Contacts of the helix formed by residues 3 - 34 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12 MET 4.0 0.4 + - - -
22 LEU* 1.3 75.1 - - - +
42 GLU* 1.3 65.7 + - - +
52 ARG* 3.8 2.7 + - - -
62 MET* 3.0 12.9 + - - +
72 LEU* 3.0 22.5 + - - +
1112 GLU* 2.6 37.9 + - - -
1132 ASP* 5.4 1.0 + - - -
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Residues in contact with GLU 4 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22 LEU 3.9 1.2 + - - -
32 SER* 1.3 72.9 - - - +
52 ARG* 1.3 60.4 + - - +
72 LEU* 3.8 8.9 + - + +
82 LYS* 3.4 23.4 + - - +
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Residues in contact with ARG 5 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 SER* 3.2 2.3 + - - +
42 GLU* 1.3 75.8 - - - +
62 MET* 1.3 59.6 + - - +
82 LYS* 3.6 7.3 + - + +
92 ALA* 3.1 27.4 + - - +
1072 LEU* 4.3 23.4 - - + +
1112 GLU* 3.7 20.2 - - - +
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Residues in contact with MET 6 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22 LEU* 3.8 13.9 - - + -
32 SER* 3.0 24.6 + - - +
52 ARG* 1.3 76.7 - - - +
72 LEU* 1.3 59.5 + - - +
92 ALA* 3.1 5.1 + - - +
102 LEU* 2.8 37.5 + - + +
1042 LEU* 4.4 12.8 - - - +
1072 LEU* 3.8 20.4 - - + +
1082 ALA* 3.7 32.5 - - + +
1112 GLU* 3.6 19.2 + - - +
1132 ASP* 3.8 23.6 - - + +
1162 THR* 3.8 18.4 - - - +
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Residues in contact with LEU 7 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22 LEU* 4.2 23.0 - - + +
32 SER 3.0 15.9 + - - +
42 GLU* 4.1 7.9 - - + +
62 MET* 1.3 76.3 - - - +
82 LYS* 1.3 54.8 + - - +
102 LEU* 3.4 4.7 + - - +
112 ASN* 2.7 55.3 + - - +
612 ILE* 3.8 16.4 - - + -
662 GLY* 4.2 4.9 - - - -
672 ARG* 3.6 35.4 - - + +
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Residues in contact with LYS 8 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42 GLU 3.4 16.0 + - - +
52 ARG* 3.8 7.6 - - + +
62 MET 3.2 0.4 - - - -
72 LEU* 1.3 78.0 - - - +
92 ALA* 1.3 58.1 + - - +
112 ASN* 3.5 6.9 + - - +
122 ASP* 3.0 55.4 + - - +
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Residues in contact with ALA 9 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52 ARG* 3.1 18.4 + - + +
62 MET 3.1 5.1 + - - +
82 LYS* 1.3 77.9 - - - +
102 LEU* 1.3 59.6 + - - +
122 ASP* 3.6 9.3 + - - +
132 GLN* 3.3 21.0 + - - +
162 ARG* 4.9 1.7 + - - -
1042 LEU* 3.8 24.2 - - + +
1072 LEU* 3.9 18.2 - - + -
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Residues in contact with LEU 10 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22 LEU* 3.8 34.8 - - + -
62 MET* 2.8 24.7 + - + +
72 LEU* 3.8 3.8 - - - +
92 ALA* 1.3 74.6 - - - +
112 ASN* 1.3 58.5 + - - +
132 GLN* 3.3 4.0 + - - +
142 LEU* 3.0 27.4 + - - +
572 PHE* 3.9 30.9 - - + -
602 TYR* 4.0 19.5 - - + -
612 ILE* 3.9 18.8 - - + +
1042 LEU* 4.1 11.9 - - + -
1162 THR* 4.0 19.3 - - + -
1192 PHE* 4.1 8.7 - - + -
1202 LEU* 5.2 0.9 - - + -
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Residues in contact with ASN 11 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72 LEU* 2.7 41.1 + - - +
82 LYS* 3.7 8.2 - - + +
92 ALA 3.4 0.2 - - - -
102 LEU* 1.3 76.9 - - - +
122 ASP* 1.3 64.4 + - - +
142 LEU* 3.5 9.5 - - - +
152 ASN* 3.2 22.2 + - - +
612 ILE* 4.1 8.0 - - - +
672 ARG 3.5 17.2 + - - -
682 VAL* 3.4 12.6 - - - +
692 GLU* 3.1 41.0 + - + +
712 ASP* 4.7 5.2 - - - +
