Contacts of the helix formed by residues 31 - 60 (chain A) in PDB entry 5VEY
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 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 1.3 77.1 - - - +
32A SER* 1.4 68.5 + - - +
33A LYS* 3.1 13.9 + - - +
34A ALA* 2.9 17.0 + - - +
35A MET* 3.0 11.9 + - - +
166A ARG* 4.2 22.0 - - - +
167A ILE 3.1 19.6 + - - -
168A ILE* 4.5 10.5 - - - -
169A PRO* 5.2 1.3 - - - -
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE 3.9 1.0 + - - -
31A SER* 1.4 76.3 + - - +
33A LYS* 1.3 63.0 + - - +
35A MET* 3.4 18.0 + - - +
36A GLY* 3.3 16.5 + - - -
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.1 8.8 + - - +
32A SER* 1.3 80.6 + - - +
34A ALA* 1.3 63.9 + - - +
36A GLY* 3.2 3.9 + - - +
37A ILE* 3.1 35.2 + - + +
169A PRO* 4.0 28.5 - - + +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 3.3 20.0 - - + -
31A SER* 2.9 13.4 + - - +
33A LYS* 1.3 78.6 - - - +
35A MET* 1.3 63.6 + - - +
37A ILE* 3.2 9.2 + - - +
38A MET* 3.1 26.2 + - - +
167A ILE 3.8 16.4 - - - +
168A ILE* 4.6 3.6 - - - -
169A PRO* 4.6 1.5 - - - +
172A LEU* 3.7 25.1 - - + +
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Residues in contact with MET 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 2.9 49.6 - - - +
15A ILE* 4.8 1.3 - - + -
17A VAL* 4.1 7.6 - - + +
18A TYR* 3.6 23.3 - - + -
30A ILE* 3.7 32.3 - - + +
31A SER 3.0 17.6 + - - +
32A SER* 3.5 17.9 - - - +
33A LYS 3.2 0.2 - - - -
34A ALA* 1.3 75.2 - - - +
36A GLY* 1.3 58.6 + - - +
38A MET* 3.2 8.0 + - - +
39A ASN* 2.7 32.8 + - - -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 5.1 2.9 + - - +
14A SER* 5.5 0.2 - - - -
32A SER 3.3 7.0 + - - -
33A LYS* 3.2 7.6 + - - -
35A MET* 1.3 77.7 - - - +
37A ILE* 1.3 64.1 + - - +
39A ASN* 3.1 20.8 + - - +
40A SER* 3.2 12.1 + - - -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 3.1 26.1 + - + +
34A ALA* 3.2 10.7 + - - +
36A GLY* 1.3 75.5 - - - +
38A MET* 1.3 64.4 + - + +
40A SER* 2.5 29.0 + - - +
41A PHE* 3.1 8.3 + - + +
169A PRO* 3.4 44.9 - - + -
172A LEU* 4.5 10.3 - - + -
191A ILE* 3.8 38.1 - - + +
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Residues in contact with MET 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.3 19.3 - - + -
30A ILE* 4.5 7.6 - - + -
34A ALA 3.1 17.1 + - - +
35A MET 3.4 8.3 - - - +
37A ILE* 1.3 77.2 - - - +
39A ASN* 1.3 63.3 + - - +
41A PHE* 3.1 20.8 + - + +
42A VAL* 3.1 19.4 + - + +
148A THR* 3.5 48.9 - - + +
151A ILE* 4.0 33.4 - - + -
152A LEU* 4.3 7.2 - - + -
172A LEU* 4.4 13.5 - - + -
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.3 19.3 - - - +
11A GLU 3.8 8.1 - - - +
12A SER* 4.8 0.7 - - - -
13A TYR* 2.6 40.7 + - + +
14A SER* 3.4 23.4 - - - +
17A VAL* 5.3 0.4 - - - +
35A MET 2.7 33.1 + - - -
36A GLY* 3.1 12.7 + - - +
38A MET* 1.3 76.1 - - - +
40A SER* 1.3 61.9 + - - +
42A VAL* 3.3 10.5 + - - +
43A ASN* 2.8 26.9 + - - +
----------------------------------------------------------
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.5 19.0 - - - +
36A GLY 3.2 7.4 + - - -
37A ILE* 2.5 28.2 + - - +
39A ASN* 1.3 76.2 - - - +
41A PHE* 1.3 59.7 + - - +
43A ASN* 3.3 4.6 + - - +
44A ASP* 2.9 40.4 + - - +
