Contacts of the helix formed by residues 46 - 76 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 2.6 41.5 + - - +
46A ASN* 4.3 17.7 - - + -
46E ASN* 4.2 11.4 - - + +
155E HIS* 4.8 1.1 - - - -
45L PRO* 1.3 82.5 - - + +
47L PHE* 1.3 64.7 + - - +
48L ILE 3.7 1.1 - - - -
49L GLY* 3.6 11.8 + - - +
50L VAL* 3.8 9.8 + - - +
102L VAL* 3.6 31.9 - - - +
103L GLN* 4.8 3.9 + - - +
155L HIS* 4.4 4.2 - - - -
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Residues in contact with PHE 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E TRP* 4.1 14.4 - + - -
151E PHE* 3.4 31.6 - + - -
154E ALA* 3.6 26.9 - - + +
155E HIS* 3.3 26.6 + + + +
39L HIS 4.9 1.6 - - - -
42L VAL* 3.5 37.9 - - + -
44L GLY 3.7 19.4 + - - +
45L PRO 3.2 4.4 + - - -
46L ASN* 1.3 75.9 - - - +
48L ILE* 1.3 78.1 + - + +
49L GLY 3.1 0.9 + - - -
50L VAL* 3.1 4.0 + - - +
51L HIS* 3.0 53.2 + + + -
102L VAL* 4.7 6.7 - - - -
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Residues in contact with ILE 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLY* 4.1 24.0 - - - +
53E MET* 3.3 41.7 - - + -
151E PHE* 4.0 27.1 - - + -
155E HIS* 3.5 15.2 + - + +
47L PHE* 1.3 84.2 - - + +
49L GLY* 1.3 74.0 + - - +
50L VAL 3.1 0.2 + - - -
51L HIS* 4.1 8.1 - - + -
52L GLU* 3.0 49.9 + - - +
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Residues in contact with GLY 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 4.0 24.2 - - - +
49A GLY* 5.2 5.4 - - - -
49E GLY* 5.3 5.1 - - - -
46L ASN* 3.6 9.2 + - - +
47L PHE 3.1 2.0 + - - -
48L ILE* 1.3 85.5 - - - +
50L VAL* 1.3 59.6 + - - +
52L GLU* 4.0 2.5 - - - +
53L MET* 3.1 20.7 + - - +
155L HIS* 5.5 0.7 - - - -
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Residues in contact with VAL 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L VAL* 5.4 0.4 - - + -
42L VAL* 4.6 13.5 - - + -
46L ASN* 3.8 5.9 + - - +
47L PHE 3.1 7.1 + - - +
49L GLY* 1.3 71.3 - - - +
51L HIS* 1.3 59.8 + - - +
53L MET* 2.6 40.4 + - + +
54L ILE* 3.1 30.4 + - + +
102L VAL* 3.2 34.3 - - + -
105L HIS* 6.5 0.4 - - + -
106L LEU* 3.9 21.5 - - + -
155L HIS* 4.0 17.9 - - + +
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Residues in contact with HIS 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E TRP* 4.3 12.3 - + - -
151E PHE* 3.8 26.3 - + - -
70F GLU* 3.2 23.7 + - + -
212F FE 3.9 0.8 - - - -
39L HIS* 2.7 78.6 + + - +
42L VAL* 5.4 2.9 - - - +
47L PHE* 3.0 33.1 + + + +
48L ILE* 3.5 15.9 - - + +
50L VAL* 1.3 81.8 - - - +
52L GLU* 1.3 68.5 + - + +
54L ILE* 3.7 11.0 + - - +
55L ASP 4.1 0.5 + - - -
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Residues in contact with GLU 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E MET* 6.1 1.2 - - - -
151E PHE* 6.0 0.5 - - - -
39L HIS* 5.1 1.8 - - - -
48L ILE* 3.0 40.9 + - + +
49L GLY* 4.1 2.2 - - - +
51L HIS* 1.3 81.9 - - + +
53L MET* 1.3 66.0 + - - +
54L ILE 3.1 3.5 + - - -
55L ASP* 3.5 9.0 + - + +
56L PRO* 3.3 18.4 - - - +
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Residues in contact with MET 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.3 38.4 - - + -
52A GLU* 6.1 1.3 - - - -
49L GLY 3.1 15.6 + - - +
