Contacts of the helix formed by residues 37 - 66 (chain s) in PDB entry 3J9X
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 VAL 37 (chain s).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767 T 3.9 22.2 - - - +
777 A 3.9 4.3 - - - +
16r LYS* 4.7 10.3 - - + -
19r ALA* 3.7 18.4 - - + -
20r LYS* 3.6 30.5 - - + -
33s ILE 3.0 20.9 + - - +
34s LEU* 3.5 15.7 - - + +
36s ASN* 1.3 76.3 - - - +
38s SER* 1.3 69.2 + - - +
39s PRO* 3.5 1.6 - - - -
40s VAL* 3.3 8.2 + - + +
41s ALA* 2.9 19.7 + - + +
21t PHE* 4.5 9.4 - - + -
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Residues in contact with SER 38 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34s LEU 2.6 23.5 + - - -
35s SER* 3.3 15.5 - - - -
36s ASN 3.3 0.2 - - - -
37s VAL* 1.3 80.8 - - - +
39s PRO* 1.4 73.9 - - - +
41s ALA* 2.9 10.0 + - - +
42s GLN* 2.9 27.1 + - - +
21t PHE* 3.5 21.8 - - - -
22t ASN* 5.5 2.0 + - - -
25t SER* 4.7 4.9 + - - -
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Residues in contact with PRO 39 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35s SER 4.0 4.5 - - - +
36s ASN 3.6 12.3 - - - +
37s VAL 3.5 1.6 - - - -
38s SER* 1.4 97.4 - - - +
40s VAL* 1.3 69.1 + - + +
42s GLN* 3.5 20.6 - - + +
43s GLN* 3.1 22.2 + - - +
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Residues in contact with VAL 40 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767 T 4.8 2.2 - - - +
12r GLN* 5.0 2.0 - - - +
15r ALA* 4.1 29.4 - - + +
16r LYS* 3.9 32.1 - - + +
19r ALA* 4.5 3.8 - - + -
36s ASN 4.3 13.2 - - - +
37s VAL* 3.5 12.8 - - + +
38s SER 3.0 0.8 - - - -
39s PRO* 1.3 79.4 - - + +
41s ALA* 1.3 67.1 + - - +
43s GLN* 3.1 9.4 + - + +
44s ASN* 3.1 32.2 + - - +
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Residues in contact with ALA 41 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757 A 3.9 4.4 - - - +
767 T 3.5 39.7 - - - +
37s VAL 2.9 17.9 + - - +
38s SER 3.4 3.4 - - - +
40s VAL* 1.3 76.6 - - - +
42s GLN* 1.3 58.0 + - - +
44s ASN* 3.1 3.2 + - - +
45s PHE* 2.8 31.5 + - - +
17t TRP* 4.2 15.0 - - + -
21t PHE* 4.5 9.0 - - + -
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Residues in contact with GLN 42 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38s SER* 2.9 21.7 + - - +
39s PRO* 3.5 29.5 - - - +
40s VAL 3.1 0.2 - - - -
41s ALA* 1.3 76.8 - - - +
43s GLN* 1.3 62.9 + - - +
45s PHE* 3.7 0.9 - - - +
46s GLN* 2.9 35.3 + - - +
14t TYR* 3.9 8.7 + - - +
17t TRP* 4.2 13.0 - - + -
18t GLN* 3.2 41.4 - - - +
21t PHE* 5.8 0.9 - - + -
22t ASN* 4.6 2.4 + - - -
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Residues in contact with GLN 43 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12r GLN* 5.3 7.4 - - + +
39s PRO 3.1 11.0 + - - +
40s VAL* 3.3 11.4 - - - +
42s GLN* 1.3 80.9 - - - +
44s ASN* 1.3 59.9 + - - +
46s GLN* 3.4 11.8 + - - +
47s THR* 2.6 60.7 + - - +
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Residues in contact with ASN 44 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757 A 3.6 24.0 - - - +
767 T 2.9 20.0 + - - -
8r ARG* 3.7 25.1 - - - +
12r GLN* 2.9 34.7 + - - +
16r LYS* 5.5 3.4 - - - +
40s VAL* 3.1 21.3 + - - +
41s ALA 3.1 7.5 + - - +
43s GLN* 1.3 76.4 - - - +
45s PHE* 1.3 64.9 + - - +
47s THR* 3.4 5.0 + - - -
48s ASN* 3.1 24.9 + - - +
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Residues in contact with PHE 45 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747 T 4.5 10.1 - - - -
757 A 3.5 27.7 - - - -
2768 T 5.3 6.3 - - - -
41s ALA 2.8 16.3 + - - +
42s GLN 3.7 3.8 - - - +
44s ASN* 1.3 76.5 - - - +
46s GLN* 1.3 59.4 + - - +
49s VAL* 2.9 69.0 + - + +
10t TYR* 5.1 0.4 - + - -
13t ARG* 4.4 5.8 - - + -
14t TYR* 3.5 44.0 - + + -
17t TRP* 3.5 57.9 - + + -
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Residues in contact with GLN 46 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42s GLN* 2.9 27.9 + - - +