----------------------------------------------------------
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.1 8.9 + - + +
38A MET* 3.2 21.8 - - + +
40A SER* 1.3 83.5 + - - +
42A VAL* 1.3 69.3 + - + +
44A ASP* 3.3 7.4 + - + +
45A ILE* 3.0 59.1 + - + +
144A LEU* 5.4 2.7 - - + -
147A LEU* 3.5 30.5 - - + -
148A THR* 4.8 3.1 - - - -
151A ILE* 3.5 34.5 - - + -
182A LEU* 5.8 0.9 - - + -
185A LEU* 4.4 8.5 - - + -
186A LEU* 3.7 38.1 - - + -
189A VAL* 6.0 1.3 - - + -
191A ILE* 6.0 4.9 - - + -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.7 32.3 - - + +
38A MET* 3.1 16.5 + - + +
39A ASN* 3.3 8.0 + - - +
41A PHE* 1.3 84.0 - - + +
43A ASN* 1.3 56.3 + - - +
45A ILE* 3.4 1.9 + - - +
46A PHE* 2.9 29.6 + - + +
114A PHE* 4.3 21.8 - - + -
144A LEU* 4.0 34.6 - - + +
148A THR* 4.6 13.0 - - + +
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.7 29.3 + - + +
10A LYS* 3.6 17.9 - - - +
11A GLU* 2.7 33.5 + - - +
13A TYR* 5.0 1.6 - - - -
39A ASN 2.8 10.7 + - - +
40A SER* 3.3 9.2 + - - +
42A VAL* 1.3 81.0 - - - +
44A ASP* 1.3 63.2 + - - +
46A PHE* 3.4 6.4 + - - +
47A GLU* 3.1 35.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 2.9 27.1 + - - +
41A PHE* 3.3 8.9 + - + +
43A ASN* 1.3 76.3 - - - +
45A ILE* 1.3 68.9 + - + +
47A GLU* 3.4 15.7 + - - +
48A ARG* 3.2 30.5 + - - +
186A LEU* 6.1 0.4 - - + -
189A VAL* 4.1 33.2 - - + +
----------------------------------------------------------
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.0 58.3 + - + +
42A VAL 3.9 3.4 - - - +
44A ASP* 1.3 74.6 - - + +
46A PHE* 1.3 66.5 + - - +
48A ARG* 3.3 14.3 + - + +
49A ILE* 3.0 56.7 + - + +
78A LEU* 6.1 1.6 - - + -
144A LEU* 3.7 19.1 - - + -
147A LEU* 4.1 12.1 - - + -
185A LEU* 4.1 25.4 - - + -
186A LEU* 5.2 3.8 - - + -
189A VAL* 6.5 0.7 - - + -
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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
----------------------------------------------------------
42A VAL* 2.9 20.4 + - + +
43A ASN* 3.6 7.6 - - - +
45A ILE* 1.3 78.2 - - - +
47A GLU* 1.3 63.1 + - + +
49A ILE* 4.1 3.7 - - - +
50A ALA* 2.8 39.5 + - + +
119A VAL* 3.8 18.4 - - + -
122A LEU* 3.5 46.7 - - + -
123A LEU* 3.4 27.1 - - + -
128A TYR* 5.3 5.4 - + - -
140A LEU* 3.2 37.0 - - + +
144A LEU* 4.7 11.2 - - + +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN* 3.1 23.5 + - - +
44A ASP* 3.7 18.6 - - - +
45A ILE 3.3 0.2 - - - -
46A PHE* 1.3 83.8 - - + +
48A ARG* 1.3 62.8 + - + +
50A ALA* 3.7 4.4 - - - +
51A GLY* 3.1 20.8 + - - -
128A TYR* 4.0 13.8 + - - +
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.2 20.4 + - - +
45A ILE* 3.8 12.9 - - + +
47A GLU* 1.3 77.3 - - + +
49A ILE* 1.3 64.0 + - + +
51A GLY* 4.1 0.5 - - - -
52A GLU* 3.1 23.9 + - - +
77A LEU* 3.5 38.1 + - + +
184A LYS 5.2 3.4 + - - -
185A LEU* 2.7 36.5 + - - +
186A LEU* 5.8 0.2 - - - +
188A ARG* 4.9 23.2 - - - +
189A VAL* 4.6 19.8 - - - +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.0 44.2 + - + +
46A PHE 4.1 1.6 - - - +
48A ARG* 1.3 72.2 - - + +
50A ALA* 1.3 62.5 + - - +
52A GLU* 3.2 3.0 + - - +
53A ALA* 2.8 32.2 + - + +
70A ILE* 4.4 16.8 - - + -
73A ALA* 4.5 9.4 - - + +
74A VAL* 4.8 9.4 - - + -
77A LEU* 3.6 25.1 - - + -
78A LEU* 5.9 4.5 - - + -
