Contacts of the helix formed by residues 83 - 111 (chain J) in PDB entry 1BCF
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 VAL 83 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J PHE* 3.6 24.7 - - + -
35J TRP* 4.4 8.9 - - + -
37J LEU* 5.1 5.4 - - + -
40J LEU* 4.0 14.1 - - + -
82J ASP* 1.3 71.4 - - + +
84J GLU* 1.3 59.6 + - - +
86J MET* 3.5 12.0 - - - +
87J LEU* 2.9 48.6 + - + +
141J ILE* 4.5 2.0 - - + -
146J LEU* 4.6 9.0 - - + -
149J TYR* 4.3 10.3 - - + -
150J LEU* 4.1 24.7 - - + -
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Residues in contact with GLU 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J ASP* 3.3 9.9 + - - +
83J VAL* 1.3 80.9 - - - +
85J GLU* 1.3 62.5 + - - +
88J ARG* 2.8 68.1 + - - +
138J LEU* 3.7 13.0 - - + +
141J ILE* 3.8 38.2 - - + +
142J GLN* 6.1 0.5 - - - +
146J LEU* 5.5 4.9 - - + -
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Residues in contact with GLU 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J ASN* 5.3 4.4 + - - +
80J GLY* 3.3 14.6 - - - -
81J GLU* 3.2 22.0 + - - +
82J ASP* 2.8 45.7 + - - +
84J GLU* 1.3 77.5 + - - +
86J MET* 1.3 62.0 + - - +
88J ARG* 3.3 8.8 + - - +
89J SER* 3.2 25.8 + - - +
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Residues in contact with MET 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J HIS* 3.4 38.7 + - + +
31J MET* 3.7 33.4 - - + -
32J PHE* 3.6 25.4 - - + -
35J TRP* 3.5 28.3 - - + -
79J ILE 3.7 9.9 - - - +
80J GLY 3.6 22.2 - - - +
82J ASP 2.8 20.9 + - - +
83J VAL* 3.2 9.6 + - - +
85J GLU* 1.3 75.8 - - - +
87J LEU* 1.3 61.5 + - - +
89J SER* 3.2 6.1 + - - -
90J ASP* 3.1 19.2 + - - +
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Residues in contact with LEU 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J PHE* 3.6 31.2 - - + -
40J LEU* 4.9 6.5 - - + -
44J GLU* 5.0 3.4 - - - +
83J VAL* 2.9 30.8 + - + +
84J GLU 4.0 3.8 - - - +
86J MET* 1.3 77.1 - - - +
88J ARG* 1.3 57.2 + - - +
90J ASP* 3.4 9.8 - - - +
91J LEU* 3.0 24.4 + - - +
133J TRP* 5.0 6.7 - - + -
134J LEU* 3.5 24.7 - - + +
137J GLU* 4.1 16.6 - - + -
138J LEU* 4.2 14.6 - - + +
141J ILE* 4.0 15.5 - - + -
149J TYR* 4.0 17.3 - - - +
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Residues in contact with ARG 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J GLU* 2.8 51.5 + - - +
85J GLU* 3.3 9.2 + - - +
87J LEU* 1.3 74.6 - - - +
89J SER* 1.3 60.8 + - - +
91J LEU* 3.4 6.1 + - + +
92J ALA* 3.0 28.4 + - - +
138J LEU* 3.5 39.2 + - + +
142J GLN* 6.3 0.2 - - - +
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Residues in contact with SER 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLN* 3.3 8.9 - - - +
28J HIS* 4.4 0.2 - - - -
78J ASN* 2.9 49.5 + - - +
79J ILE 3.8 6.0 + - - -
80J GLY* 4.9 0.5 - - - -
85J GLU* 3.2 15.3 + - - +
86J MET 3.2 8.3 + - - -
88J ARG* 1.3 72.0 - - - +
90J ASP* 1.3 66.3 + - - +
92J ALA* 3.2 6.5 + - - +
93J LEU* 3.0 25.5 + - - +
