Contacts of the helix formed by residues 113 - 145 (chain P) in PDB entry 3IS7
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 ASP 113 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I ARG* 4.0 9.3 + - - +
128I GLU* 4.7 0.3 - - - +
3P GLY* 6.0 0.2 - - - -
4P ASP* 5.6 2.5 + - + +
7P VAL* 3.5 17.3 - - + +
61P ARG* 2.9 25.5 + - - -
65P LEU* 3.9 9.3 - - - +
108P CYS* 2.9 22.3 + - + +
111P VAL* 3.3 14.1 + - + -
112P HIS* 1.3 73.1 - - - +
114P TYR* 1.3 60.7 + - - +
115P VAL* 3.8 1.6 + - - +
116P SER* 2.8 29.2 + - - -
117P ARG* 3.2 16.0 + - - +
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Residues in contact with TYR 114 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I ARG* 3.9 13.6 + - + +
105I ILE* 3.6 41.7 - - + -
106I VAL* 3.4 19.8 + - - +
117I ARG* 3.9 17.5 - - - +
121I LYS* 4.6 19.2 - - + +
124I LEU* 4.2 15.5 - - + -
109P GLU* 3.6 33.5 + - - -
112P HIS* 3.1 60.9 + - + -
113P ASP* 1.3 70.5 - - - +
115P VAL* 1.3 60.2 + - - +
117P ARG* 3.3 10.6 + - - +
118P ASP* 2.9 28.1 + - - +
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Residues in contact with VAL 115 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I LYS* 5.0 3.6 - - + +
124I LEU* 4.0 13.9 - - + -
125I GLU* 3.9 44.2 - - + +
128I GLU* 3.3 34.1 + - + +
61P ARG* 3.5 23.8 - - - +
113P ASP* 3.3 1.2 + - - -
114P TYR* 1.3 72.5 - - + +
116P SER* 1.3 65.6 + - - +
118P ASP* 3.1 7.2 + - + +
119P LEU* 3.0 23.0 + - + +
----------------------------------------------------------
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Residues in contact with SER 116 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P VAL* 4.0 4.2 - - - +
11P LEU* 4.2 9.2 - - - +
61P ARG* 3.0 26.9 + - - +
65P LEU* 3.8 7.4 - - - +
108P CYS* 3.6 17.3 - - - -
113P ASP* 2.8 33.9 + - - -
115P VAL* 1.3 75.7 - - - +
117P ARG* 1.3 64.7 + - - +
119P LEU* 3.4 8.4 + - - +
120P LEU* 3.0 26.9 + - - +
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Residues in contact with ARG 117 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ARG* 4.4 13.5 - - - +
105P ILE* 3.8 26.8 - - + +
108P CYS* 4.0 15.0 - - + -
109P GLU* 3.0 42.5 + - - +
113P ASP 3.2 12.6 + - - +
114P TYR* 3.3 14.8 - - - +
115P VAL 3.1 0.4 - - - -
116P SER* 1.3 82.2 - - - +
118P ASP* 1.3 58.0 + - - +
120P LEU* 3.3 6.2 + - - +
121P LYS* 2.8 32.5 + - + +
109Q GLU* 2.5 41.6 + - - -
114Q TYR* 3.8 17.8 + - - +
117Q ARG* 4.2 15.2 - - - +
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Residues in contact with ASP 118 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I LYS* 4.2 23.0 - - + +
125I GLU* 4.4 14.4 - - - +
114P TYR 2.9 16.0 + - - +
115P VAL* 3.1 8.3 + - + +
117P ARG* 1.3 78.0 - - - +
119P LEU* 1.3 66.4 + - - +
121P LYS* 3.2 28.8 + - - +
122P ASP* 3.0 32.6 + - - +
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Residues in contact with LEU 119 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P LEU* 5.7 1.6 - - + -
57P LYS* 4.1 19.5 - - + +
58P LEU* 3.8 20.4 - - + +
61P ARG* 3.7 39.7 - - + -
115P VAL* 3.0 13.0 + - + +
116P SER* 3.4 9.4 - - - +
118P ASP* 1.3 78.4 + - - +
120P LEU* 1.3 65.9 + - + +
122P ASP* 3.2 11.2 + - - +
123P ILE* 3.1 45.8 + - + +
