Contacts of the helix formed by residues 4 - 36 (chain J) 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 4 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLY* 1.3 70.3 - - - -
5J LYS* 1.3 66.3 + - - +
6J LYS* 3.2 6.6 + - - +
7J VAL* 2.9 43.9 + - + +
8J ILE* 3.2 22.7 + - - +
65J LEU* 5.6 1.2 - - - +
107J HIS* 3.0 17.1 + - - -
111J VAL* 4.0 24.4 - - + +
113J ASP* 5.8 1.2 + - - +
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Residues in contact with LYS 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLY 3.6 4.0 + - - -
4J ASP* 1.3 77.3 + - - +
6J LYS* 1.3 60.4 + - + +
8J ILE* 3.4 9.8 + - + +
9J GLN* 3.1 47.0 + - + +
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Residues in contact with LYS 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J ASP* 3.2 4.3 + - - +
5J LYS* 1.3 79.6 - - + +
7J VAL* 1.3 58.3 + - - +
9J GLN* 3.5 19.3 - - - +
10J HIS* 2.9 35.6 + - + -
107J HIS* 3.1 31.6 - - + +
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Residues in contact with VAL 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J ASP* 2.9 34.3 + - + +
6J LYS* 1.3 75.3 - - - +
8J ILE* 1.3 51.7 + - + +
10J HIS* 3.1 7.2 + - - +
11J LEU* 2.8 52.9 + - + +
65J LEU* 4.4 5.8 - - + -
107J HIS* 3.8 12.1 - - + -
108J CYS* 4.3 15.7 - - - -
111J VAL* 3.7 22.4 - - + -
113J ASP* 3.4 28.0 - - + +
116J SER* 4.0 2.9 - - - +
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Residues in contact with ILE 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLY 4.2 8.3 - - - +
4J ASP 3.2 14.7 + - - +
5J LYS* 3.6 11.7 - - + +
6J LYS 3.2 0.2 - - - -
7J VAL* 1.3 72.3 - - - +
9J GLN* 1.3 61.8 + - + +
11J LEU* 3.8 8.0 - - + +
12J ASN* 2.8 45.3 + - - +
62J ILE* 4.3 7.8 - - + +
65J LEU* 3.8 37.0 - - + +
66J GLU 4.4 1.3 - - - +
67J GLY* 3.7 33.2 - - - +
68J LEU 4.7 1.1 - - - +
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Residues in contact with GLN 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LYS* 3.1 33.2 + - + +
6J LYS* 3.5 22.6 - - - +
8J ILE* 1.3 78.5 - - + +
10J HIS* 1.3 63.2 + - + +
12J ASN* 3.3 5.8 + - - +
13J LYS* 2.8 22.2 + - - +
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Residues in contact with HIS 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J LYS* 2.9 26.4 + - + -
7J VAL* 3.1 8.9 + - - +
9J GLN* 1.3 75.5 - - + +
11J LEU* 1.3 52.3 + - + +
13J LYS* 2.7 35.1 + - + +
14J ILE* 2.7 25.0 + - - +
100J ASP 4.7 2.4 + - - -
103J GLU* 4.0 22.4 + - + -
104J ALA* 3.6 34.2 + - + +
107J HIS* 3.9 30.9 + + + +
108J CYS* 6.1 1.8 - - - -
120J LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J VAL* 2.8 42.4 + - + +
8J ILE* 3.8 4.0 - - - +
10J HIS* 1.3 71.3 - - + +
12J ASN* 1.4 50.6 - - - +
14J ILE* 3.1 6.4 + - - +
15J LEU* 2.8 34.5 + - - +
58J LEU* 3.8 16.8 - - + +
61J ARG* 4.4 7.6 - - + -
62J ILE* 3.7 30.0 - - + +
65J LEU* 4.1 17.3 - - + -
116J SER* 4.2 11.9 - - - +
119J LEU* 5.2 4.5 - - + -
120J LEU* 3.8 38.4 - - + -
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Residues in contact with ASN 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ILE* 2.8 35.7 + - - +
9J GLN* 3.8 6.3 - - - +
11J LEU* 1.4 71.6 - - - +
13J LYS* 1.3 58.3 + - - +
15J LEU* 3.4 12.6 + - - +
16J GLY* 2.9 24.6 + - - -
62J ILE* 3.8 6.3 - - - +
68J LEU 2.9 23.8 + - - -
69J PRO* 3.5 4.0 - - - +
70J ASN* 2.7 41.1 + - + +
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Residues in contact with LYS 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J GLN 2.8 12.6 + - - +