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Residues in contact with ASP 12 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 LYS* 3.0 49.8 + - - +
92 ALA* 3.7 9.0 - - - +
102 LEU 3.2 0.4 - - - -
112 ASN* 1.3 78.2 - - - +
132 GLN* 1.3 56.2 + - - +
152 ASN* 3.3 8.3 + - - +
162 ARG* 3.0 48.7 + - - +
712 ASP* 3.9 14.7 - - - +
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Residues in contact with GLN 13 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 ALA 3.3 7.7 + - - +
102 LEU 3.3 4.5 + - - +
122 ASP* 1.3 75.8 - - - +
142 LEU* 1.3 65.7 + - - +
162 ARG* 3.1 19.4 + - - +
172 GLU* 3.0 48.2 + - - +
572 PHE* 3.5 28.3 - - + -
972 ILE* 3.8 10.9 - - - +
1002 SER* 2.9 39.7 + - - +
1012 ILE* 3.6 16.2 - - + +
1042 LEU* 3.6 21.1 - - + +
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Residues in contact with LEU 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 LEU 3.0 12.9 + - - +
112 ASN* 3.5 13.2 - - - +
132 GLN* 1.3 77.7 - - - +
152 ASN* 1.3 60.9 + - + +
172 GLU* 3.4 5.4 + - - +
182 LEU* 3.2 41.9 + - + +
542 ALA* 3.6 16.8 - - + +
572 PHE* 4.0 15.3 - - + -
582 TYR* 3.6 34.8 - - + +
612 ILE* 4.1 5.2 - - + -
682 VAL* 4.0 23.1 - - + -
692 GLU 6.0 0.4 - - - +
702 LEU* 3.8 18.4 - - + -
25K PHE* 4.5 7.0 - - + -
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Residues in contact with ASN 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112 ASN 3.2 10.1 + - - +
122 ASP* 3.5 11.6 - - - +
132 GLN 3.2 0.2 - - - -
142 LEU* 1.3 79.6 - - + +
162 ARG* 1.3 60.8 + - - +
182 LEU* 3.4 9.6 + - - +
192 TYR* 3.1 25.5 + - - +
702 LEU* 5.8 0.6 - - + +
712 ASP* 3.1 51.7 + - - +
722 GLU 3.4 14.7 + - - +
732 ILE* 4.5 4.7 - - - +
742 PRO* 4.9 6.1 - - - +
22K TYR* 3.6 8.7 + - - -
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Residues in contact with ARG 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 ALA 4.9 1.4 + - - -
122 ASP* 3.0 40.9 + - - +
132 GLN* 3.1 40.0 + - - +
152 ASN* 1.3 76.3 - - - +
172 GLU* 1.3 58.9 + - - +
192 TYR* 3.4 9.3 + - - +
202 SER* 3.0 30.0 + - - -
962 PHE* 3.9 33.0 - - + -
972 ILE* 4.1 8.8 - - + +
1002 SER* 3.8 22.7 + - - -
1042 LEU* 5.9 0.4 - - - +
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Residues in contact with GLU 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 GLN* 3.0 38.1 + - - +
142 LEU 3.7 5.4 - - - +
162 ARG* 1.3 75.6 - - - +
182 LEU* 1.3 58.8 + - - +
202 SER* 3.4 4.8 + - - -
212 ALA* 3.1 21.0 + - - +
502 GLU* 2.8 52.7 - - - +
532 HIS* 3.6 23.0 + - + +
542 ALA* 3.9 9.0 - - + +
572 PHE* 4.2 12.6 - - + -
972 ILE* 4.0 14.6 - - - +
1012 ILE* 4.6 1.4 - - - +
1232 PHE* 4.2 13.5 - - - -
1272 GLN* 4.3 4.3 + - - -
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Residues in contact with LEU 18 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142 LEU* 3.2 36.4 + - + +
152 ASN* 3.7 10.1 - - - +
162 ARG 3.3 0.2 - - - -
172 GLU* 1.3 75.0 - - - +
192 TYR* 1.3 63.6 + - - +
212 ALA* 3.5 7.1 - - + +
222 TYR* 3.2 20.1 + - - +
512 ILE* 4.9 20.4 - - + -
542 ALA* 3.8 16.4 - - + -
702 LEU* 4.0 2.7 - - + -
732 ILE* 4.2 18.0 - - + +
22K TYR* 3.6 37.5 - - + +
25K PHE* 4.2 11.4 - - + -
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Residues in contact with TYR 19 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 ASN* 3.1 14.7 + - - +
162 ARG* 3.7 10.1 - - - +
172 GLU 3.3 0.2 - - - -
182 LEU* 1.3 74.7 - - - +
202 SER* 1.3 55.2 + - - +
222 TYR* 2.9 4.0 + - + -
232 LEU* 2.6 49.2 + - + +
732 ILE* 4.0 13.4 - - + +
742 PRO* 3.8 46.7 - - + -
752 LYS 4.7 2.2 + - - -