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Residues in contact with LEU 120 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P LEU* 4.1 20.0 - - + -
14P ILE* 3.9 16.8 - - + -
58P LEU* 4.3 12.6 - - + -
101P LEU* 3.6 26.5 - - + +
104P ALA* 3.7 29.6 - - + -
105P ILE* 3.8 14.8 - - + +
108P CYS* 3.9 20.2 - - - -
116P SER 3.0 20.9 + - - +
117P ARG 3.7 4.3 - - - +
119P LEU* 1.3 78.5 - - + +
121P LYS* 1.3 58.8 + - - +
123P ILE* 3.3 7.8 + - + +
124P LEU* 3.0 27.4 + - - +
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Residues in contact with LYS 121 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P ILE* 4.1 11.4 - - + +
117P ARG* 2.8 24.3 + - + +
118P ASP* 3.2 33.8 + - - +
120P LEU* 1.3 76.9 - - - +
122P ASP* 1.3 81.5 + - - +
124P LEU* 3.1 6.4 + - + +
125P GLU* 3.0 34.6 + - + +
114Q TYR* 4.5 25.1 - - + +
115Q VAL* 4.9 3.1 - - + +
118Q ASP* 3.0 46.7 + - + +
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Residues in contact with ASP 122 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P HIS* 5.3 1.6 - - - -
118P ASP* 3.0 27.8 + - - +
119P LEU* 3.6 9.7 - - - +
121P LYS* 1.3 98.1 + - - +
123P ILE* 1.3 65.4 + - + +
125P GLU* 3.3 8.3 + - - +
126P SER* 3.1 23.2 + - - -
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Residues in contact with ILE 123 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ILE* 4.9 0.4 - - + -
18P GLU* 3.6 20.9 - - - +
54P HIS* 3.5 36.1 - - + +
57P LYS* 5.9 0.7 - - + -
58P LEU* 4.0 26.5 - - + -
101P LEU* 3.9 22.0 - - + -
119P LEU* 3.1 37.6 + - + +
120P LEU* 3.5 12.8 - - + +
122P ASP* 1.3 76.5 - - + +
124P LEU* 1.3 58.2 + - - +
126P SER* 3.3 3.8 + - - -
127P GLU* 2.9 36.5 + - - +
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Residues in contact with LEU 124 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P THR* 3.3 30.5 - - - +
101P LEU* 4.1 24.7 - - + -
102P ARG* 3.8 27.4 - - + +
105P ILE* 4.2 12.8 - - + -
120P LEU 3.0 13.7 + - - +
121P LYS* 3.1 9.2 + - - +
123P ILE* 1.3 74.0 - - - +
125P GLU* 1.3 63.1 + - - +
127P GLU* 3.1 2.8 + - - +
128P GLU* 2.7 44.5 + - + +
114Q TYR* 4.2 20.0 - - + -
115Q VAL* 3.9 19.3 - - + -
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Residues in contact with GLU 125 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P LYS* 3.0 20.8 + - + +
122P ASP* 3.3 8.0 + - - +
124P LEU* 1.3 76.7 - - - +
126P SER* 1.3 63.4 + - - +
128P GLU* 3.3 3.2 + - - +
129P GLU* 3.1 42.9 + - + +
115Q VAL* 3.8 31.8 - - + +
118Q ASP* 4.0 17.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 126 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P ASP* 5.2 6.2 + - - +
54P HIS* 3.1 30.8 - - - -
122P ASP 3.1 13.8 + - - -
123P ILE 3.6 6.7 - - - -
124P LEU 3.1 0.2 - - - -
125P GLU* 1.3 78.9 - - - +
127P GLU* 1.3 63.5 + - - +
129P GLU* 3.2 13.2 + - - +
130P HIS* 3.0 21.5 + - - +
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Residues in contact with GLU 127 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P GLU* 3.1 19.4 - - - +
51P GLU* 3.0 27.4 - - - +
54P HIS* 3.9 2.4 + - - -
94P GLU* 2.3 46.6 - - - +
97P ALA* 5.0 5.6 - - + -
98P THR* 4.1 13.9 - - - +
101P LEU* 4.0 20.6 - - + -
123P ILE* 2.9 23.0 + - - +
124P LEU* 3.1 6.0 + - - +
126P SER* 1.3 78.3 - - - +
128P GLU* 1.3 58.7 + - - +