10J HIS* 2.7 29.8 + - + +
12J ASN* 1.3 73.4 - - - +
14J ILE* 1.3 60.6 + - + +
16J GLY* 3.0 10.6 + - - -
17J ASN* 3.1 15.7 + - - +
96J LYS* 4.1 10.2 - - - +
100J ASP* 3.2 42.1 + - + +
103J GLU* 5.0 5.9 + - - -
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Residues in contact with ILE 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J HIS* 2.7 24.4 + - - +
11J LEU* 3.6 6.1 - - - +
13J LYS* 1.3 71.4 - - + +
15J LEU* 1.3 66.6 + - - +
17J ASN* 3.0 11.5 + - + +
18J GLU* 2.9 32.3 + - - +
58J LEU* 3.7 18.2 - - + -
97J ALA 4.8 0.7 - - - +
100J ASP* 3.6 45.1 - - + +
101J LEU* 3.6 35.0 - - + +
104J ALA* 4.3 5.6 - - + -
120J LEU* 4.0 15.3 - - + -
123J ILE* 4.9 1.8 - - + -
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Residues in contact with LEU 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LEU 2.8 16.4 + - - +
12J ASN* 3.6 23.8 - - - +
14J ILE* 1.3 76.7 - - - +
16J GLY* 1.3 58.0 + - - +
18J GLU* 3.1 2.2 + - - +
19J LEU* 2.9 47.2 + - + +
55J ALA* 3.7 40.2 - - + +
58J LEU* 3.8 15.5 - - + +
59J ILE* 3.9 15.9 - - + -
62J ILE* 4.2 9.0 - - + -
69J PRO* 4.3 0.9 - - + -
70J ASN 3.7 16.8 - - - +
71J LEU* 3.9 15.0 - - + -
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Residues in contact with GLY 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ASN 2.9 14.7 + - - -
13J LYS* 3.0 4.9 + - - -
15J LEU* 1.3 77.4 - - - +
17J ASN* 1.3 62.5 + - - +
19J LEU* 3.3 14.3 + - - +
20J ILE* 3.2 28.3 + - - +
70J ASN 5.6 1.3 - - - -
73J ASP 5.2 8.6 - - - +
74J LEU* 5.1 0.5 - - - +
75J GLY 5.2 1.0 + - - -
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Residues in contact with ASN 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LYS* 3.1 14.4 + - - +
14J ILE* 3.0 13.8 + - + +
16J GLY* 1.3 74.8 - - - +
18J GLU* 1.3 60.8 + - + +
20J ILE* 3.2 18.5 + - - +
21J ALA* 3.0 27.9 + - - +
51J GLU* 5.1 0.2 - - - -
93J LEU* 4.9 7.3 - - + +
96J LYS* 3.7 16.6 + - - +
97J ALA* 4.1 25.5 - - + +
100J ASP* 2.8 37.8 + - - +
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Residues in contact with GLU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J ILE* 2.9 22.3 + - + +
15J LEU 3.5 6.1 - - - +
17J ASN* 1.3 79.4 - - + +
19J LEU* 1.4 58.0 + - - +
21J ALA* 3.2 2.4 + - - +
22J ILE* 2.9 35.4 + - - +
51J GLU* 2.3 51.1 - - - +
54J HIS* 3.7 12.5 - - + +
55J ALA* 4.2 16.8 - - + -
58J LEU* 3.9 17.5 - - + -
97J ALA* 6.1 0.9 - - - +
101J LEU* 5.2 1.2 - - - +
123J ILE* 3.4 19.2 - - - +
127J GLU* 2.9 17.5 - - - +
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Residues in contact with LEU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ASN* 4.8 6.3 - - - +
15J LEU* 2.9 37.3 + - + +
16J GLY* 3.8 9.4 - - - +
17J ASN 3.3 0.2 - - - -
18J GLU* 1.4 73.5 - - - +
20J ILE* 1.3 63.5 + - - +
22J ILE* 3.6 11.8 + - + +
23J ASN* 3.5 19.9 + - - +
55J ALA* 4.6 2.0 - - + -
70J ASN 3.7 22.7 - - - +
71J LEU* 4.0 20.9 - - + +
73J ASP 5.4 5.6 - - - +
74J LEU* 3.8 20.5 - - + +
159J HEM 3.6 34.3 - - + -
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Residues in contact with ILE 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J GLY 3.2 16.7 + - - +
17J ASN* 3.2 17.9 + - - +
19J LEU* 1.3 76.2 - - - +
21J ALA* 1.3 58.5 + - - +
23J ASN* 3.2 4.2 + - - +
24J GLN* 2.8 28.1 + - - +
74J LEU* 3.9 6.3 - - + -
75J GLY* 3.5 43.5 - - - +
76J LYS 3.6 21.1 - - - +
77J LEU* 4.1 14.1 - - + +
93J LEU* 3.7 27.1 - - + -