50L VAL* 2.6 32.3 + - + +
52L GLU* 1.3 72.5 - - - +
54L ILE* 1.3 60.1 + - + +
56L PRO* 3.7 11.3 - - - +
57L GLN 4.5 1.9 + - - -
106L LEU* 4.1 25.6 - - + -
109L LEU* 6.4 0.2 - - + -
148L PHE* 4.1 28.8 - - + -
151L PHE* 4.0 21.8 - - + -
152L VAL* 4.7 2.5 - - - -
155L HIS* 3.8 16.6 - - + +
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Residues in contact with ILE 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L LEU* 3.5 31.0 - - + +
38L VAL* 3.1 33.7 - - + +
39L HIS* 3.9 15.9 - - + -
50L VAL* 3.1 31.4 + - + +
51L HIS* 3.8 7.6 - - - +
52L GLU 3.1 0.6 - - - -
53L MET* 1.3 86.0 - - + +
55L ASP* 1.3 67.2 + - - +
56L PRO 3.3 0.4 - - - -
57L GLN* 3.1 13.7 + - - +
58L VAL* 3.1 25.0 + - + +
106L LEU* 6.2 1.1 - - + -
109L LEU* 5.4 2.9 - - + -
148L PHE* 4.7 8.7 - - + -
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Residues in contact with ASP 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F FE 3.9 4.9 - - - -
36L LYS* 3.2 28.4 + - - -
39L HIS* 3.3 26.5 + - - -
51L HIS 4.1 2.4 + - - +
52L GLU* 3.5 11.2 + - + +
54L ILE* 1.3 75.3 - - - +
56L PRO* 1.4 65.3 - - + +
58L VAL* 3.0 8.9 + - - +
59L GLU* 2.8 37.4 + - + +
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Residues in contact with PRO 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLU 3.3 14.8 - - - +
53L MET* 3.7 8.5 - - - +
54L ILE 3.5 3.6 - - - -
55L ASP* 1.4 95.2 - - + +
57L GLN* 1.3 56.0 + - - +
59L GLU* 3.4 7.2 + - + +
60L LEU* 2.9 33.4 + - - +
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Residues in contact with GLN 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L LEU* 4.6 4.5 - - + -
53L MET 4.5 1.2 + - - +
54L ILE* 3.1 8.1 + - - +
56L PRO* 1.3 78.6 - - - +
58L VAL* 1.3 56.9 + - - +
60L LEU* 3.5 20.4 - - - +
61L VAL* 2.9 43.5 + - + +
64L TYR* 5.6 0.8 - - - -
113L TYR* 3.2 28.5 + - - +
144L GLU* 4.2 5.6 + - - +
145L LEU* 3.6 26.9 - - - +
148L PHE* 3.1 58.3 - - + +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ARG* 2.8 38.0 + - - +
32L HIS* 4.2 7.0 - - + +
35L LEU* 3.3 31.2 - - + -
36L LYS* 3.6 25.6 - - + +
54L ILE* 3.1 24.2 - - + +
55L ASP* 3.0 11.2 - - - +
57L GLN* 1.3 73.7 - - - +
59L GLU* 1.3 56.9 + - + +
60L LEU 2.7 14.5 + - - -
61L VAL* 2.9 5.5 + - - +
62L ARG* 2.9 24.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 59 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F GLU* 3.8 29.7 - - - +
62F ARG* 3.8 19.3 + - - +
55L ASP* 2.8 23.6 + - + +
56L PRO* 3.9 7.2 - - + +
58L VAL* 1.3 73.8 - - + +
60L LEU* 1.3 58.5 + - - +
62L ARG* 4.4 4.3 - - - +
63L GLY* 3.5 14.2 + - - -
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Residues in contact with LEU 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L PRO 2.9 17.4 + - - +
57L GLN* 3.5 19.7 - - - +
58L VAL 2.7 1.0 + - - -
59L GLU* 1.3 77.6 - - - +
61L VAL* 1.3 60.2 + - - +
62L ARG 3.2 1.1 - - - -
63L GLY* 2.8 18.2 + - - -
64L TYR* 2.9 44.6 + - + +
144L GLU* 3.5 33.4 - - + +
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Residues in contact with VAL 61 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 3.7 28.5 - - + +
31L LEU* 3.6 31.6 - - + -
32L HIS* 3.4 26.9 - - + -
35L LEU* 5.1 1.6 - - + -