130P HIS* 3.1 6.2 + - - +
131P ILE* 2.9 31.5 + - + +
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Residues in contact with GLU 128 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P THR* 4.4 5.8 - - - +
102P ARG* 2.7 34.7 + - - +
124P LEU* 2.7 28.1 + - + +
125P GLU* 3.7 6.1 - - - +
127P GLU* 1.3 73.2 - - - +
129P GLU* 1.4 57.1 + - - +
131P ILE* 3.1 12.9 + - + +
132P ASP* 2.8 27.9 + - - +
61Q ARG* 2.9 40.3 + - - +
64Q PHE* 3.6 20.8 - - + -
113Q ASP* 4.8 0.2 - - - +
115Q VAL* 3.6 19.3 - - + +
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Residues in contact with GLU 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P GLU* 3.1 43.5 + - + +
126P SER* 3.2 11.7 + - - +
128P GLU* 1.4 75.5 - - - +
130P HIS* 1.3 58.1 + - - +
132P ASP* 3.3 10.8 - - - +
133P TYR* 3.0 25.3 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P TYR* 3.6 33.9 - + - -
44P GLU* 4.6 4.2 + - - -
47P GLU* 3.1 46.1 + - + +
51P GLU* 6.0 0.2 - - - -
90P ASP* 4.5 3.6 - - + -
94P GLU* 3.1 23.2 + - - +
126P SER 3.0 12.8 + - - +
127P GLU* 3.5 9.6 - - - +
129P GLU* 1.3 75.6 - - - +
131P ILE* 1.3 60.6 + - - +
133P TYR* 3.2 12.4 + + - -
134P LEU* 2.9 55.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P LEU* 3.9 14.4 - - + -
94P GLU* 3.6 31.9 - - + +
95P LEU* 4.2 17.7 - - + -
98P THR* 4.0 22.9 - - + +
127P GLU 2.9 19.4 + - - +
128P GLU* 3.1 17.0 + - + +
130P HIS* 1.3 75.2 - - - +
132P ASP* 1.3 64.6 + - - +
134P LEU* 3.2 5.7 + - - -
135P GLU* 2.9 48.4 + - - +
64Q PHE* 4.3 10.1 - - + -
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Residues in contact with ASP 132 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P GLU 2.8 12.3 + - - +
129P GLU* 3.3 14.7 - - - +
131P ILE* 1.3 77.8 - - - +
133P TYR* 1.3 61.4 + - - +
135P GLU* 4.0 3.9 - - - +
136P THR* 2.8 38.2 + - - -
64Q PHE* 3.7 30.4 - - + +
34R ASP* 4.7 11.6 - - - +
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Residues in contact with TYR 133 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P LEU* 3.8 22.0 - - - +
43P HIS* 3.5 54.3 - + + +
44P GLU* 5.2 3.6 - - - -
47P GLU* 4.8 0.9 - - - +
87P LEU* 4.7 3.8 - - + +
129P GLU 3.0 13.3 + - - +
130P HIS* 3.2 24.0 + + + +
132P ASP* 1.3 76.2 - - - +
134P LEU* 1.3 75.6 + - + +
136P THR* 3.2 4.8 + - - -
137P GLN* 2.8 75.4 + - + +
153P HIS* 5.1 3.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P GLU* 5.5 0.7 - - - +
87P LEU* 3.9 38.8 - - + +
90P ASP* 4.0 18.8 - - + +
91P LEU* 4.0 28.0 - - + +
94P GLU* 4.4 3.6 - - + -
130P HIS* 2.9 59.0 + - + +
131P ILE* 3.7 5.8 - - - +
133P TYR* 1.3 85.7 - - + +
135P GLU* 1.3 67.5 + - - +
137P GLN* 3.1 5.2 + - - +
138P LEU* 3.0 28.9 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P LEU* 4.2 20.6 - - + +
95P LEU* 6.0 1.2 - - - +
131P ILE* 2.9 36.0 + - + +
132P ASP* 4.1 3.8 - - - +
134P LEU* 1.3 75.1 - - - +
136P THR* 1.3 58.9 + - - +
138P LEU* 3.3 8.1 + - - +
139P GLY* 2.8 27.0 + - - -
64Q PHE* 4.6 13.3 - - - +
66Q GLU* 4.4 20.1 - - - +
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Residues in contact with THR 136 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P ASP* 2.8 30.6 + - - -
133P TYR* 3.5 6.5 - - - -
135P GLU* 1.3 76.8 - - - +
137P GLN* 1.3 67.0 + - - +