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J ASN 3.0 11.6 + - - +
18J GLU 3.6 2.9 - - - +
20J ILE* 1.3 74.1 - - - +
22J ILE* 1.3 67.1 + - - +
24J GLN* 4.4 0.7 - - - -
25J TYR* 2.7 44.5 + - + +
51J GLU* 3.0 35.4 - - + +
93J LEU* 3.7 18.8 - - + +
94J GLU* 5.3 0.2 - - - +
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Residues in contact with ILE 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J GLU 2.9 24.0 + - - +
19J LEU* 3.8 17.9 - - + +
20J ILE 3.3 0.2 - - - -
21J ALA* 1.3 76.3 - - - +
23J ASN* 1.3 71.0 + - - +
26J PHE* 2.9 15.1 + - - +
48J SER* 2.9 29.7 + - - +
51J GLU* 3.6 23.3 - - + +
52J MET* 3.7 29.2 - - + +
55J ALA* 4.3 5.2 - - + -
159J HEM 3.8 51.4 - - + -
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Residues in contact with ASN 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 4.5 11.9 - - - +
71I LEU* 3.3 49.5 + - + +
19J LEU 3.5 10.3 + - - +
20J ILE 3.2 6.4 + - - +
22J ILE* 1.3 77.6 - - - +
24J GLN* 1.3 67.0 + - - +
26J PHE* 3.2 1.7 + - - -
27J LEU* 3.0 26.0 + - - +
74J LEU* 3.7 13.9 - - - +
77J LEU* 4.2 13.2 - - + -
159J HEM 3.2 23.7 - - - +
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Residues in contact with GLN 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ILE* 2.8 18.9 + - - +
21J ALA* 3.9 2.5 - - - +
23J ASN* 1.3 79.4 - - - +
25J TYR* 1.3 64.0 + - + +
27J LEU* 3.4 1.2 + - - +
28J HIS* 2.9 36.2 + - + -
77J LEU* 4.2 9.2 - - + +
78J LEU* 2.9 52.1 + - - +
79J ILE* 4.3 9.9 - - + -
89J CYS 3.3 22.4 + - - -
90J ASP* 2.9 25.7 + - - +
93J LEU* 3.5 19.6 - - - +
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Residues in contact with TYR 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ALA* 2.7 38.8 + - + +
24J GLN* 1.3 81.4 - - + +
26J PHE* 1.3 58.7 + - - +
28J HIS 3.3 0.2 + - - -
29J SER* 2.9 25.3 + - - -
44J GLU* 3.1 29.4 - - - +
47J GLU* 3.8 18.2 - - + -
48J SER* 3.8 15.0 - - - -
51J GLU* 3.8 17.3 - - + -
90J ASP* 3.3 40.9 + - + -
93J LEU* 4.1 11.6 - - + +
94J GLU* 2.5 38.0 + - - +
130J HIS* 3.5 18.1 - + - -
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Residues in contact with PHE 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I ASP* 3.6 22.9 - - + -
59I ILE* 4.2 13.5 - - + -
71I LEU* 4.9 2.0 - - + -
22J ILE 2.9 20.0 + - - +
23J ASN* 3.8 4.7 - - - +
24J GLN 3.2 0.4 - - - -
25J TYR* 1.3 78.5 - - - +
27J LEU* 1.3 61.1 + - - +
29J SER* 3.3 6.2 + - - -
30J ARG* 3.1 52.5 + - + +
45J TYR* 3.7 25.6 - + - -
48J SER* 3.5 20.4 + - - +
52J MET* 4.0 5.2 - - + -
159J HEM 3.3 56.8 - + + -
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Residues in contact with LEU 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ILE* 4.5 7.2 - - + -
63I LEU* 4.6 1.6 - - + -
69I PRO* 3.9 49.4 - - + +
71I LEU* 4.3 17.7 - - + +
23J ASN 3.0 16.1 + - - +
24J GLN 4.1 2.5 - - - +
26J PHE* 1.3 75.5 - - - +
28J HIS* 1.3 69.5 + - - +
30J ARG* 3.1 3.6 + - - -
31J MET* 2.9 45.0 + - + +
77J LEU* 5.3 4.7 - - + -
79J ILE* 3.7 36.6 - - + -
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Residues in contact with HIS 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLN* 2.9 20.5 + - + +
25J TYR 3.7 0.7 - - - +
27J LEU* 1.3 77.4 - - - +
29J SER* 1.3 63.0 + - - +
31J MET* 3.1 14.3 + - - +
32J TRP* 2.8 31.5 + - + -
44J GLU* 3.4 19.2 + - + +
78J LEU 3.4 18.8 - - - -
79J ILE* 3.5 11.3 - - + +
80J GLY 3.1 21.9 + - - -
86J MET* 3.5 48.9 + - + +
89J CYS* 4.2 0.2 - - + -
90J ASP* 2.9 27.5 + - - -
