Contacts of the helix formed by residues 3 - 34 (chain Q) in PDB entry 2X17
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 SER 3 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Q MET 3.9 0.8 + - - -
2Q LEU* 1.3 75.0 - - - +
4Q GLU* 1.3 65.8 + - - +
5Q ARG* 4.0 3.0 + - - -
6Q MET* 2.9 12.7 + - - +
7Q LEU* 2.9 22.1 + - - +
111Q GLU* 2.6 37.5 + - - -
113Q ASP* 5.4 1.0 + - - -
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Residues in contact with GLU 4 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q LEU 3.9 0.8 + - - -
3Q SER* 1.3 72.7 - - - +
5Q ARG* 1.3 61.6 + - - +
7Q LEU* 3.7 10.3 + - + +
8Q LYS* 3.3 22.9 + - - +
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Residues in contact with ARG 5 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q SER* 3.2 2.6 + - - +
4Q GLU* 1.3 78.2 - - - +
6Q MET* 1.3 62.0 + - - +
8Q LYS* 3.7 7.3 + - + +
9Q ALA* 3.3 21.7 + - - +
107Q LEU* 4.4 18.0 - - + +
111Q GLU* 3.9 18.2 - - - +
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Residues in contact with MET 6 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q LEU* 4.0 15.0 - - + -
3Q SER* 2.9 26.2 + - - +
5Q ARG* 1.3 77.2 - - - +
7Q LEU* 1.3 60.0 + - - +
9Q ALA* 3.1 3.5 + - - +
10Q LEU* 3.0 33.4 + - + +
104Q LEU* 4.3 13.5 - - - +
107Q LEU* 3.9 26.5 - - + +
108Q ALA* 3.7 36.8 - - + +
111Q GLU* 3.9 10.9 + - - +
113Q ASP* 3.7 20.2 - - + +
116Q THR* 3.8 17.9 - - + +
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Residues in contact with LEU 7 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q LEU* 4.0 26.8 - - + +
3Q SER 2.9 14.8 + - - +
4Q GLU* 4.0 9.2 - - + +
6Q MET* 1.3 76.1 - - - +
8Q LYS* 1.3 55.6 + - - +
10Q LEU* 3.5 3.1 + - - +
11Q ASN* 2.8 48.7 + - - +
61Q ILE* 3.8 15.3 - - + -
66Q GLY* 4.0 4.0 - - - -
67Q ARG* 3.6 43.1 - - + +
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Residues in contact with LYS 8 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q GLU 3.3 14.3 + - - +
5Q ARG* 3.8 7.4 - - + +
6Q MET 3.2 0.6 - - - -
7Q LEU* 1.3 79.5 - - - +
9Q ALA* 1.3 56.8 + - - +
11Q ASN* 3.4 7.2 + - + +
12Q ASP* 2.9 56.4 + - - +
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Residues in contact with ALA 9 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q ARG 3.3 12.1 + - - +
6Q MET* 3.1 9.3 + - - +
8Q LYS* 1.3 78.9 - - - +
10Q LEU* 1.3 60.0 + - - +
12Q ASP* 3.7 8.3 + - - +
13Q GLN* 3.3 21.7 + - - +
16Q ARG* 4.5 2.1 + - - -
104Q LEU* 3.7 25.6 - - + +
107Q LEU* 3.9 17.7 - - + -
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Residues in contact with LEU 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q LEU* 3.8 39.0 - - + -
6Q MET* 3.0 28.5 + - + +
7Q LEU* 3.8 4.3 - - - +
9Q ALA* 1.3 76.1 - - - +
11Q ASN* 1.3 58.6 + - - +
13Q GLN* 3.4 3.6 + - - +