139P GLY* 3.3 2.9 + - - -
140P LEU* 2.7 31.1 + - + +
33R ASN 5.1 1.1 + - - +
34R ASP 3.3 14.6 + - - +
35R TRP* 3.6 7.2 - - - +
36R GLY* 3.5 38.6 - - - +
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Residues in contact with GLN 137 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P LEU* 4.1 17.5 - - + -
133P TYR* 2.8 69.0 + - + +
134P LEU* 3.1 4.5 + - - +
136P THR* 1.3 88.3 - - - +
138P LEU* 1.3 61.9 + - - +
140P LEU* 3.2 13.2 + - - +
141P ILE* 3.0 28.8 + - - +
149P TYR* 2.5 45.6 + - - +
153P HIS* 3.9 10.1 + - - -
154R MET* 5.2 0.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P GLN* 3.7 37.1 + - + +
87P LEU* 3.8 33.2 - - + +
88P GLN* 3.9 28.9 - - - +
91P LEU* 4.0 20.4 - - + -
134P LEU 3.0 21.8 + - - +
135P GLU* 3.7 5.2 - - - +
137P GLN* 1.3 74.5 - - - +
139P GLY* 1.3 63.2 + - - +
141P ILE* 3.1 15.3 + - + +
142P GLN* 3.4 15.6 + - - +
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Residues in contact with GLY 139 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P GLU 2.8 15.2 + - - -
136P THR* 3.5 4.0 - - - -
138P LEU* 1.3 77.6 - - - +
140P LEU* 1.3 61.4 + - - +
141P ILE 3.3 0.2 + - - -
142P GLN* 3.3 9.7 + - - +
143P LYS* 3.1 40.9 + - - +
35R TRP 5.5 0.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P THR* 2.7 18.6 + - + +
137P GLN* 3.2 25.8 + - - +
139P GLY* 1.3 73.4 - - - +
141P ILE* 1.3 63.9 + - - +
143P LYS* 4.3 7.9 - - + +
144P VAL* 2.9 33.9 + - + +
149P TYR* 3.9 11.2 - - + -
35R TRP 3.2 24.4 + - - +
36R GLY* 4.1 19.5 - - - +
37R LEU* 4.3 11.2 - - + -
154R MET* 3.7 43.7 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P THR* 4.9 1.6 - - + -
84P GLN* 4.0 30.1 - - + +
87P LEU* 3.8 23.3 - - + -
137P GLN 3.0 18.6 + - - +
138P LEU* 3.1 15.0 + - + +
140P LEU* 1.3 77.2 - - - +
142P GLN* 1.3 63.0 + - - +
145P GLY* 2.9 30.3 + - - -
146P LEU* 4.1 30.1 - - + +
149P TYR* 3.4 40.2 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P GLN* 4.2 22.0 + - - +
138P LEU 3.4 9.8 + - - +
139P GLY* 3.3 10.9 + - - +
140P LEU 3.2 0.2 - - - -
141P ILE* 1.3 84.9 - - - +
143P LYS* 1.3 63.4 + - + +
145P GLY* 4.2 2.4 + - - -
147R GLU* 4.6 4.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 143 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P GLY* 3.1 28.6 + - - +
140P LEU* 3.1 11.6 + - + +
142P GLN* 1.3 79.1 - - + +
144P VAL* 1.3 64.1 + - + +
35R TRP* 3.8 52.5 + - + +
37R LEU* 4.8 12.3 - - + -
146R LEU* 5.4 1.4 - - - +
147R GLU* 3.5 17.5 - - - +
150R LEU* 3.8 28.7 - - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P LEU* 2.9 25.2 + - + +
143P LYS* 1.3 84.7 - - + +
145P GLY* 1.3 72.4 + - - +
148P ASN* 3.1 29.0 + - + +
149P TYR* 3.5 22.4 - - + +
147R GLU* 3.5 25.5 - - - +
150R LEU* 3.9 12.3 - - + +
151R GLN* 3.8 25.1 - - + +
154R MET* 4.3 16.4 - - - -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P ILE 2.9 17.2 + - - -
142P GLN 4.2 2.0 + - - -
143P LYS 3.5 1.8 - - - -
144P VAL* 1.3 83.6 - - - +
146P LEU* 1.3 66.2 + - - -
147P GLU 3.3 3.0 + - - -
148P ASN 3.3 1.2 + - - -
149P TYR* 2.9 19.9 + - - +
147R GLU* 3.6 13.8 + - - -
----------------------------------------------------------
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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