - - - +
16B ALA* 4.9 1.4 - - - +
96B VAL* 2.8 19.5 + - - +
97B GLU* 3.5 11.5 + - - +
99B LEU* 1.3 77.6 - - - +
101B CYS* 1.3 56.7 + - - +
103B TYR* 3.1 8.4 + - + +
104B ILE* 2.8 47.7 + - + +
154B ASN* 2.6 43.6 + - - +
157B ASP* 2.8 30.5 + - - +
158B LEU* 3.9 21.2 - - + +
161B ILE* 4.0 15.6 - - - +
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Residues in contact with CYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A CYS* 6.1 5.2 - - - -
13B ARG* 4.1 7.4 - - - -
97B GLU* 3.0 39.6 + - - -
98B ASP* 3.6 11.9 - - - +
99B LEU 3.3 0.2 - - - -
100B ARG* 1.3 75.2 - - - +
102B LYS* 1.3 57.8 + - + +
104B ILE* 3.4 9.0 + - - +
105B SER* 2.9 29.7 + - - -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 3.3 20.6 + - - +
99B LEU* 3.2 14.3 + - + +
101B CYS* 1.3 75.3 - - + +
103B TYR* 1.3 65.9 + - - +
105B SER* 3.3 8.0 + - - -
106B LEU* 3.0 22.7 + - - +
118B TYR* 3.7 16.8 - - + -
125B GLN* 3.2 38.2 + - + +
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU 3.0 10.6 + - - +
100B ARG* 3.3 15.0 - - + +
102B LYS* 1.3 77.1 - - - +
104B ILE* 1.3 73.2 + - + +
106B LEU* 3.1 4.8 + - + +
107B ILE* 3.0 50.2 + - + +
108B TYR* 6.5 0.2 - + - -
118B TYR* 3.4 17.7 + + - +
158B LEU* 5.2 0.2 - - + -
161B ILE* 3.6 44.2 + - + +
162B HIS* 4.0 21.3 - + + -
165B LEU* 4.2 22.4 - - + -
203B ILE* 3.7 12.0 - - + +
204B ASN* 3.1 35.0 + - - -
209B GLN* 4.4 6.6 + - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.4 43.5 - - + +
100B ARG* 2.8 33.5 + - + +
101B CYS* 3.7 6.3 - - - +
103B TYR* 1.3 83.9 - - + +
105B SER* 1.3 63.5 + - - +
107B ILE* 3.4 1.7 + - - -
108B TYR* 3.0 50.5 + - + +
204B ASN* 5.8 1.3 - - - +
210B VWW 6.1 4.7 - - + -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B CYS 2.9 18.9 + - - -
102B LYS* 3.5 8.5 - - - -
103B TYR 3.2 0.2 - - - -
104B ILE* 1.3 76.8 - - - +
106B LEU* 1.3 58.5 + - - +
108B TYR* 5.4 0.2 - - - -
109B THR* 2.8 50.7 + - - +
110B ASN* 3.7 3.3 + - - -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS 3.0 12.7 + - - +
103B TYR* 3.1 9.6 + - + +
105B SER* 1.3 76.9 - - - +
107B ILE* 1.3 64.1 + - + +
110B ASN* 3.2 36.1 + - - +
111B TYR* 2.9 38.2 + - + -
114B GLY* 3.5 25.8 - - - +
115B LYS* 3.6 9.0 - - - +
118B TYR* 3.6 39.5 - - + -
165B LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.0 49.4 + - + +
104B ILE* 3.4 4.7 + - - +
106B LEU* 1.3 81.0 - - + +
108B TYR* 1.3 67.8 + - + +
111B TYR* 3.8 31.2 + - + +
165B LEU* 4.6 4.7 - - + -
204B ASN* 3.6 28.0 - - + +
206B ASN* 2.9 40.7 + - - +
208B LYS* 3.8 14.4 + - + +
209B GLN* 4.4 9.0 - - - +
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.0 46.5 + - + +
105B SER* 5.4 0.4 - - - -
107B ILE* 1.3 87.8 - - + +
109B THR* 1.3 63.5 + - - +
204B ASN* 3.6 15.1 + - + +
205B GLY 2.9 25.2 + - - -
206B ASN* 4.1 31.7 + - + +
210B VWW 3.5 43.5 - + + +
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 2.8 37.0 + - - +
108B TYR* 1.3 78.3 + - - +
110B ASN* 1.3 69.8 + - + +
111B TYR 4.1 0.4 - - - -
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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