762 PRO* 3.9 15.2 - - + +
772 PRO* 3.8 22.7 - - - +
932 HIS* 3.6 31.2 - + - -
962 PHE* 5.9 2.0 - + - -
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Residues in contact with SER 20 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162 ARG 3.0 15.6 + - - -
172 GLU* 3.4 11.7 + - - -
192 TYR* 1.3 76.1 - - - +
212 ALA* 1.3 59.9 + - - +
232 LEU* 3.4 3.3 + - - +
242 TYR* 3.0 36.6 + - - -
502 GLU* 3.6 24.6 + - - -
932 HIS* 3.1 26.7 + - - -
942 GLU* 5.7 0.4 - - - -
972 ILE* 3.4 14.6 - - - +
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Residues in contact with ALA 21 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172 GLU 3.1 12.5 + - - +
182 LEU* 3.5 13.5 - - + +
202 SER* 1.3 77.2 - - - +
222 TYR* 1.3 56.9 + - - +
252 PHE* 3.2 23.4 + - - +
472 ALA* 3.3 40.1 - - + +
502 GLU* 3.5 5.1 - - + +
512 ILE* 3.7 21.3 - - + -
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Residues in contact with TYR 22 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LEU 3.2 11.7 + - - +
192 TYR* 2.9 10.1 + + + +
212 ALA* 1.3 76.5 - - - +
232 LEU* 1.3 60.0 + - - +
252 PHE* 3.5 10.8 + + + +
262 ALA* 3.0 26.5 + - - +
732 ILE* 3.8 23.6 - - + -
742 PRO 4.0 4.0 - - - -
762 PRO* 3.6 32.6 - - + +
15K ASN* 3.6 11.1 + - - -
18K LEU* 3.6 28.5 - - + +
70K LEU* 3.5 31.4 - - + +
71K ASP 2.7 29.2 + - - -
73K ILE* 3.7 20.4 - - + +
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Residues in contact with LEU 23 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192 TYR* 2.6 34.9 + - + +
202 SER* 3.9 4.7 - - - +
212 ALA 3.4 0.2 - - - -
222 TYR* 1.3 71.2 - - - +
242 TYR* 1.3 64.4 + - + +
262 ALA* 3.2 6.6 + - - +
272 MET* 3.0 54.8 + - + +
762 PRO* 4.3 5.1 - - + +
772 PRO* 3.8 29.6 - - + -
802 TRP* 4.2 7.6 - - + -
892 ALA 5.2 0.7 - - - +
932 HIS* 3.5 47.6 - - + +
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Residues in contact with TYR 24 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202 SER* 3.0 26.4 + - - +
232 LEU* 1.3 80.3 - - + +
252 PHE* 1.3 60.1 + - - +
262 ALA 3.3 0.2 - - - -
272 MET* 3.5 13.1 + - + +
282 ALA* 2.9 27.9 + - - +
422 TRP* 5.9 0.7 - + - -
432 MET* 3.4 46.3 - - + +
462 GLN* 3.7 22.2 - - + -
472 ALA* 4.1 6.3 - - + -
502 GLU* 3.6 31.2 - - + -
902 ALA* 4.1 26.1 + - + +
932 HIS* 4.5 9.6 - + - -
942 GLU* 2.5 35.5 + - - +
1342 VAL* 4.8 5.5 - - + +
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Residues in contact with PHE 25 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212 ALA 3.2 19.3 + - - +
222 TYR* 3.6 16.8 - + + +
232 LEU 3.2 0.2 - - - -
242 TYR* 1.3 77.0 - - - +
262 ALA* 1.3 56.9 + - - +
282 ALA* 3.4 9.2 + - + +
292 ALA* 3.1 25.8 + - - +
442 LYS* 4.9 7.6 - - + +
472 ALA* 4.2 8.9 - - + +
14K LEU* 4.5 5.8 - - + -
18K LEU* 4.2 19.3 - - + -
54K ALA* 5.2 4.0 - - + -
55K LEU* 3.8 31.0 - - + -
58K TYR* 3.7 35.0 - + + -
70K LEU* 3.6 37.5 - - + +
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Residues in contact with ALA 26 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 TYR 3.0 14.7 + - - +
232 LEU* 3.2 10.1 + - - +
252 PHE* 1.3 75.2 - - - +
272 MET* 1.3 62.4 + - - +
292 ALA* 3.5 6.7 + - - +
302 TYR* 3.2 19.6 + - - +
762 PRO* 3.7 19.5 - - + -
772 PRO 3.6 22.0 - - - +
782 LYS* 4.5 3.8 - - - +
802 TRP* 4.0 6.9 - - + -
67K ARG* 5.1 0.5 + - - -
70K LEU* 3.6 12.1 - - + +
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Residues in contact with MET 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 LEU* 3.0 35.2 + - + +
