Contacts of the helix formed by residues 23 - 55 (chain A) in PDB entry 6XXD
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 ASN 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 1.3 73.5 - - - +
24A LEU* 1.3 61.9 + - - +
25A LEU* 3.4 4.7 + - - +
26A ALA* 2.9 36.9 + - + +
27A ALA* 3.5 19.1 + - - +
3E LEU* 5.2 1.4 - - - +
42K ASP* 5.2 2.4 + - - -
46K PHE* 3.7 21.1 - - + -
68K GLY* 2.8 34.6 + - - -
70K LYS* 4.8 8.0 - - - +
105L PRO 4.1 2.7 - - - -
106L ASP* 3.1 35.2 + - - +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.4 4.3 - - + -
22A PRO* 3.8 20.4 - - + +
23A ASN* 1.3 70.3 - - - +
25A LEU* 1.3 66.8 + - - +
27A ALA* 3.2 4.3 + - - +
28A ARG* 3.1 28.5 + - - +
4F ILE* 4.0 20.6 - - + -
8F ILE* 3.4 34.0 - - + +
44L VAL* 3.5 20.9 - - + -
48L GLU* 3.8 19.7 - - + +
57L TYR* 5.5 0.4 - - - +
88L TYR* 3.5 24.5 - - - +
104L THR 5.3 0.4 - - - +
105L PRO* 3.0 20.8 + - + +
108L GLY* 6.2 1.1 - - - -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.4 0.6 + - - -
24A LEU* 1.3 78.4 - - - +
26A ALA* 1.3 60.9 + - - +
28A ARG* 3.5 8.3 + - + +
29A LYS* 3.3 47.4 + - + +
96A GLY* 5.9 2.5 - - - +
57L TYR* 6.1 0.4 - - - -
86L ASN* 3.0 31.0 - - + +
87L SER* 4.9 7.0 - - - +
105L PRO* 3.7 17.1 + - + +
106L ASP* 3.8 38.8 - - + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 2.9 26.9 + - + +
25A LEU* 1.3 74.4 - - - +
27A ALA* 1.3 65.7 + - - +
29A LYS* 3.4 27.2 + - - +
30A ARG* 3.8 5.0 + - - +
46K PHE* 3.7 24.7 - - + -
49K MET* 3.8 23.6 - - + +
67K LEU 4.4 7.0 - - - +
68K GLY* 4.9 0.7 - - - -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN 3.5 13.4 + - - +
24A LEU 3.2 9.1 + - - +
26A ALA* 1.3 79.7 - - - +
28A ARG* 1.3 60.5 + - - +
30A ARG* 3.8 6.4 + - - +
31A ALA* 3.6 17.0 + - - +
3E LEU* 4.4 26.5 - - + -
7E LEU* 5.6 7.3 - - + +
10E ILE* 5.3 3.6 - - - +
8F ILE* 4.2 15.3 - - + -
12F ILE* 4.8 5.6 - - + +
49K MET* 5.3 2.9 - - - -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU 3.1 17.1 + - - +
25A LEU* 3.9 8.7 - - + +
26A ALA 3.3 0.2 - - - -
27A ALA* 1.3 75.0 - - - +
29A LYS* 1.3 56.1 + - - +
31A ALA* 3.2 8.7 + - - +
32A ASN* 2.7 52.8 + - - +
8F ILE* 3.7 18.8 - - + +
11F ALA* 4.2 15.6 - - - +
12F ILE* 4.2 9.1 - - + +
15F ILE* 3.4 29.3 - - - +
48L GLU* 3.0 23.5 + - - -
51L GLN* 3.4 38.1 + - - +
52L ILE* 5.6 0.4 - - - +
57L TYR* 3.6 22.7 - - - -
86L ASN* 6.0 1.8 - - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.3 45.6 + - + +
26A ALA* 3.4 16.7 + - - +
28A ARG* 1.3 77.0 - - - +
30A ARG* 1.3 61.2 + - + +