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Residues in contact with ASP 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLN* 3.2 14.5 - - - +
25J TYR* 3.7 17.8 + - + -
28J HIS* 2.9 23.1 - - - -
44J GLU* 2.7 35.2 - - - +
86J MET 3.1 9.3 + - - +
87J LEU* 3.4 12.1 - - - +
89J SER* 1.3 80.2 - - - +
91J LEU* 1.3 60.9 + - - +
93J LEU* 3.6 6.4 + - - +
94J GLU* 3.1 28.1 + - - +
134J LEU* 3.6 17.4 - - + +
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Residues in contact with LEU 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J LEU 3.0 16.1 + - - +
88J ARG* 3.6 9.0 - - + +
89J SER 3.2 0.2 - - - -
90J ASP* 1.3 74.6 - - - +
92J ALA* 1.3 60.5 + - - +
94J GLU* 3.2 4.2 + - - +
95J LEU* 2.9 46.2 + - + +
131J ILE* 4.0 39.0 - - + +
134J LEU* 3.8 13.9 - - + +
135J GLU* 4.2 21.3 - - + +
138J LEU* 4.0 22.0 - - + -
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Residues in contact with ALA 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ARG 3.0 17.0 + - - +
89J SER* 3.7 6.7 - - - +
91J LEU* 1.3 73.2 - - - +
93J LEU* 1.3 65.7 + - - +
95J LEU* 3.3 11.2 + - - +
96J ASP* 3.0 31.5 + - - +
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Residues in contact with LEU 93 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J ASN* 5.3 2.9 - - + +
20J VAL* 4.2 25.1 - - + -
21J ALA* 4.0 31.2 - - + -
24J GLN* 3.7 32.5 - - + +
25J TYR* 6.3 1.8 - - + -
76J LYS 5.3 2.7 - - - +
89J SER 3.0 15.6 + - - +
90J ASP* 3.7 6.5 - - - +
92J ALA* 1.3 75.7 - - - +
94J GLU* 1.3 63.8 + - + +
96J ASP* 3.2 12.3 + - + +
97J GLY* 3.1 19.2 + - - -
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Residues in contact with GLU 94 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ALA* 5.3 3.1 - - - +
25J TYR* 3.1 21.0 + - + +
51J GLU* 3.1 5.4 - - - +
90J ASP 3.1 18.1 + - - +
91J LEU* 3.2 10.5 + - - +
93J LEU* 1.3 79.2 - - + +
95J LEU* 1.3 57.6 + - - +
97J GLY* 3.5 1.5 + - - -
98J ALA* 3.0 28.8 + - - +
127J GLU* 3.1 27.8 - - - +
130J HIS* 3.6 9.4 - - + -
131J ILE* 3.6 17.4 - - + +
134J LEU* 4.1 8.7 - - + -
600J MN 2.0 38.0 + - - -
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Residues in contact with LEU 95 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 4.9 11.4 - - + -
91J LEU* 2.9 32.0 + - + +
92J ALA* 3.4 12.3 - - - +
93J LEU 3.2 0.2 - - - -
94J GLU* 1.3 75.5 - - - +
96J ASP* 1.3 66.5 + - - +
98J ALA* 3.4 5.0 + - + +
99J LYS* 3.2 20.8 + - - +
131J ILE* 3.7 34.1 - - + -
135J GLU* 5.6 1.6 - - - +
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Residues in contact with ASP 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J ALA* 3.0 22.3 + - - +
93J LEU* 3.6 12.5 - - + +
95J LEU* 1.3 77.3 - - - +
97J GLY* 1.3 62.7 + - - +
99J LYS* 3.1 34.6 + - - +
100J ASN* 3.2 16.0 + - - +
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Residues in contact with GLY 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J LEU* 5.2 0.5 - - - +
