Contacts of the helix formed by residues 46 - 76 (chain K) in PDB entry 1VEQ
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 46 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO* 2.6 39.2 + - - +
46F ASN* 4.1 20.1 - - + +
46G ASN* 4.2 11.7 - - + +
155G HIS* 4.8 0.7 - - - -
45K PRO* 1.3 82.0 - - + +
47K PHE* 1.3 65.2 + - - +
48K ILE 3.7 1.3 - - - -
49K GLY* 3.6 10.9 + - - +
50K VAL* 3.7 9.4 + - - +
102K VAL* 3.6 32.5 - - - +
103K GLN* 4.7 3.7 + - - +
155K HIS* 4.4 3.4 + - - -
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Residues in contact with PHE 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G TRP* 4.1 14.1 - + - -
151G PHE* 3.3 33.0 - + - -
154G ALA* 3.7 22.4 - - + +
155G HIS* 3.3 32.7 + + + +
39K HIS 5.0 1.3 - - - -
40K TRP 5.6 0.2 - - - -
42K VAL* 3.4 38.5 - - + +
44K GLY 3.6 17.8 + - - +
45K PRO 3.2 4.2 + - - -
46K ASN* 1.3 76.1 - - - +
48K ILE* 1.3 76.0 + - + +
49K GLY 3.0 1.2 + - - -
50K VAL* 3.0 3.8 + - - +
51K HIS* 3.0 51.3 + + + -
102K VAL* 4.7 7.2 - - - -
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Residues in contact with ILE 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLY* 4.0 24.2 - - - +
53G MET* 3.2 42.6 - - + -
151G PHE* 4.2 27.1 - - + -
155G HIS* 3.6 13.8 + - + +
46K ASN 3.7 0.2 - - - -
47K PHE* 1.3 83.3 - - + +
49K GLY* 1.3 73.9 + - - +
51K HIS* 3.1 8.7 + - + -
52K GLU* 3.0 50.1 + - + +
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Residues in contact with GLY 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ILE* 4.0 23.6 - - - +
49F GLY* 5.2 5.8 - - - -
49G GLY* 5.2 5.5 - - - -
46K ASN* 3.6 9.4 + - - -
47K PHE 3.0 2.0 + - - -
48K ILE* 1.3 84.8 - - - +
50K VAL* 1.3 60.3 + - - +
52K GLU* 4.0 2.6 - - - +
53K MET* 3.1 20.5 + - - +
155K HIS* 5.6 0.4 - - - -
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Residues in contact with VAL 50 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K VAL* 5.4 0.7 - - + -
42K VAL* 4.6 13.5 - - + -
46K ASN* 3.7 6.0 + - - +
47K PHE 3.0 7.1 + - - +
49K GLY* 1.3 70.9 - - - +
51K HIS* 1.3 61.1 + - - +
53K MET* 2.6 41.9 + - + +
54K ILE* 3.1 29.4 + - + +
102K VAL* 3.2 34.3 - - + -
105K HIS* 6.5 0.4 - - + -
106K LEU* 3.9 21.3 - - + -
155K HIS* 4.0 17.3 - - + +
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Residues in contact with HIS 51 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G TRP* 4.4 8.1 - + - -
151G PHE* 3.8 25.2 - + - -
70H GLU* 3.3 20.0 + - + -
211H FE 4.1 0.8 - - - -
39K HIS* 2.7 80.2 + + - +
42K VAL* 5.4 3.3 - - - +
47K PHE* 3.0 38.2 + + + +
48K ILE* 3.5 15.3 - - + +
50K VAL* 1.3 82.3 - - - +
52K GLU* 1.3 67.8 + - + +
54K ILE* 3.6 11.7 + - - +
55K ASP 4.1 0.7 + - - -
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Residues in contact with GLU 52 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G MET* 6.1 1.2 - - - -
48K ILE* 3.0 38.5 + - + +
49K GLY* 4.1 2.0 - - - +
50K VAL 2.9 0.8 + - - -
51K HIS* 1.3 80.0 - - + +
53K MET* 1.3 66.2 + - - +
54K ILE 3.1 3.0 + - - -
55K ASP* 3.5 11.5 + - + +
56K PRO* 3.3 18.2 - - - +
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Residues in contact with MET 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ILE* 3.2 40.2 - - + -