32A ASN* 3.4 3.1 + - - +
33A ASP* 3.1 34.3 + - - +
96A GLY* 3.6 23.5 + - - +
97A GLY* 3.6 18.6 - - - +
98A THR* 4.1 17.7 - - + -
49K MET* 5.9 1.1 - - + -
67K LEU 5.5 4.2 + - - +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 4.0 10.3 + - - +
27A ALA 3.8 6.4 + - - +
28A ARG 3.2 0.4 - - - -
29A LYS* 1.3 76.0 - - - +
31A ALA* 1.3 63.5 + - - +
33A ASP* 3.4 15.7 + - - +
34A THR* 2.9 25.7 + - - -
98A THR* 3.7 25.5 + - - +
111A LYS* 5.2 3.6 - - - +
7E LEU* 4.3 20.0 - - + -
10E ILE* 3.5 20.5 - - + +
49K MET* 3.5 40.4 + - + +
52K ILE* 4.3 21.1 - - + +
53K ASP* 2.7 41.7 + - - -
67K LEU* 4.2 10.9 + - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 3.6 7.1 + - - +
28A ARG* 3.2 7.3 + - - +
30A ARG* 1.3 79.0 - - - +
32A ASN* 1.3 61.2 + - - +
34A THR* 3.3 11.6 + - - -
35A VAL* 3.2 25.7 + - - +
10E ILE* 4.5 7.0 - - + +
12F ILE* 3.2 46.2 - - + -
15F ILE* 5.2 5.2 - - + -
16F LEU* 4.7 5.6 - - + +
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Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 2.7 37.7 + - - +
29A LYS 3.5 6.1 - - - +
31A ALA* 1.3 72.6 - - - +
33A ASP* 1.3 63.6 + - - +
35A VAL* 3.4 8.9 + - - +
36A VAL* 3.2 26.5 + - - +
94A HIS* 3.2 44.1 + - + -
96A GLY 2.9 23.7 + - - +
97A GLY* 4.3 1.3 - - - -
15F ILE* 5.7 4.7 - - - +
86L ASN* 3.5 14.0 + - - +
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Residues in contact with ASP 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS 3.1 17.9 + - - +
30A ARG* 3.6 19.6 + - - +
31A ALA 3.3 0.4 - - - -
32A ASN* 1.3 73.6 - - - +
34A THR* 1.3 57.0 + - - +
36A VAL* 3.3 3.9 + - - +
37A THR* 2.7 38.5 + - - +
94A HIS* 5.5 0.7 - - - +
97A GLY* 3.8 4.0 - - - -
98A THR* 2.7 48.8 + - - +
99A VAL 4.7 0.5 - - - +
101A PHE* 3.8 27.0 - - + -
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG 2.9 15.5 + - - -
31A ALA* 3.3 11.4 + - - -
33A ASP* 1.3 77.2 - - - +
35A VAL* 1.3 55.3 - - - +
37A THR* 4.0 5.5 - - - -
38A ALA* 2.8 32.6 + - - +
10E ILE* 3.2 20.5 + - + +
13E ILE* 4.3 19.3 - - + -
16F LEU* 4.4 19.7 - - + -
19F VAL* 4.8 1.3 - - + -
20F LEU* 3.9 25.6 - - + -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA 3.2 12.2 + - - +
32A ASN* 3.6 12.8 - - - +
33A ASP 3.3 0.4 - - - -
34A THR* 1.3 76.8 - - - +
36A VAL* 1.3 58.1 + - - +
38A ALA* 3.9 1.2 - - - +
39A TYR* 3.0 28.8 + - - +
73A PRO* 3.9 29.4 - - + -
74A ALA 5.7 0.2 - - - +
76A VAL* 4.3 10.8 - - + -
94A HIS* 4.6 6.3 - - + +
15F ILE* 3.3 33.9 - - + -