14Q LEU* 3.1 26.7 + - - +
57Q PHE* 3.8 33.0 - - + -
60Q TYR* 4.1 14.1 - - + -
61Q ILE* 4.0 18.1 - - + +
104Q LEU* 4.3 8.5 - - + -
116Q THR* 3.9 19.5 - - + -
119Q PHE* 4.2 8.3 - - + -
120Q LEU* 5.2 0.7 - - + -
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Residues in contact with ASN 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q LEU* 2.8 37.3 + - - +
8Q LYS* 3.4 7.9 + - + +
10Q LEU* 1.3 76.9 - - - +
12Q ASP* 1.3 64.2 + - - +
14Q LEU* 3.4 8.7 - - - +
15Q ASN* 3.2 20.1 + - - +
61Q ILE* 3.8 9.3 - - - +
67Q ARG 3.3 17.4 + - - -
68Q VAL* 3.3 12.0 - - - +
69Q GLU* 3.0 44.2 + - + +
71Q ASP* 4.7 3.6 - - - +
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Residues in contact with ASP 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q LYS* 2.9 49.4 + - - +
9Q ALA* 3.8 8.0 - - - +
10Q LEU 3.3 0.4 - - - -
11Q ASN* 1.3 77.3 - - - +
13Q GLN* 1.3 57.6 + - - +
15Q ASN* 3.3 9.2 + - - +
16Q ARG* 3.0 52.6 + - - +
71Q ASP* 3.7 15.8 - - - +
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Residues in contact with GLN 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q ALA 3.3 7.5 + - - +
10Q LEU 3.4 4.5 + - - +
12Q ASP* 1.3 76.6 - - - +
14Q LEU* 1.3 60.3 + - - +
16Q ARG* 3.4 21.8 + - - +
17Q GLU* 2.9 58.9 + - - +
57Q PHE* 3.4 30.5 - - + -
97Q ILE* 4.0 11.1 - - - +
100Q SER* 2.9 38.6 + - - +
101Q ILE* 4.1 9.8 - - + +
104Q LEU* 3.7 20.4 - - + +
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Residues in contact with LEU 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 PHE* 4.2 7.9 - - + -
10Q LEU 3.1 12.3 + - - +
11Q ASN* 3.4 12.6 - - - +
13Q GLN* 1.3 76.4 - - - +
15Q ASN* 1.3 59.4 + - - +
17Q GLU* 3.6 5.3 + - - +
18Q LEU* 3.2 41.5 + - + +
54Q ALA* 3.6 18.7 - - + +
57Q PHE* 4.0 10.0 - - + -
58Q TYR* 3.6 31.9 - - + +
61Q ILE* 3.9 17.7 - - + -
68Q VAL* 3.9 16.2 - - + -
69Q GLU 6.1 0.2 - - - +
70Q LEU* 3.8 17.7 - - + -
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Residues in contact with ASN 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228 TYR* 3.9 7.6 + - - -
11Q ASN 3.2 10.4 + - - +
12Q ASP* 3.4 12.5 - - - +
13Q GLN 3.2 0.4 - - - -
14Q LEU* 1.3 78.0 - - - +
16Q ARG* 1.3 61.4 + - - +
18Q LEU* 3.3 8.1 + - - +
19Q TYR* 2.9 29.4 + - - +
70Q LEU* 6.4 0.2 - - - -
71Q ASP* 3.5 33.9 + - + +
72Q GLU 3.1 28.2 + - - +
73Q ILE* 4.2 5.9 - - - +
74Q PRO* 4.9 6.2 - - - +
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Residues in contact with ARG 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q ALA 4.5 2.4 + - - -
12Q ASP* 3.0 34.8 + - - +
13Q GLN* 3.2 57.8 + - - +
15Q ASN* 1.3 75.9 - - - +
17Q GLU* 1.3 60.4 + - - +
19Q TYR* 3.4 9.1 + - - +
20Q SER* 2.9 32.1 + - - -
96Q PHE* 4.2 27.6 - - + -
97Q ILE* 4.0 8.9 - - + +
100Q SER* 3.9 22.5 + - - -
104Q LEU* 5.5 1.2 - - - +