140A LEU* 3.4 37.9 - - + -
143A VAL* 4.9 10.8 - - + -
----------------------------------------------------------
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 2.8 26.2 + - + +
47A GLU* 3.7 2.0 - - - +
49A ILE* 1.3 78.5 - - - +
51A GLY* 1.3 57.9 + - - +
53A ALA* 3.7 5.5 - - - +
54A SER* 3.0 29.6 + - - -
65A ILE* 5.6 0.7 - - - +
123A LEU* 4.4 20.9 - - + -
128A TYR* 3.5 35.9 - - + +
140A LEU* 5.8 0.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 3.1 15.6 + - - -
48A ARG 4.1 0.9 - - - -
50A ALA* 1.3 76.7 - - - +
52A GLU* 1.3 58.1 + - - +
54A SER* 2.5 20.7 + - - -
55A ARG* 3.1 20.9 + - - +
128A TYR* 3.5 17.6 - - - -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG 3.1 16.4 + - - +
49A ILE 3.6 3.8 - - - +
51A GLY* 1.3 73.2 - - - +
53A ALA* 1.3 64.8 + - - +
55A ARG* 3.3 12.5 + - + +
56A LEU* 3.2 27.3 + - + +
73A ALA* 3.0 22.2 - - + +
76A LEU* 3.1 37.2 - - + +
77A LEU* 2.8 36.2 - - + +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 2.8 19.2 + - + +
50A ALA* 3.7 7.0 - - - +
52A GLU* 1.3 73.5 - - - +
54A SER* 1.3 66.8 + - - +
56A LEU* 3.2 13.9 + - - +
57A ALA* 3.0 22.4 + - - +
65A ILE* 4.3 24.5 - - + +
69A GLU* 4.4 6.1 - - - +
70A ILE* 4.4 21.1 - - + +
73A ALA* 4.3 2.2 - - + +
123A LEU* 6.4 0.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA 3.0 14.3 + - - -
51A GLY* 2.5 27.9 + - - -
53A ALA* 1.3 77.4 - - - +
55A ARG* 1.3 58.3 + - - +
57A ALA* 3.2 8.8 + - - +
58A HIS* 2.6 38.0 + - - -
65A ILE* 4.8 6.2 - - - +
128A TYR* 3.7 36.7 - - - -
129A SER* 6.0 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY* 3.1 18.3 + - - +
52A GLU* 3.5 13.0 - - + +
54A SER* 1.3 84.6 + - - +
56A LEU* 1.3 63.7 + - + +
58A HIS* 3.2 12.3 + - - +
59A TYR* 3.2 19.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.2 19.4 + - + +
53A ALA* 3.2 7.8 + - - +
55A ARG* 1.3 75.3 - - + +
57A ALA* 1.3 64.9 + - - +
59A TYR* 3.2 13.7 + - + +
60A ASN* 3.0 32.6 + - - +
69A GLU* 3.1 38.8 - - + +
72A THR* 3.9 19.3 - - + -
73A ALA* 3.9 20.9 - - + +
76A LEU* 5.4 4.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 3.0 12.1 + - - +
54A SER* 3.2 13.2 + - - +
56A LEU* 1.3 76.0 - - - +
58A HIS* 1.3 60.3 + - + +
60A ASN* 3.3 3.2 + - - +
61A LYS* 2.8 23.0 + - - -
62A ARG* 2.9 33.9 + - + +
63A SER 5.1 1.1 - - - +
64A THR 5.3 1.1 - - - +
65A ILE* 4.4 16.4 - - + -
69A GLU* 4.2 12.1 - - + +
129A SER* 5.7 1.8 - - - -
----------------------------------------------------------
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 2.6 31.8 + - - -
55A ARG* 3.5 10.6 - - - +
56A LEU 3.2 0.2 - - - -
57A ALA* 1.3 77.1 - - + +
59A TYR* 1.3 65.1 + - - +
61A LYS* 3.0 29.9 + - - +
128A TYR 4.4 15.9 + - - -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG 3.2 9.1 + - - +
56A LEU* 3.2 18.8 + - + +
58A HIS* 1.3 79.0 - - - +
60A ASN* 1.3 74.3 + - - +
61A LYS* 3.5 8.0 + - - +
----------------------------------------------------------
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.0 22.5 + - - +
57A ALA* 3.9 3.6 - - - +
59A TYR* 1.3 90.0 - - - +
61A LYS* 1.3 70.9 + - - +
62A ARG* 3.1 27.5 + - + +
69A GLU* 3.5 24.6 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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