19F VAL* 4.0 25.2 - - + +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN 3.2 14.8 + - - +
33A ASP* 3.7 8.7 - - - +
35A VAL* 1.3 76.1 - - - +
37A THR* 1.3 58.6 + - - +
39A TYR* 3.5 4.1 + - - +
40A LEU* 3.0 32.0 + - + +
76A VAL* 4.5 10.1 - - + -
92A ALA* 3.5 32.3 - - + +
93A GLY 3.7 4.0 - - - +
94A HIS* 3.4 35.4 - - + +
101A PHE* 3.6 27.4 - - + -
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 2.7 29.5 + - - +
34A THR* 4.0 7.2 - - - -
36A VAL* 1.3 74.3 - - - +
38A ALA* 1.3 56.2 + - - +
40A LEU* 3.6 1.8 + - - +
41A ASN* 2.9 31.3 + - + +
101A PHE* 3.3 22.0 - - + -
109A VAL* 4.3 23.6 - - + +
13E ILE* 6.1 3.4 - - + -
14E ALA* 5.6 7.7 - - - +
17E ALA* 4.0 27.8 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR 2.8 19.9 + - - +
35A VAL 3.9 3.6 - - - +
37A THR* 1.3 76.1 - - - +
39A TYR* 1.3 56.9 + - - +
41A ASN* 3.3 8.1 + - - +
42A ASP* 2.8 35.2 + - - +
19F VAL* 3.9 35.0 - - + +
20F LEU* 4.0 13.2 - - + -
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL 3.0 19.2 + - - +
36A VAL* 4.0 4.7 - - - +
38A ALA* 1.3 74.0 - - - +
40A LEU* 1.3 56.1 + - + +
42A ASP* 3.4 9.0 + - - +
43A ALA* 2.8 33.6 + - - +
61A GLN* 3.1 21.1 + - - -
69A LEU* 3.8 24.1 - - + +
70A LYS* 2.9 29.3 + - + -
71A SER 3.4 19.7 - - - -
72A THR* 3.5 6.2 + - - -
73A PRO* 3.7 25.8 - - + -
76A VAL* 5.4 4.0 - - + -
78A PHE* 3.6 44.0 - + + -
92A ALA* 5.7 0.9 - - + -
19F VAL* 5.7 0.4 - - - +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.0 24.8 + - + +
37A THR 3.9 0.2 - - - +
39A TYR* 1.3 73.3 - - + +
41A ASN* 1.3 61.5 + - - +
43A ALA* 3.5 3.5 - - - +
44A VAL* 2.9 35.0 + - - +
78A PHE* 3.9 18.2 - - + -
90A MET* 3.8 21.7 - - + +
92A ALA* 3.6 21.8 - - + -
101A PHE* 3.3 43.3 - - + +
102A ALA 3.9 1.6 - - - +
103A ALA* 3.8 8.5 - - + -
109A VAL* 3.8 25.6 - - + -
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 2.9 22.5 + - + +
38A ALA* 3.3 9.1 + - - +
40A LEU* 1.3 75.3 - - - +
42A ASP* 1.3 61.9 + - - +
44A VAL* 3.7 6.3 + - - +
45A LYS* 3.5 49.0 + - - +
109A VAL* 4.0 11.8 - - + +
4B ILE* 5.0 4.0 - - - +
5C GLU* 6.0 0.8 + - - -
17E ALA* 5.8 6.7 - - + +
21E ILE* 3.8 30.2 - - - +
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Residues in contact with ASP 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA 2.8 22.5 + - - +
39A TYR* 3.6 10.1 - - + +
41A ASN* 1.3 76.2 + - - +
43A ALA* 1.3 64.6 + - - +
45A LYS* 3.1 33.7 + - - +
46A PHE* 3.2 24.9 + - + -
69A LEU* 3.7 18.6 - - + -
70A LYS* 5.4 5.4 + - - -
19F VAL 3.7 17.8 - - - +
20F LEU 6.1 0.2 - - - -
21F ILE 5.3 0.9 - - - +