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Residues in contact with GLU 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Q GLN* 2.9 39.4 + - - +
14Q LEU 3.9 4.7 - - - +
16Q ARG* 1.3 75.7 - - - +
18Q LEU* 1.3 59.4 + - - +
20Q SER* 3.5 3.1 + - - -
21Q ALA* 3.2 20.3 + - - +
50Q GLU* 2.9 51.2 - - - +
53Q HIS* 3.4 25.8 + - + +
54Q ALA* 4.0 8.5 - - + +
57Q PHE* 4.1 20.4 - - + -
97Q ILE* 3.8 15.7 - - - +
101Q ILE* 4.7 2.3 - - - +
123Q PHE* 4.3 8.0 - - - -
127Q GLN* 4.7 3.5 + - - -
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Residues in contact with LEU 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228 TYR* 3.6 37.9 - - + +
258 PHE* 4.3 9.9 - - + -
14Q LEU* 3.2 40.8 + - + +
15Q ASN* 3.7 6.5 - - - +
16Q ARG 3.3 0.2 - - - -
17Q GLU* 1.3 76.1 - - - +
19Q TYR* 1.3 62.8 + - - +
21Q ALA* 3.4 7.8 - - + +
22Q TYR* 3.2 19.4 + - - +
50Q GLU 5.1 0.2 - - - -
51Q ILE* 4.9 20.0 - - + -
54Q ALA* 3.8 16.2 - - + -
70Q LEU* 4.0 2.5 - - + -
73Q ILE* 4.4 16.6 - - + +
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Residues in contact with TYR 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q ASN* 2.9 18.5 + - - +
16Q ARG* 3.7 8.3 - - - +
17Q GLU 3.4 0.2 - - - -
18Q LEU* 1.3 73.2 - - - +
20Q SER* 1.3 55.0 + - - +
22Q TYR* 2.9 4.7 + - + -
23Q LEU* 2.7 46.0 + - + +
73Q ILE* 4.1 14.3 - - + +
74Q PRO* 3.8 47.3 - - + -
75Q LYS 4.5 2.9 + - - -
76Q PRO* 4.0 14.3 - - + +
77Q PRO* 3.8 21.8 - - - +
93Q HIS* 3.7 30.7 - + - -
96Q PHE* 6.1 2.0 - + - -
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Residues in contact with SER 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q ARG 2.9 21.5 + - - -
17Q GLU* 3.5 4.4 - - - -
18Q LEU 3.3 0.2 - - - -
19Q TYR* 1.3 75.3 - - - +
21Q ALA* 1.3 61.1 + - - +
23Q LEU* 3.8 2.6 - - - +
24Q TYR* 2.9 36.2 + - - -
50Q GLU* 3.4 25.7 + - - -
93Q HIS* 2.8 33.1 + - - -
94Q GLU* 5.7 0.4 - - - -
97Q ILE* 3.4 14.6 - - - +
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Residues in contact with ALA 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q GLU 3.2 5.9 + - - +
18Q LEU* 3.4 13.2 - - + +
20Q SER* 1.3 79.2 - - - +
22Q TYR* 1.3 57.4 + - - +
25Q PHE* 3.1 25.5 + - - +
47Q ALA* 3.3 35.6 - - + +
50Q GLU* 3.6 13.8 - - + +
51Q ILE* 3.8 19.1 - - + +
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Residues in contact with TYR 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158 ASN* 3.5 11.4 + - - -
188 LEU* 3.6 27.5 - - + +
708 LEU* 3.4 30.8 - - + +
718 ASP 2.7 29.8 + - - -
728 GLU* 4.9 0.9 - - - -
738 ILE* 3.7 19.3 - - + +
18Q LEU 3.2 9.9 + - - +
19Q TYR* 2.9 11.9 + + + +
21Q ALA* 1.3 77.6 - - - +
23Q LEU* 1.3 58.5 + - - +
25Q PHE* 3.4 10.0 + + - +
26Q ALA* 2.9 27.6 + - - +
73Q ILE* 3.9 21.8 - - + -
74Q PRO 4.0 4.5 - - - -
76Q PRO* 3.6 32.4 - - + +