52F GLU* 6.1 0.9 - - - -
49K GLY 3.1 15.6 + - - +
50K VAL* 2.6 30.5 + - + +
52K GLU* 1.3 73.5 - - - +
54K ILE* 1.3 60.8 + - + +
56K PRO* 3.6 10.9 - - - +
57K GLN* 4.5 2.4 + - - +
106K LEU* 4.1 26.0 - - + -
148K PHE* 4.1 29.3 - - + -
151K PHE* 4.0 20.9 - - + -
152K VAL 4.7 2.0 - - - +
155K HIS* 3.9 16.6 - - + +
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Residues in contact with ILE 54 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K LEU* 3.6 29.8 - - + +
38K VAL* 3.1 33.4 - - + +
39K HIS* 3.9 17.3 - - + -
42K VAL* 4.9 0.4 - - + -
50K VAL* 3.4 29.4 - - + +
51K HIS* 3.8 7.6 - - - +
52K GLU 3.1 0.8 - - - -
53K MET* 1.3 86.2 - - + +
55K ASP* 1.3 69.4 + - - +
57K GLN* 3.1 13.0 + - - +
58K VAL* 3.1 24.9 + - + -
106K LEU* 6.1 1.3 - - + -
109K LEU* 5.5 2.7 - - + -
148K PHE* 4.7 9.2 - - + -
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Residues in contact with ASP 55 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H FE 3.9 4.5 - - - -
36K LYS* 3.2 29.5 + - - +
39K HIS* 3.3 25.0 + - - -
51K HIS 4.1 2.5 + - - +
52K GLU* 3.5 11.2 + - + +
54K ILE* 1.3 76.5 - - - +
56K PRO* 1.4 67.3 - - + +
58K VAL* 2.9 9.5 + - - +
59K GLU* 2.8 35.2 + - + +
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Residues in contact with PRO 56 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K GLU 3.3 14.8 - - - +
53K MET* 3.6 8.1 - - - +
54K ILE 3.5 3.4 - - - -
55K ASP* 1.4 93.4 - - + +
57K GLN* 1.3 56.3 + - - +
59K GLU* 3.3 7.5 + - + +
60K LEU* 2.8 33.7 + - - +
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Residues in contact with GLN 57 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K LEU* 4.6 4.9 - - + -
53K MET 4.5 1.5 + - - +
54K ILE* 3.1 8.6 + - - +
56K PRO* 1.3 79.0 - - - +
58K VAL* 1.3 57.4 + - - +
60K LEU* 3.5 19.3 - - - +
61K VAL* 2.9 43.1 + - + +
64K TYR* 5.6 1.0 - - - -
113K TYR* 3.1 28.7 + - - +
144K GLU* 4.2 5.5 + - - +
145K LEU* 3.5 27.7 - - - +
148K PHE* 3.0 60.0 - - + +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ARG* 2.8 37.0 + - - +
32K HIS* 4.2 7.6 - - + +
35K LEU* 3.4 31.6 - - + -
36K LYS* 3.6 24.9 - - + +
39K HIS* 5.7 0.2 - - + -
54K ILE* 3.1 24.2 - - + +
55K ASP* 2.9 11.6 + - - +
57K GLN* 1.3 74.6 - - - +
59K GLU* 1.3 57.0 + - + +
60K LEU 2.7 13.7 + - - -
61K VAL* 2.9 5.9 + - - +
62K ARG* 2.9 24.1 + - - +
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Residues in contact with GLU 59 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H GLU* 3.7 30.1 - - - +
62H ARG* 3.7 18.6 + - - +
55K ASP* 2.8 24.4 + - + +
56K PRO* 3.6 7.6 - - + +
58K VAL* 1.3 74.0 - - + +
60K LEU* 1.3 58.4 + - - +
62K ARG* 4.5 4.6 - - - +
63K GLY* 3.6 14.3 + - - -
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Residues in contact with LEU 60 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K PRO 2.8 18.0 + - - +
57K GLN* 3.5 19.3 - - - +
58K VAL 2.7 1.4 + - - -
59K GLU* 1.3 78.8 - - - +
61K VAL* 1.3 59.0 + - - +
62K ARG 3.2 0.9 - - - -
63K GLY* 2.8 18.3 + - - -
64K TYR* 3.0 44.8 + - + +
144K GLU* 3.5 33.2 - - + +
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Residues in contact with VAL 61 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K TYR* 3.7 31.7 - - + +
31K LEU* 3.6 30.1 - - + -