22F PRO* 4.5 14.8 - - - +
23F ASN 5.2 1.5 + - - -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 2.8 21.4 + - + +
40A LEU* 3.3 10.1 + - - +
42A ASP* 1.3 73.8 - - - +
44A VAL* 1.3 55.8 + - - +
46A PHE* 3.6 2.0 + - - +
47A GLN* 3.1 32.9 + - - +
64A LEU* 4.5 2.9 - - + +
69A LEU* 4.0 17.9 - - + +
78A PHE* 4.0 20.9 - - + -
90A MET* 3.6 19.5 - - + -
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Residues in contact with VAL 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU 2.9 20.7 + - - +
41A ASN* 3.8 9.2 - - - +
42A ASP 3.3 0.2 - - - -
43A ALA* 1.3 74.3 - - - +
45A LYS* 1.3 62.8 + - - +
47A GLN* 3.5 6.1 + - - +
48A GLU* 3.2 21.7 + - - +
88A TYR* 3.4 25.3 + - + +
90A MET* 4.0 13.9 - - + -
103A ALA* 4.3 7.0 - - + -
104A THR 5.3 2.2 - - - +
108A GLY* 5.6 2.0 - - - -
109A VAL* 3.9 20.0 - - + +
4B ILE* 4.1 12.6 - - + -
21E ILE* 5.6 7.0 - - + -
24E LEU* 3.5 19.3 - - + -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.5 41.6 + - - +
42A ASP* 3.1 24.6 + - - +
44A VAL* 1.3 77.4 - - - +
46A PHE* 1.3 64.0 + - + +
48A GLU* 3.1 3.6 + - - +
49A MET* 3.0 24.4 + - - +
3B LEU* 4.0 38.7 - - + +
4B ILE* 3.8 30.3 - - + +
7B LEU* 3.4 24.4 - - + +
5C GLU* 4.5 8.7 - - - +
22F PRO* 4.2 11.6 - - + +
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 3.2 27.9 + - + +
43A ALA 4.3 2.0 - - - +
45A LYS* 1.3 80.9 - - + +
47A GLN* 1.3 58.4 + - - +
48A GLU 3.4 0.2 - - - -
49A MET* 3.5 29.7 - - - +
50A TYR* 3.2 21.7 + - - +
64A LEU* 3.4 27.8 - - + +
67A LEU* 3.9 20.0 - - + +
68A GLY* 3.3 23.6 - - - -
69A LEU* 3.3 42.6 - - + -
23F ASN* 3.7 28.7 - - + -
26F ALA* 3.7 9.2 - - + -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA 3.1 25.7 + - - +
44A VAL* 3.6 8.3 - - - +
45A LYS 3.2 0.4 - - - -
46A PHE* 1.3 77.4 - - - +
48A GLU* 1.3 57.3 + - - +
50A TYR* 3.5 4.1 + - - +
51A GLN* 3.1 26.5 + - - +
57A TYR* 3.5 29.9 - - + -
58A THR* 3.0 52.1 + - - +
64A LEU* 3.8 7.2 - - + +
80A ILE* 4.3 3.4 - - - +
88A TYR* 4.0 22.4 - - + +
90A MET* 3.4 32.4 - - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL 3.2 13.0 + - - +
45A LYS 3.1 9.2 + - - +
47A GLN* 1.3 74.5 - - - +
49A MET* 1.3 63.8 + - - +
51A GLN* 3.4 6.1 + - - +
52A ILE* 3.2 29.0 + - + +
57A TYR* 3.0 28.3 + - - -
88A TYR* 4.5 2.3 - - - +
4B ILE* 3.7 20.6 - - + -
7B LEU* 4.5 8.7 - - + -
8B ILE* 3.5 23.2 - - + +
11B ALA* 4.8 1.8 - - + +
24E LEU* 3.7 21.3 - - + +
28E ARG* 3.0 28.2 + - - -
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Residues in contact with MET 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 3.0 17.9 + - - +