43s GLN* 3.8 13.7 + - - +
45s PHE* 1.3 79.1 - - - +
47s THR* 1.3 64.2 + - - +
50s PRO* 3.1 24.7 - - - +
10t TYR* 5.2 11.8 + - - +
14t TYR* 3.4 48.1 + - + -
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Residues in contact with THR 47 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12r GLN* 4.9 12.4 + - - +
43s GLN* 2.6 47.6 + - - +
44s ASN* 3.7 6.1 - - - -
45s PHE 3.2 0.2 - - - -
46s GLN* 1.3 80.1 - - - +
48s ASN* 1.3 72.5 + - - +
50s PRO* 4.3 2.1 - - - +
51s LYS* 3.4 24.0 - - - +
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Residues in contact with ASN 48 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747 T 3.8 18.6 + - - +
757 A 3.0 20.4 + - - -
7r SER* 4.5 8.5 + - - -
8r ARG* 3.8 13.3 - - - +
12r GLN* 5.5 3.8 - - - +
44s ASN* 3.1 10.5 + - - +
47s THR* 1.3 86.0 - - - +
49s VAL* 1.3 67.0 + - - +
50s PRO* 3.4 1.6 - - - -
51s LYS* 2.9 49.8 + - + +
52s PHE* 3.4 11.9 - - + -
88s ASN* 4.9 5.6 + - - -
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Residues in contact with VAL 49 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747 T 3.6 31.9 - - + +
45s PHE* 2.9 58.3 + - + +
48s ASN* 1.3 74.0 - - - +
50s PRO* 1.3 64.0 - - + +
52s PHE* 2.9 26.9 + - + +
53s THR* 3.0 12.6 + - - +
10t TYR* 4.6 6.7 - - + -
13t ARG* 3.8 29.2 - - + +
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Residues in contact with PRO 50 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45s PHE 3.8 1.1 - - - +
46s GLN 3.1 26.7 - - - +
47s THR 4.2 2.5 - - - +
48s ASN 3.4 2.7 - - - -
49s VAL* 1.3 95.4 - - + +
51s LYS* 1.3 61.1 + - + +
53s THR* 3.7 1.8 - - - +
54s SER* 3.2 23.9 + - - -
10t TYR* 3.7 49.1 - - + -
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Residues in contact with LYS 51 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47s THR* 3.4 23.8 + - - +
48s ASN* 2.9 35.7 + - - +
49s VAL 3.0 0.4 - - - -
50s PRO* 1.3 79.6 - - + +
52s PHE* 1.3 63.9 + - + +
54s SER* 2.9 19.2 + - - -
55s VAL* 3.3 13.2 - - - +
84s ALA* 5.5 0.3 - - - +
88s ASN* 3.9 27.6 + - - +
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Residues in contact with PHE 52 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737 A 3.7 16.4 - - + +
747 T 3.4 40.4 - - - +
48s ASN* 3.4 20.4 - - + -
49s VAL* 2.9 8.3 + - + +
51s LYS* 1.3 78.1 - - + +
53s THR* 1.3 66.8 + - - +
54s SER 3.2 1.1 - - - -
55s VAL* 3.1 7.1 + - - +
56s ASN* 2.9 27.3 + - - +
81s LEU* 3.7 30.2 - - + +
84s ALA* 3.6 26.0 - - + -
85s ARG* 3.6 14.6 - - - -
88s ASN* 3.3 31.6 - - - -
13t ARG* 4.5 5.6 - - - +
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Residues in contact with THR 53 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49s VAL* 3.0 7.5 + - - +
50s PRO 3.4 6.0 + - - -
52s PHE* 1.3 77.5 - - - +
54s SER* 1.3 62.9 + - - +
56s ASN* 3.1 9.5 + - + +
57s GLU* 3.0 23.1 + - + +
8t ARG 4.7 4.7 - - - +
9t SER* 4.2 7.2 - - - -
10t TYR* 3.1 45.4 - - + +
13t ARG* 2.7 29.2 + - - +
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Residues in contact with SER 54 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50s PRO 3.2 10.5 + - - -
51s LYS* 2.9 22.3 + - - -
53s THR* 1.3 78.8 - - - +
55s VAL* 1.3 57.9 + - - +
57s GLU* 3.4 6.6 + - - +
58s ASN* 3.0 41.2 + - - -
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Residues in contact with VAL 55 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51s LYS 3.3 17.9 - - - +
52s PHE* 3.1 10.3 + - - +
53s THR 3.1 0.4 - - - -
54s SER* 1.3 77.1 + - - +
56s ASN* 1.3 60.9 + - - +
57s GLU 3.2 0.2 + - - -
58s ASN* 4.9 2.7 - - - +
59s VAL* 2.8 52.1 + - + +
77s GLN* 5.2 0.9 - - - +
80s GLY 4.1 14.1 - - - +
81s LEU* 4.3 10.5 - - + +
84s ALA* 4.0 20.2 - - + -
125s ILE* 3.9 26.0 - - + -
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Residues in contact with ASN 56 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2778 A 4.8 4.6 + - - +