57L GLN* 2.9 41.7 + - + +
58L VAL* 2.9 1.6 + - - +
60L LEU* 1.3 69.7 - - - +
62L ARG* 1.3 59.9 + - - +
63L GLY 2.9 4.7 - - - -
64L TYR* 2.8 27.6 + - + +
65L ALA* 3.0 10.2 + - - +
113L TYR* 4.4 2.0 - - - +
145L LEU* 4.6 4.3 - - + -
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Residues in contact with ARG 62 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 3.3 28.3 + - - -
36F LYS* 4.6 18.6 - - + +
58F VAL* 2.8 37.5 + - - +
59F GLU* 3.8 23.2 + - - +
62F ARG* 3.3 64.1 - - - +
32L HIS* 4.2 20.1 + - + +
58L VAL 2.9 9.2 + - - +
59L GLU* 4.5 7.0 - - - +
61L VAL* 1.3 78.3 - - - +
63L GLY* 1.3 61.6 + - - +
65L ALA* 3.2 21.6 + - + +
66L ASP* 3.5 8.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 63 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L GLU 3.5 9.7 + - - -
60L LEU* 2.8 16.0 + - - -
62L ARG* 1.3 80.6 - - - +
64L TYR* 1.3 62.5 + - - +
66L ASP* 3.9 4.5 + - - +
67L GLU* 3.4 24.1 + - - +
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Residues in contact with TYR 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 3.6 13.2 - + + -
57L GLN* 5.6 1.1 - - - -
60L LEU* 2.9 46.2 + - + +
61L VAL* 2.8 19.3 + - + +
63L GLY* 1.3 76.0 - - - +
65L ALA* 1.3 59.7 + - - +
67L GLU* 3.4 14.1 - - - -
68L VAL* 2.9 35.9 + - - +
140L ALA* 4.5 3.2 + - + -
141L HIS* 3.2 54.3 - + + +
144L GLU* 3.4 27.7 + - + +
145L LEU* 4.1 23.3 - - + -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LYS* 6.2 1.3 - - + -
40F TRP* 4.2 13.9 - - + -
25L LEU* 4.3 5.8 - - + +
28L TYR* 4.2 13.0 - - + -
29L ASN* 4.3 19.5 - - - +
32L HIS* 5.1 1.8 - - + +
61L VAL 3.0 7.0 + - - +
62L ARG* 3.3 20.4 - - + +
63L GLY 3.2 0.2 - - - -
64L TYR* 1.3 75.4 - - - +
66L ASP* 1.3 67.8 + - - +
67L GLU 3.0 0.9 - - - -
68L VAL* 3.0 4.6 + - - +
69L ALA* 2.9 25.3 + - - +
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Residues in contact with ASP 66 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LYS* 3.0 26.5 + - - +
39F HIS* 3.1 7.8 + - - -
40F TRP* 3.2 14.3 + - - +
62L ARG 3.5 7.9 + - - +
63L GLY* 4.3 6.1 - - - +
65L ALA* 1.3 76.2 - - - +
67L GLU* 1.3 57.8 + - - +
70L GLU* 2.7 55.5 + - - +
206L FE 2.3 31.0 - - - -
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Residues in contact with GLU 67 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K LYS* 5.1 10.0 + - - +
63L GLY 3.4 16.0 + - - +
64L TYR* 3.4 17.3 - - - +
65L ALA 3.0 0.6 - - - -
66L ASP* 1.3 80.2 - - - +
68L VAL* 1.3 62.2 + - - +
70L GLU* 4.0 3.1 - - - +
71L ARG* 3.2 21.7 + - - +
137L LEU* 4.7 17.6 - - + +
141L HIS* 3.0 28.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L LEU* 3.6 44.4 - - + +
24L GLN* 4.7 4.7 - - + -
25L LEU* 4.2 14.1 - - + +
28L TYR* 3.6 21.8 - - + -
64L TYR 2.9 22.6 + - - +
65L ALA* 3.0 3.4 + - - +
67L GLU* 1.3 70.3 - - - +
69L ALA* 1.3 60.1 + - - +
71L ARG* 2.7 32.9 + - - +
72L ILE* 2.9 7.9 + - + +
137L LEU* 4.5 9.0 - - + -
138L LEU* 4.9 2.5 - - + -
141L HIS* 3.9 12.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F TRP* 3.3 37.0 - - + +
25L LEU* 3.2 28.6 - - + +
65L ALA 2.9 11.8 + - - +
68L VAL* 1.3 72.7 - - - +
70L GLU* 1.3 56.5 + - - +
71L ARG 2.7 10.9 + - - -
72L ILE* 2.7 16.9 + - - +
73L ALA 3.0 10.0 + - - -