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Residues in contact with SER 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J TYR 2.9 14.2 + - - -
26J PHE* 3.5 11.0 - - - -
27J LEU 3.2 0.2 - - - -
28J HIS* 1.3 76.2 - - - +
30J ARG* 1.3 80.0 + - - +
32J TRP 3.3 0.5 + - - -
33J ASN* 2.8 31.4 + - - -
41J GLY* 2.5 32.3 + - - -
44J GLU* 3.7 8.5 - - - +
45J TYR* 3.5 16.7 - - - +
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Residues in contact with ARG 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I ASP* 2.9 41.6 + - - +
59I ILE* 4.0 13.7 - - + -
60I GLU* 3.6 23.5 + - + +
63I LEU* 3.6 19.1 - - + +
26J PHE* 3.1 34.1 + - + +
27J LEU 3.1 3.6 + - - +
29J SER* 1.3 94.2 + - - +
31J MET* 1.3 60.0 + - - +
33J ASN* 3.6 19.2 + - + +
34J ASP* 2.8 30.7 + - - +
41J GLY 4.5 0.2 + - - -
45J TYR* 3.3 32.3 - - - +
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Residues in contact with MET 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LEU* 4.2 16.6 - - + -
27J LEU* 2.9 44.9 + - + +
28J HIS* 3.6 17.0 - - + +
30J ARG* 1.3 74.2 - - - +
32J TRP* 1.3 65.9 + - - +
34J ASP* 3.2 6.5 + - - +
35J TRP* 2.9 58.5 + - + -
79J ILE* 4.1 9.2 - - + -
80J GLY 3.4 24.2 - - - +
81J GLU* 4.9 2.5 - - - -
86J MET* 4.0 11.2 - - + -
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Residues in contact with TRP 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J HIS* 2.8 24.5 + - + +
29J SER* 3.8 3.1 - - - +
31J MET* 1.3 76.6 - - - +
33J ASN* 1.3 62.0 + - - +
35J TRP* 3.2 14.1 + + - +
36J GLY 3.0 4.0 + - - -
37J LEU* 2.9 54.9 + - + +
40J LEU* 3.7 28.8 - - + +
41J GLY 3.8 4.5 - - - +
44J GLU* 3.6 46.4 - - + -
83J THR* 2.8 41.5 + - + +
86J MET* 3.4 37.8 - - + +
87J LEU* 4.1 22.4 - - + -
90J ASP* 4.7 1.3 - - - -
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Residues in contact with ASN 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I GLU* 5.3 1.8 - - - +
29J SER* 2.8 21.6 + - - +
30J ARG* 3.6 31.7 + - + +
32J TRP* 1.3 72.4 - - - +
34J ASP* 1.3 65.2 + - - +
36J GLY* 2.9 14.8 + - - +
37J LEU 4.8 2.2 - - - +
38J LYS* 3.8 26.5 + - + +
41J GLY* 3.2 29.6 - - - -
42J ALA 4.1 0.6 - - - +
136Q THR* 5.0 1.0 - - - +
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Residues in contact with ASP 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LEU* 4.0 44.7 - - + +
64I PHE* 4.5 4.0 - - - +
30J ARG 2.8 22.9 + - - +
31J MET* 3.5 4.3 - - - +
33J ASN* 1.3 74.1 - - - +
35J TRP* 1.3 76.6 + - - +
132Q ASP* 4.5 12.3 - - - +
136Q THR* 3.4 20.1 + - - +
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Residues in contact with TRP 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J MET* 2.9 35.3 + - + +
32J TRP* 3.7 25.1 - + - +
34J ASP* 1.3 93.3 + - - +
36J GLY* 1.3 59.7 + - - +
37J LEU* 3.6 13.2 + - + -
81J GLU 3.4 25.6 - - - -
82J ASN* 4.0 7.9 - - + -
83J THR* 4.3 3.8 - - - -
86J MET* 3.6 32.5 - - + -
136Q THR* 3.6 10.7 - - - +
139Q GLY 5.6 0.3 - - - -
140Q LEU* 3.4 19.8 + - - +
143Q LYS* 3.7 39.0 + - - +
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Residues in contact with GLY 36 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33J ASN 2.9 14.5 + - - -
34J ASP 3.3 1.0 + - - -
35J TRP* 1.3 78.8 - - - +
37J LEU* 1.3 61.9 + - - +
38J LYS* 3.3 16.8 + - - +
154J MET* 3.4 24.8 - - - +
136Q THR* 3.5 16.8 - - - -
140Q LEU* 4.0 7.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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