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Residues in contact with LEU 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q TYR* 2.7 32.7 + - + +
20Q SER* 3.8 4.5 - - - +
21Q ALA 3.4 0.2 - - - -
22Q TYR* 1.3 73.4 - - - +
24Q TYR* 1.3 61.4 + - + +
26Q ALA* 3.2 7.2 + - - +
27Q MET* 2.9 43.4 + - + +
76Q PRO* 4.3 5.1 - - + +
77Q PRO* 3.8 29.8 - - + -
80Q TRP* 3.9 20.0 - - + -
89Q ALA 5.1 0.9 - - - +
93Q HIS* 3.5 46.2 - - + +
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Residues in contact with TYR 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q SER* 2.9 28.1 + - - +
23Q LEU* 1.3 77.6 - - + +
25Q PHE* 1.3 60.7 + - - +
27Q MET* 3.7 12.1 - - + +
28Q ALA* 2.9 22.7 + - - +
42Q TRP* 5.9 0.4 - + - -
43Q MET* 3.4 49.3 - - + +
46Q GLN* 3.8 21.5 - - + -
47Q ALA* 4.0 6.7 - - + -
50Q GLU* 3.8 24.5 - - + -
90Q ALA* 3.8 29.2 + - + +
93Q HIS* 4.2 9.7 - + - -
94Q GLU* 2.6 41.6 + - - +
134Q VAL* 4.8 5.0 - - + +
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Residues in contact with PHE 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148 LEU* 4.3 10.1 - - + -
188 LEU* 4.3 14.1 - - + -
548 ALA* 5.0 3.6 - - + -
558 LEU* 3.9 27.1 - - + -
588 TYR* 3.6 40.3 - + + -
708 LEU* 3.6 36.4 - - + +
21Q ALA 3.1 19.7 + - - +
22Q TYR* 3.6 15.3 - + + +
23Q LEU 3.3 0.2 - - - -
24Q TYR* 1.3 75.2 - - - +
26Q ALA* 1.3 56.8 + - - +
28Q ALA* 3.5 10.4 - - + +
29Q ALA* 3.1 24.1 + - - +
44Q LYS* 4.7 8.7 - - + -
47Q ALA* 4.1 9.4 - - + +
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Residues in contact with ALA 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678 ARG* 5.3 0.2 + - - -
708 LEU* 3.6 11.6 - - + +
22Q TYR 2.9 13.9 + - - +
23Q LEU 3.3 9.9 - - - +
25Q PHE* 1.3 75.6 - - - +
27Q MET* 1.3 59.1 + - - +
29Q ALA* 3.3 7.5 + - - +
30Q TYR* 3.0 24.9 + - - +
76Q PRO* 3.8 24.2 - - + -
77Q PRO 3.8 16.4 - - - +
78Q LYS 4.6 3.6 - - - +
80Q TRP* 4.2 5.7 - - + -
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Residues in contact with MET 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q LEU* 2.9 36.9 + - + +
24Q TYR* 3.7 17.5 - - + +
26Q ALA* 1.3 73.7 - - - +
28Q ALA* 1.3 60.5 + - - +
30Q TYR* 3.2 2.8 + - - +
31Q PHE* 2.9 40.7 + - + -
43Q MET* 3.7 32.3 - - + -
80Q TRP* 3.5 39.0 - - + -
86Q ALA* 3.4 28.9 - - + +
89Q ALA* 4.4 3.1 - - + -
90Q ALA* 3.8 20.4 - - + +
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Residues in contact with ALA 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588 TYR* 2.9 16.1 + - - +
24Q TYR 2.9 18.3 + - - +
25Q PHE* 3.5 11.4 - - + +
27Q MET* 1.3 76.8 - - - +
29Q ALA* 1.3 56.0 + - - +
32Q GLU* 3.0 22.7 + - - +
40Q ALA* 3.4 29.5 - - - +
43Q MET* 3.8 9.8 - - + +
44Q LYS* 3.8 18.4 - - + +