17J ASN* 4.0 25.2 - - - +
93J LEU 3.1 10.4 + - - -
94J GLU* 3.9 3.6 - - - -
96J ASP* 1.3 76.4 - - - +
98J ALA* 1.3 63.8 + - - +
100J ASN* 3.0 5.8 + - - +
101J LEU* 2.9 26.1 + - - +
127J GLU* 6.1 0.7 - - - -
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Residues in contact with ALA 98 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 6.2 0.7 - - - -
94J GLU 3.0 17.6 + - - +
95J LEU* 3.7 6.5 - - + +
96J ASP 3.3 0.2 - - - -
97J GLY* 1.3 73.5 - - - +
99J LYS* 1.3 62.9 + - - +
101J LEU* 3.1 13.5 + - - +
102J ARG* 3.0 41.8 + - - +
124J LEU* 4.0 18.6 - - + +
127J GLU* 5.2 5.2 - - + +
128J GLU* 5.6 0.9 - - + -
131J ILE* 4.3 15.5 - - + -
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Residues in contact with LYS 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J LEU 3.2 10.4 + - - +
96J ASP* 3.1 30.1 + - - +
97J GLY 3.1 0.4 - - - -
98J ALA* 1.3 80.1 - - - +
100J ASN* 1.3 68.1 + - - +
102J ARG* 3.5 11.8 + - - +
103J GLU* 3.4 21.9 + - - +
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Residues in contact with ASN 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J TYR* 4.9 2.3 - - - -
13J LYS* 3.8 27.1 + - + +
14J LEU* 3.6 17.1 - - + +
17J ASN* 2.6 32.3 + - - +
96J ASP* 3.2 14.0 + - - +
97J GLY* 3.0 7.4 + - - +
99J LYS* 1.3 83.1 - - - +
101J LEU* 1.3 65.8 + - - +
103J GLU* 3.3 15.3 + - - +
104J ALA* 3.1 23.6 + - - +
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Residues in contact with LEU 101 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J LEU* 4.4 10.3 - - + -
58J TYR* 3.8 21.3 - - - +
97J GLY 2.9 14.9 + - - +
98J ALA* 3.2 10.5 - - - +
100J ASN* 1.3 77.7 - - - +
102J ARG* 1.3 56.1 + - - +
104J ALA* 3.3 5.6 + - - +
105J ILE* 2.9 36.6 + - + +
120J MET* 3.6 35.2 - - + +
123J ILE* 4.4 5.4 - - + -
124J LEU* 3.6 41.1 - - + +
127J GLU* 3.9 17.5 - - + -
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Residues in contact with ARG 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 4.6 15.1 - - - +
112F HIS* 3.0 49.0 + - + +
113F ASP* 4.3 13.3 + - - +
114F TYR* 3.8 17.5 + - + +
115F VAL 5.5 0.2 - - - +
98J ALA* 3.0 37.4 + - - +
99J LYS* 3.8 9.6 - - - +
100J ASN 3.3 0.2 - - - -
101J LEU* 1.3 71.8 - - - +
103J GLU* 1.3 65.1 + - - +
105J ILE* 3.4 1.3 + - - -
106J GLY* 3.2 18.9 + - - -
124J LEU* 4.2 17.6 - - + +
128J GLU* 2.7 29.7 + - - -
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Residues in contact with GLU 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F HIS* 6.0 0.4 - - - -
10J TYR* 2.9 34.3 + - + +
13J LYS* 6.1 1.0 - - - +
99J LYS* 3.4 11.5 + - - +
100J ASN* 3.3 19.3 + - - +
102J ARG* 1.3 78.7 - - - +
104J ALA* 1.3 62.7 + - - +
106J GLY* 3.5 1.0 + - - -
107J TYR* 3.3 21.7 + - - +
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Residues in contact with ALA 104 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J TYR* 3.8 30.7 - - + -
14J LEU* 3.7 26.2 - - + -
100J ASN 3.1 13.9 + - - +