32K HIS* 3.5 24.9 - - + -
35K LEU* 5.1 2.2 - - + -
57K GLN* 2.9 42.1 + - + +
58K VAL* 2.9 2.7 + - - +
60K LEU* 1.3 70.2 - - - +
62K ARG* 1.3 66.5 + - - +
63K GLY 2.9 1.6 - - - -
64K TYR* 2.9 22.6 + - + +
65K ALA* 3.1 10.0 + - - +
113K TYR* 4.4 1.6 - - - +
145K LEU* 4.6 4.0 - - + -
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Residues in contact with ARG 62 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H HIS* 3.3 29.7 + - - -
36H LYS* 4.6 17.8 - - + +
58H VAL* 2.8 37.1 + - - +
59H GLU* 3.8 22.2 + - - +
62H ARG* 3.3 65.6 - - - +
32K HIS* 4.2 17.7 - - + +
58K VAL 2.9 9.0 + - - +
59K GLU* 4.5 6.5 - - - +
61K VAL* 1.3 78.4 - - - +
63K GLY* 1.3 60.6 + - - +
65K ALA* 3.1 22.6 + - + +
66K ASP* 3.4 8.8 + - - +
----------------------------------------------------------
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Residues in contact with GLY 63 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K GLU 3.6 9.7 + - - -
60K LEU* 2.8 16.0 + - - -
62K ARG* 1.3 81.0 - - - +
64K TYR* 1.3 62.0 + - - +
66K ASP* 3.9 4.6 + - - +
67K GLU* 3.3 24.4 + - - +
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Residues in contact with TYR 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K TYR* 3.5 14.3 - + + -
57K GLN* 5.6 1.1 - - - -
60K LEU* 3.0 49.0 + - + +
61K VAL* 2.9 20.4 + - + +
63K GLY* 1.3 76.0 - - - +
65K ALA* 1.3 59.8 + - - +
67K GLU* 3.5 13.9 - - - -
68K VAL* 2.9 35.9 + - - +
140K ALA* 4.5 3.0 + - + -
141K HIS* 3.2 52.4 - + + -
144K GLU* 3.4 25.8 + - + +
145K LEU* 4.0 23.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LYS* 6.1 0.9 - - + -
40H TRP* 4.0 14.1 - - + -
25K LEU* 4.4 6.1 - - + +
28K TYR* 4.4 13.0 - - + -
29K ASN* 4.3 18.8 - - - +
32K HIS* 5.1 1.6 - - + -
61K VAL 3.1 8.5 + - - +
62K ARG* 3.1 20.4 + - + +
64K TYR* 1.3 74.3 - - - +
66K ASP* 1.3 69.4 + - - +
67K GLU 3.0 1.3 + - - -
68K VAL* 3.0 3.7 + - - +
69K ALA* 2.9 24.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 66 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LYS* 2.9 28.3 + - - +
39H HIS* 3.0 9.0 + - - -
40H TRP* 3.1 17.1 + - - +
62K ARG 3.4 5.7 + - - +
63K GLY* 4.3 6.1 - - - +
65K ALA* 1.3 77.6 - - - +
67K GLU* 1.3 64.4 + - - +
70K GLU* 2.8 45.5 + - - +
208K FE 2.2 32.5 - - - -
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Residues in contact with GLU 67 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J LYS* 5.1 9.1 + - - +
63K GLY 3.3 16.0 + - - +
64K TYR* 3.5 16.9 - - - +
65K ALA 3.0 0.6 - - - -
66K ASP* 1.3 83.0 - - - +
68K VAL* 1.3 62.4 + - - +
70K GLU* 4.0 4.6 - - - +
71K ARG* 3.2 19.1 + - - +
137K LEU* 4.7 18.5 - - + +
141K HIS* 3.0 28.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU* 3.6 43.1 - - + +
24K GLN* 4.8 1.8 - - + -
25K LEU* 4.3 14.1 - - + +
28K TYR* 3.6 21.5 - - + -
64K TYR 2.9 19.0 + - - +
65K ALA* 3.0 3.8 + - - +
67K GLU* 1.3 71.9 - - - +
69K ALA* 1.3 68.8 + - - +
71K ARG* 2.8 17.8 + - - +
72K ILE* 2.9 13.4 + - + +
137K LEU* 4.5 9.0 - - + -
138K LEU* 4.9 5.8 - - + -
141K HIS* 3.9 12.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H TRP* 3.2 38.6 - - + +
25K LEU* 3.2 28.2 - - + +
65K ALA 2.9 11.4 + - - +
68K VAL* 1.3 69.2 - - - +
70K GLU* 1.3 55.6 + - - +
71K ARG 2.6 16.1 + - - -