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Residues in contact with ALA 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588 TYR* 3.4 18.3 + - + -
628 TYR* 2.6 30.2 + - - +
678 ARG* 4.0 9.1 + - - +
688 VAL* 4.2 15.9 - - + +
708 LEU* 5.4 2.0 - - + -
25Q PHE 3.1 14.1 + - - +
26Q ALA* 3.4 12.1 - - - +
27Q MET 3.2 0.2 - - - -
28Q ALA* 1.3 75.7 - - - +
30Q TYR* 1.3 62.1 + - - +
32Q GLU 3.5 0.3 + - - -
33Q ASP* 3.3 15.8 + - - +
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Residues in contact with TYR 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678 ARG* 3.9 21.7 - - - +
26Q ALA 3.0 13.2 + - - +
27Q MET* 3.2 8.3 + - - +
29Q ALA* 1.3 76.4 - - - +
31Q PHE* 1.3 74.9 + + - +
33Q ASP* 3.5 12.4 + - - +
34Q LEU* 3.6 40.8 + - + +
78Q LYS 4.1 5.6 - - - +
79Q GLU* 4.3 4.7 - - + -
80Q TRP* 3.1 60.1 + + + -
81Q GLU 3.9 1.7 + - - -
82Q SER* 3.3 23.7 - - - -
83Q PRO* 3.5 2.4 - - - +
86Q ALA* 4.0 24.2 - - + -
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Residues in contact with PHE 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q MET* 2.9 31.1 + - + +
28Q ALA 4.0 1.3 - - - +
30Q TYR* 1.3 82.9 - + - +
32Q GLU* 1.3 62.2 + - - +
34Q LEU* 3.4 8.4 + - + +
36Q LEU* 2.9 42.6 + - + +
39Q PHE* 3.5 27.8 - + + -
40Q ALA 3.8 17.7 - - - +
43Q MET* 4.1 22.2 - - + -
83Q PRO* 3.7 29.6 - - + -
86Q ALA* 3.9 21.3 - - + -
87Q PHE* 3.7 34.3 - + - -
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Residues in contact with GLU 32 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588 TYR* 3.0 23.5 + - - +
628 TYR* 3.7 33.2 - - + -
28Q ALA 3.0 15.5 + - - +
29Q ALA 3.7 5.2 - - - +
30Q TYR 3.3 0.2 - - - -
31Q PHE* 1.3 77.7 - - - +
33Q ASP* 1.3 56.6 + - - +
35Q GLY* 3.0 19.6 + - - -
36Q LEU 4.4 2.2 - - - +
37Q GLU* 3.5 30.0 - - - +
40Q ALA* 3.4 14.4 - - - +
41Q ASN* 5.1 0.2 - - - +
44Q LYS* 3.1 21.8 + - - -
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Residues in contact with ASP 33 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628 TYR* 3.7 9.5 - - + -
668 GLY 4.4 8.3 - - - +
678 ARG* 3.3 42.8 + - - +
29Q ALA 3.3 5.7 + - - +
30Q TYR* 3.6 10.4 - - - +
31Q PHE 3.3 0.2 - - - -
32Q GLU* 1.3 74.7 - - - +
34Q LEU* 1.3 61.9 + - - +
35Q GLY* 3.0 8.3 + - - -
79Q GLU* 5.6 1.0 - - - +
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Residues in contact with LEU 34 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439 PHE* 5.3 10.4 - - - -
30Q TYR* 3.6 50.2 + - + +
31Q PHE* 3.4 9.5 + - + +
32Q GLU 3.3 0.8 - - - -
33Q ASP* 1.3 79.8 - - + +
35Q GLY* 1.3 60.5 + - - +
36Q LEU* 3.3 18.7 + - + +
83Q PRO* 4.3 18.6 - - + -
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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) + - + + + + + -
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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