46A PHE* 3.5 33.7 - - + +
47A GLN 3.3 0.4 - - - -
48A GLU* 1.3 75.2 - - - +
50A TYR* 1.3 62.1 + - - +
52A ILE* 3.4 9.9 + - - +
53A ASP* 3.2 28.4 + - - +
67A LEU* 3.6 18.8 - - + +
7B LEU* 4.0 26.0 - - + -
26F ALA* 3.8 35.9 - - + +
27F ALA* 5.3 1.3 - - - -
29F LYS* 5.9 1.6 - - + -
30F ARG* 3.6 31.3 + - + +
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE 3.2 17.7 + - - +
47A GLN* 3.7 6.5 - - - +
48A GLU 3.4 0.2 - - - -
49A MET* 1.3 74.4 - - - +
51A GLN* 1.3 59.9 + - - +
53A ASP* 4.5 2.5 - - - +
54A ASN* 2.8 68.9 + - + +
56A SER* 3.5 20.8 - - - +
57A TYR 4.8 1.8 - - - -
58A THR* 3.3 38.6 - - + -
63A ALA* 3.8 16.9 - - + +
64A LEU* 4.7 0.4 - - + -
67A LEU* 3.4 27.5 - - + +
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Residues in contact with GLN 51 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN 3.1 14.1 + - - +
48A GLU* 3.4 14.6 - - - +
49A MET 3.3 0.2 - - - -
50A TYR* 1.3 74.7 - - - +
52A ILE* 1.3 63.5 + - - +
55A ASN* 3.2 52.3 + - - +
56A SER 3.0 26.6 + - - +
57A TYR* 3.2 27.8 - - + +
85A ALA 3.4 8.7 + - - +
86A ASN* 5.6 3.2 - - - +
15B ILE* 6.1 0.2 - - - +
28E ARG* 3.4 39.4 + - - +
75E ASN* 4.7 3.4 - - - +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLU 3.2 15.7 + - - +
49A MET* 3.5 15.3 - - - +
50A TYR 3.3 0.6 - - - -
51A GLN* 1.3 78.4 - - - +
53A ASP* 1.3 69.6 + - - +
55A ASN* 4.0 7.7 + - - +
7B LEU* 4.5 13.9 - - + +
10B ILE* 5.1 1.8 - - + -
11B ALA* 3.2 43.5 - - + +
14B ALA* 4.9 16.2 - - + -
15B ILE* 6.5 2.0 - - + -
28E ARG* 5.6 1.1 - - - +
30F ARG* 4.3 24.9 - - + +
111F LYS* 3.7 13.8 + - - +
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET 3.2 12.6 + - - +
50A TYR* 3.3 5.4 + - + +
52A ILE* 1.3 82.0 - - - +
54A ASN* 1.3 78.0 + - - +
55A ASN* 3.9 5.2 + - - +
67A LEU* 4.6 10.0 - - - +
30F ARG* 2.7 40.6 + - - -
111F LYS* 3.9 18.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 2.8 63.4 + - + +
53A ASP* 1.3 89.2 + - - +
55A ASN* 1.3 72.5 + - - +
56A SER* 3.5 6.9 + - - +
67A LEU* 5.7 0.8 - - - +
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Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 3.2 34.6 + - - +
52A ILE* 4.0 10.7 + - - +
53A ASP 4.5 3.8 - - - +
54A ASN* 1.3 81.8 - - - +
56A SER* 1.3 59.4 + - - +
15B ILE* 5.7 7.9 - - - +
74E ALA* 3.3 34.3 - - + +
75E ASN* 2.7 34.1 + - - +
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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