72K ILE* 2.7 17.7 + - - +
73K ALA 3.0 10.2 + - - -
79K PRO* 3.5 13.9 - - + +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H TRP* 3.5 13.7 - - + -
51H HIS* 3.2 24.8 + - - -
147J LYS* 2.8 44.5 + - - +
150J TRP* 4.3 18.7 - - + -
151J PHE* 5.1 1.1 - - - -
66K ASP* 2.8 43.8 + - - +
67K GLU* 4.1 0.8 - - - +
69K ALA* 1.3 72.5 - - - +
71K ARG* 1.3 50.9 + - - +
73K ALA* 4.1 7.3 - - - +
74K THR* 2.5 32.6 + - - -
208K FE 2.1 27.2 - - - -
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Residues in contact with ARG 71 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J ARG* 3.9 1.4 - - - +
143J GLY* 4.3 9.5 + - - -
146J GLU* 3.0 39.7 + - - +
147J LYS* 5.2 1.2 - - - +
6K ILE* 5.3 0.4 - - - -
21K LEU* 3.8 18.8 - - + -
67K GLU 3.2 13.7 + - - +
68K VAL* 2.8 15.8 + - - +
69K ALA 2.6 5.5 + - - -
70K GLU* 1.3 73.9 - - - +
72K ILE* 1.3 62.3 + - - +
74K THR* 3.1 22.7 + - - +
75K LEU* 3.1 27.6 + - + +
131K ASP* 2.8 28.1 + - - -
133K VAL* 3.5 23.9 - - - +
134K SER* 3.0 15.8 + - - +
137K LEU* 4.7 17.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 72 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K ALA* 4.4 9.9 - - + +
21K LEU* 3.6 21.8 - - + -
22K GLN* 3.4 46.0 - - + +
25K LEU* 4.5 4.7 - - + -
68K VAL* 2.9 21.4 + - + +
69K ALA* 2.7 17.5 + - - +
71K ARG* 1.3 72.6 - - - +
73K ALA* 1.3 57.1 + - - +
75K LEU* 2.8 31.6 + - - +
76K GLY 3.2 4.5 + - - -
77K LYS* 3.7 21.0 + - + +
78K SER 4.4 0.9 - - - -
79K PRO* 3.5 23.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H TRP* 4.2 8.7 - - + +
99H ARG* 3.6 17.4 + - - +
150J TRP* 3.5 37.2 + - + +
4K PHE* 4.0 1.6 - - - -
69K ALA 3.0 8.6 + - - +
70K GLU* 4.2 3.6 - - - +
72K ILE* 1.3 78.9 - - - +
74K THR* 1.3 63.4 + - - +
76K GLY* 3.0 11.1 + - - -
77K LYS 3.5 11.7 - - - -
79K PRO* 3.7 14.1 - - + +
----------------------------------------------------------
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Residues in contact with THR 74 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J GLU* 3.6 33.2 - - + +
147J LYS* 4.2 8.5 - - - +
149J GLN* 5.9 1.1 - - - +
150J TRP* 3.7 27.3 - - + +
153J ARG* 5.2 1.4 + - - -
4K PHE* 3.5 14.2 - - - -
6K ILE* 3.2 21.2 - - + +
70K GLU 2.5 23.9 + - - -
71K ARG* 3.1 19.9 + - - +
72K ILE 3.1 0.2 - - - -
73K ALA* 1.3 81.2 - - - +
75K LEU* 1.3 60.5 + - - +
76K GLY 3.5 0.2 + - - -
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Residues in contact with LEU 75 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K PHE* 3.9 1.8 - - - +
5K THR* 3.5 26.5 + - - -
6K ILE* 3.4 22.0 - - + -
9K LEU* 3.9 23.6 - - + -
14K ALA* 3.8 30.1 - - + +
17K VAL* 3.8 25.1 - - + -
18K ALA* 3.9 14.6 - - + +
21K LEU* 4.5 7.9 - - + -
71K ARG* 3.1 25.7 + - - +
72K ILE* 2.8 12.5 + - - +
74K THR* 1.3 81.2 - - - +
76K GLY* 1.3 55.1 + - - -
77K LYS 3.8 2.9 - - - +
131K ASP* 5.3 0.2 - - - +
134K SER* 4.9 2.5 - - - +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ARG* 3.0 27.4 + - - -
4K PHE* 4.1 22.2 - - - -
72K ILE 3.2 0.8 + - - -
73K ALA 3.0 11.2 + - - -
75K LEU* 1.3 80.6 - - - +
77K LYS* 1.3 65.0 + - - +
----------------------------------------------------------
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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