101J LEU 3.6 3.8 - - - +
103J GLU* 1.3 80.3 - - - +
105J ILE* 1.3 61.6 + - - +
107J TYR* 3.4 2.8 + - - +
108J ALA* 3.1 18.5 + - - +
120J MET* 3.8 15.8 - - + +
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Residues in contact with ILE 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TYR* 3.5 37.5 - - + -
101J LEU* 2.9 24.3 + - + +
103J GLU 3.4 0.2 - - - -
104J ALA* 1.3 73.4 - - - +
106J GLY* 1.3 64.3 + - - +
108J ALA 3.6 0.7 + - - -
109J ASP 3.5 8.8 + - - -
117J ARG* 3.3 45.3 + - + +
120J MET* 3.7 30.7 - - + +
121J ILE* 3.8 26.9 - - + +
124J LEU* 3.9 18.6 - - + -
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Residues in contact with GLY 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F HIS* 5.2 4.0 - - - -
114F TYR* 3.5 16.9 + - - -
102J ARG 3.2 9.9 + - - -
103J GLU 3.5 3.1 + - - -
105J ILE* 1.3 79.7 - - - +
107J TYR* 1.3 62.3 + - - +
109J ASP* 3.4 6.1 + - - +
110J SER* 3.1 22.3 + - - -
117J ARG* 4.2 4.7 - - - -
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Residues in contact with TYR 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J ASP* 3.3 17.4 + - - -
6J LYS* 3.2 54.2 - - + +
7J VAL* 3.7 13.9 - - + -
10J TYR* 3.8 26.9 - + + +
103J GLU 3.3 16.7 + - - +
104J ALA 3.8 3.6 - - - +
105J ILE 3.3 0.2 - - - -
106J GLY* 1.3 75.0 - - - +
108J ALA* 1.3 65.8 + - - +
110J SER* 3.0 23.4 + - - -
111J VAL* 3.0 27.9 + - + +
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J VAL* 4.6 5.4 - - + -
104J ALA 3.1 16.6 + - - +
105J ILE 4.0 0.4 - - - +
106J GLY 3.5 0.2 - - - -
107J TYR* 1.3 77.4 - - - +
109J ASP* 1.3 56.3 + - - +
111J VAL* 3.3 10.0 + - - -
112J HIS 2.8 9.5 + - - -
113J ASP* 2.8 51.5 + - + +
116J SER* 4.7 2.0 - - - -
117J ARG* 3.8 16.2 - - + +
120J MET* 4.1 11.7 - - + -
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Residues in contact with ASP 109 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ASP* 5.2 3.6 - - - +
109G ASP* 5.4 2.8 - - - +
117G ARG* 3.6 16.6 + - - -
105J ILE 3.5 2.6 + - - -
106J GLY 3.4 8.2 + - - +
107J TYR 3.1 0.8 - - - -
108J ALA* 1.3 78.4 - - - +
110J SER* 1.3 64.9 + - - +
112J HIS* 2.9 18.9 + - - -
114J TYR* 3.3 31.4 + - - -
117J ARG* 3.2 43.2 + - - +
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Residues in contact with SER 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J GLY 3.1 13.2 + - - -
107J TYR* 3.0 21.0 + - - -
109J ASP* 1.3 80.5 + - - +
111J VAL* 1.3 60.6 + - - +
112J HIS* 3.6 16.5 + - - -
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Residues in contact with VAL 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J ASP* 3.2 29.8 - - + +
7J VAL* 3.5 30.5 - - + -
107J TYR* 3.0 26.3 + - + +
108J ALA* 3.5 11.0 - - - +
110J SER* 1.3 76.0 - - - +
112J HIS* 1.3 72.5 + - - +
113J ASP* 3.6 8.7 + - + +
----------------------------------------------------------
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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