79L PRO* 3.4 14.5 - - + +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F TRP* 3.7 12.8 - - + -
51F HIS* 3.3 24.5 + - - -
147K LYS* 2.8 46.0 + - - +
150K TRP* 4.3 21.9 - - + -
151K PHE* 5.0 1.1 - - - -
66L ASP* 2.7 47.6 + - - +
67L GLU 4.0 0.9 - - - +
69L ALA* 1.3 73.1 - - - +
71L ARG* 1.3 50.6 + - - +
73L ALA* 4.0 4.1 + - - +
74L THR* 2.6 31.9 + - - -
206L FE 2.2 27.2 - - - -
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Residues in contact with ARG 71 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K ARG* 3.7 4.0 - - - +
143K GLY* 4.3 9.7 + - - -
146K GLU* 2.8 41.1 + - - +
147K LYS* 5.1 1.0 - - - +
6L ILE* 5.3 0.4 - - - -
21L LEU* 3.8 19.7 - - + -
67L GLU 3.2 13.6 + - - +
68L VAL* 2.7 17.1 + - - +
69L ALA 2.7 0.8 + - - -
70L GLU* 1.3 76.7 - - - +
72L ILE* 1.3 64.0 + - - +
74L THR* 3.1 27.2 + - - +
75L LEU* 3.1 21.6 + - + +
131L ASP* 2.8 27.1 + - - -
133L VAL* 3.5 24.0 - - - +
134L SER* 3.0 13.9 + - - +
137L LEU* 4.7 17.7 - - + -
----------------------------------------------------------
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Residues in contact with ILE 72 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L ALA* 4.5 10.5 - - + +
21L LEU* 3.6 22.7 - - + -
22L GLN* 3.5 45.8 - - + +
25L LEU* 4.5 5.4 - - + -
68L VAL* 2.9 20.2 + - + +
69L ALA* 2.7 18.4 + - - +
71L ARG* 1.3 71.8 - - - +
73L ALA* 1.3 63.3 + - - +
75L LEU* 2.8 25.6 + - - +
76L GLY 3.2 4.9 + - - -
77L LYS* 3.6 21.6 + - + +
78L SER 4.4 0.4 - - - -
79L PRO* 3.6 22.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F TRP* 4.4 6.5 - - + +
99F ARG* 3.8 11.2 + - - +
150K TRP* 3.5 41.8 + - + +
4L PHE* 4.0 1.6 - - - -
69L ALA 3.0 9.4 + - - +
70L GLU* 4.1 2.7 - - - +
72L ILE* 1.3 79.3 - - - +
74L THR* 1.3 64.2 + - - +
76L GLY* 3.1 13.7 + - - -
77L LYS 3.5 11.9 - - - -
79L PRO* 3.7 15.2 - - + +
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Residues in contact with THR 74 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K GLU* 3.4 36.8 - - + +
147K LYS* 4.1 9.2 - - - +
149K GLN* 5.7 1.6 - - - +
150K TRP* 3.8 23.8 - - + +
153K ARG* 4.9 1.6 + - - -
4L PHE* 3.5 14.6 - - - -
6L ILE* 3.2 21.0 - - + +
70L GLU 2.6 23.6 + - - -
71L ARG* 3.1 20.4 + - - +
72L ILE 3.1 0.6 - - - -
73L ALA* 1.3 80.3 - - - +
75L LEU* 1.3 60.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 75 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L PHE* 3.8 2.2 - - - +
5L THR* 3.5 26.3 + - - -
6L ILE* 3.4 22.4 - - + -
9L LEU* 4.0 23.8 - - + -
14L ALA* 3.8 25.3 - - + +
17L VAL* 3.8 29.6 - - + -
18L ALA* 3.9 14.4 - - + +
21L LEU* 4.5 10.8 - - + -
71L ARG* 3.1 24.9 + - - +
72L ILE* 2.8 12.2 + - - +
74L THR* 1.3 80.7 - - - +
76L GLY* 1.3 54.7 + - - +
77L LYS 3.8 3.1 - - - +
131L ASP* 5.3 0.2 - - - +
134L SER* 4.9 2.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ARG* 3.2 24.1 + - - -
4L PHE* 4.1 21.8 - - - -
72L ILE 3.2 0.4 + - - -
73L ALA 3.1 11.9 + - - -
74L THR 3.3 0.2 - - - -
75L LEU* 1.3 80.3 - - - +
77L LYS* 1.3 66.0 + - - +
----------------------------------------------------------
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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