2788 T 4.1 35.0 + - - +
52s PHE* 2.9 17.9 + - - +
53s THR* 3.1 8.9 + - + +
55s VAL* 1.3 76.4 - - - +
57s GLU* 1.3 57.9 + - - +
60s SER* 2.9 30.7 + - - -
77s GLN* 3.1 21.2 + - - +
81s LEU* 3.3 30.2 - - - +
13t ARG* 4.0 21.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 57 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53s THR* 3.0 14.2 + - + +
54s SER* 3.5 11.7 - - - +
56s ASN* 1.3 75.1 - - - +
58s ASN* 1.3 74.7 + - - +
60s SER* 3.2 8.8 + - - -
61s ALA* 3.0 23.4 + - + +
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Residues in contact with ASN 58 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54s SER* 3.0 22.7 + - - +
55s VAL* 4.1 2.9 - - - +
57s GLU* 1.3 88.7 - - - +
59s VAL* 1.3 62.9 + - + +
61s ALA* 3.2 9.5 + - - +
62s VAL* 3.2 25.0 + - - +
124s ILE* 3.7 27.0 - - + +
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Residues in contact with VAL 59 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55s VAL* 2.8 37.1 + - + +
58s ASN* 1.3 73.9 - - + +
60s SER* 1.3 66.0 + - - +
62s VAL* 3.1 9.3 + - - +
63s LEU* 2.9 33.4 + - + +
76s TYR 4.3 1.6 - - - +
77s GLN* 3.3 32.3 - - - +
80s GLY* 4.7 2.2 - - - -
121s VAL* 4.0 38.1 - - + +
124s ILE* 5.5 3.4 - - + -
125s ILE* 4.4 7.4 - - + -
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Residues in contact with SER 60 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2788 T 4.9 0.2 - - - -
2798 A 3.4 9.4 + - - -
56s ASN 2.9 21.2 + - - -
57s GLU* 3.4 10.3 - - - -
58s ASN 3.2 0.2 - - - -
59s VAL* 1.3 77.8 - - - +
61s ALA* 1.3 62.7 + - - +
63s LEU* 3.1 2.8 + - - -
64s THR* 3.0 12.7 + - - -
73s ARG* 2.7 40.5 + - - +
77s GLN* 3.4 12.9 - - - +
89u ARG 4.7 2.9 + - - -
90u ILE 4.7 4.0 + - - -
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Residues in contact with ALA 61 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57s GLU* 3.0 16.4 + - + +
58s ASN* 3.4 12.8 - - - +
60s SER* 1.3 76.0 - - - +
62s VAL* 1.3 63.0 + - + +
64s THR* 3.2 8.2 + - - -
65s GLN* 3.1 31.3 + - - +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58s ASN 3.4 12.8 - - - +
59s VAL* 3.1 12.1 + - + +
61s ALA* 1.3 78.4 - - + +
63s LEU* 1.3 69.2 + - + +
65s GLN* 2.9 23.9 + - - +
66s TYR* 3.0 38.9 + - + -
117s VAL 5.3 0.9 - - - +
120s ALA* 4.0 17.0 - - + +
121s VAL* 4.8 6.7 - - + +
124s ILE* 3.6 32.3 - - + -
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Residues in contact with LEU 63 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59s VAL* 2.9 35.0 + - + +
60s SER* 3.1 7.2 + - - +
62s VAL* 1.3 79.6 - - + +
64s THR* 1.3 61.0 + - - +
66s TYR* 3.2 2.5 + - - +
67s GLY 3.0 4.3 + - - -
68s ILE* 2.9 43.8 + - + -
73s ARG* 3.5 48.2 - - + +
76s TYR* 3.6 34.3 - - + -
77s GLN* 4.0 10.3 - - + +
117s VAL* 4.1 11.0 - - + -
121s VAL* 5.1 0.9 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60s SER 3.0 5.7 + - - -
61s ALA* 3.6 10.0 - - - -
62s VAL 3.2 0.2 - - - -
63s LEU* 1.3 78.0 - - - +
65s GLN* 1.3 61.4 + - + +
67s GLY 3.1 9.5 + - - -
73s ARG* 3.0 22.3 + - - +
90u ILE* 2.6 34.1 + - + +
91u GLY* 3.8 7.4 - - - +
92u SER 3.3 28.0 - - - +
93u GLY* 4.6 1.3 - - - -
94u PRO* 3.3 5.0 - - + +
95u ALA* 3.3 19.6 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61s ALA* 3.1 18.6 + - - +
62s VAL* 2.9 17.5 + - - +
64s THR* 1.3 78.8 - - + +
66s TYR* 1.3 66.8 + - + +
67s GLY 3.3 0.2 - - - -
94u PRO* 3.4 23.7 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62s VAL* 3.0 36.3 + - + +
63s LEU* 3.2 6.7 + - - +
65s GLN* 1.3 83.7 - - + +
67s GLY* 1.3 62.3 + - - +
68s ILE* 3.2 22.0 + - + +
116s GLN* 2.9 42.9 + - - -
117s VAL* 4.1 17.0 - - + -
120s ALA* 3.5 27.3 - - + +
94u PRO* 4.6 0.7 - - - -
----------------------------------------------------------
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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