242 TYR* 3.7 13.7 - - + +
252 PHE 3.3 0.4 - - - -
262 ALA* 1.3 74.0 - - - +
282 ALA* 1.3 59.9 + - - +
302 TYR* 3.1 2.9 + - - +
312 PHE* 2.9 42.6 + - + -
432 MET* 3.7 31.4 - - + -
802 TRP* 3.6 37.9 - - + -
862 ALA* 3.4 29.2 - - + +
892 ALA* 4.3 4.7 - - + -
902 ALA* 3.8 23.3 - - + +
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Residues in contact with ALA 28 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 TYR 2.9 17.9 + - - +
252 PHE* 3.5 12.1 - - + +
262 ALA 3.3 0.2 - - - -
272 MET* 1.3 76.5 - - - +
292 ALA* 1.3 56.2 + - - +
312 PHE 3.6 0.2 + - - -
322 GLU* 3.0 22.7 + - - +
402 ALA* 3.6 28.1 - - - +
432 MET* 3.8 10.5 - - + +
442 LYS* 3.8 18.4 - - + +
58K TYR* 2.9 14.8 + - - +
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Residues in contact with ALA 29 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 PHE 3.1 12.9 + - - +
262 ALA* 3.6 11.7 - - - +
282 ALA* 1.3 76.9 - - - +
302 TYR* 1.3 61.9 + - - +
322 GLU 3.5 0.2 + - - -
332 ASP* 3.3 14.7 + - - +
58K TYR* 3.4 19.6 + - + -
62K TYR* 2.6 30.9 + - - +
67K ARG* 3.8 11.1 + - - +
68K VAL* 4.0 14.4 - - + +
70K LEU* 5.5 2.7 - - + -
----------------------------------------------------------
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Residues in contact with TYR 30 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 ALA 3.2 11.2 + - - +
272 MET* 3.1 10.0 + - - +
292 ALA* 1.3 79.8 - - - +
312 PHE* 1.3 80.0 + + - +
332 ASP* 3.4 17.9 + - + +
342 LEU* 3.5 38.4 + - + +
792 GLU* 4.3 3.8 - - + -
802 TRP* 3.1 62.4 + + + -
812 GLU 4.0 1.2 + - - -
822 SER* 3.2 23.4 - - - -
832 PRO* 3.5 2.0 - - + +
862 ALA* 4.0 21.3 - - + -
67K ARG* 3.8 22.6 - - - +
----------------------------------------------------------
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Residues in contact with PHE 31 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272 MET* 2.9 33.7 + - + +
282 ALA 4.1 1.8 - - - +
302 TYR* 1.3 83.9 - + - +
322 GLU* 1.3 63.5 + - - +
342 LEU* 3.2 9.8 + - + +
362 LEU* 3.0 52.2 + - + +
392 PHE* 3.5 28.7 - + + -
402 ALA 3.9 5.6 - - - +
432 MET* 4.1 22.4 - - + -
832 PRO* 3.7 27.8 - - + -
862 ALA* 3.9 18.6 - - + -
872 PHE* 3.6 35.4 - + - -
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Residues in contact with GLU 32 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 ALA 3.0 15.7 + - - +
292 ALA 3.6 5.6 - - - +
302 TYR 3.3 0.2 - - - -
312 PHE* 1.3 76.4 - - - +
332 ASP* 1.3 62.4 + - - +
352 GLY* 3.2 13.0 + - - +
362 LEU 4.8 2.2 - - - +
372 GLU* 3.4 30.8 - - - +
402 ALA* 3.4 14.7 - - - +
442 LYS* 2.9 29.0 + - - -
58K TYR* 3.0 17.0 + - - +
59K ASN* 6.0 0.4 - - - -
62K TYR* 3.7 33.4 - - + -
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Residues in contact with ASP 33 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292 ALA 3.3 4.4 + - - +
302 TYR* 3.5 11.8 - - - +
312 PHE 3.2 0.2 - - - -
322 GLU* 1.3 76.2 - - - +
342 LEU* 1.3 63.6 + - - +
352 GLY* 3.1 8.6 + - - -
792 GLU* 5.5 1.9 - - - +
62K TYR* 3.7 7.5 - - + -
66K GLY 4.5 8.7 - - - +
67K ARG* 3.6 40.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 TYR* 3.5 51.7 + - + +
312 PHE* 3.2 9.7 + - + +
332 ASP* 1.3 82.2 - - + +
352 GLY* 1.3 60.9 + - - +
362 LEU* 3.6 18.6 + - + +
832 PRO* 4.2 19.3 - - + -
143H PHE* 5.6 7.4 - - - -
----------------------------------------------------------
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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