Contacts of the helix formed by residues 42 - 71 (chain P) in PDB entry 3A68
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 42 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ARG* 3.5 3.6 + - - +
40P LYS* 4.0 3.8 + - - -
41P TYR* 1.3 81.5 - - - +
43P ASP* 1.3 67.2 + - - +
44P GLU* 3.9 9.9 - - + +
45P SER* 3.0 30.1 + - - +
46P GLU 3.1 9.9 + - - -
157P ASN* 3.7 33.9 - - + +
159P ASP* 4.9 0.4 + - - -
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Residues in contact with ASP 43 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ARG* 3.0 24.3 + - - +
42P VAL* 1.3 74.6 - - - +
44P GLU* 1.3 57.0 + - - +
46P GLU* 3.3 13.4 + - - +
47P SER* 2.8 36.5 + - - +
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Residues in contact with GLU 44 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P VAL* 3.1 7.4 - - + +
43P ASP* 1.3 78.5 - - - +
45P SER* 1.3 57.3 + - - +
47P SER* 3.5 6.2 + - - -
48P ALA* 3.0 27.2 + - - +
153P VAL* 3.7 19.5 - - + +
156P LYS* 5.6 2.8 - - - +
157P ASN* 3.1 34.2 + - - +
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Residues in contact with SER 45 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P TYR* 4.0 17.3 - - - -
42P VAL* 3.0 23.6 + - - +
44P GLU* 1.3 76.5 - - - +
46P GLU* 1.3 65.2 + - - +
48P ALA* 3.2 3.1 + - - +
49P VAL* 3.0 28.4 + - - +
153P VAL* 4.3 9.8 - - - +
154P ALA* 4.7 1.0 - - - -
157P ASN* 4.2 13.9 + - - +
159P ASP* 4.2 9.3 + - - +
162P LEU* 3.8 23.7 - - - +
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Residues in contact with GLU 46 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ARG* 3.6 26.5 + - - +
41P TYR* 3.8 20.3 - - + -
42P VAL 3.1 12.3 + - - +
43P ASP* 3.3 18.4 + - - +
45P SER* 1.3 77.8 - - - +
47P SER* 1.3 62.8 + - - +
49P VAL 3.4 0.2 + - - -
50P ASN* 3.1 15.9 + - - +
102P GLN* 3.1 36.4 + - - +
107P GLY* 3.5 5.0 - - - -
108P LYS* 2.8 34.7 + - - +
110P LYS* 5.5 3.0 + - - -
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Residues in contact with SER 47 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P ASP* 2.8 25.4 + - - +
44P GLU* 3.7 6.7 - - - -
46P GLU* 1.3 76.4 + - - +
48P ALA* 1.3 56.1 + - - +
50P ASN* 3.2 9.9 + - - +
51P GLU* 2.9 36.0 + - - +
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Residues in contact with ALA 48 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P GLU 3.0 17.7 + - - +
45P SER* 3.6 5.2 - - - +
47P SER* 1.3 77.3 - - - +
49P VAL* 1.3 62.7 + - - +
51P GLU* 3.2 12.2 + - - +
52P GLN* 3.0 22.7 + - - +
150P LEU* 3.6 23.9 - - + +
153P VAL* 3.9 24.7 - - + -
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Residues in contact with VAL 49 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P TYR* 3.4 20.9 - - - +
45P SER 3.0 15.8 + - - +
46P GLU 3.7 4.0 - - - +
48P ALA* 1.3 75.9 - - - +
50P ASN* 1.3 58.7 + - - +
52P GLN* 3.2 5.6 + - - +
53P ILE* 2.9 30.4 + - + +
98P LEU* 3.8 33.3 - - + +
101P TYR* 4.7 4.7 - - + -
102P GLN* 3.7 20.6 - - + +
150P LEU* 4.2 12.3 - - + -
162P LEU* 3.9 26.5 - - + -
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Residues in contact with ASN 50 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P GLU* 3.1 17.4 + - - +
47P SER* 3.2 12.0 + - - +
49P VAL* 1.3 75.8 - - - +
51P GLU* 1.3 62.3 + - - +
53P ILE* 3.3 15.5 + - - +
54P ASN* 3.2 21.1 + - - +
102P GLN* 3.1 19.3 + - - +
108P LYS 3.1 21.0 + - - -
109P VAL* 3.4 4.7 - - - -
110P LYS* 3.0 46.5 + - + +
112P GLN* 4.0 10.8 - - - +
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Residues in contact with GLU 51 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ILE* 4.7 26.0 - - + +
47P SER* 2.9 22.2 + - - +
48P ALA* 3.4 13.2 - - - +
49P VAL 3.2 0.2 - - - -
50P ASN* 1.3 77.0 - - - +
52P GLN* 1.3 57.5 - - - +
54P ASN* 3.1 8.1 + - - +
55P VAL* 3.0 30.7 + - + +
112P GLN* 4.4 12.8 - - - +
149P ASN* 5.3 4.5 - - - +
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Residues in contact with GLN 52 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P ALA 3.0 13.7 + - - +
49P VAL 3.8 5.8 - - - +
51P GLU* 1.3 72.7 - - - +
53P ILE* 1.3 66.6 + - - +
55P VAL* 3.1 20.4 + - - +
56P GLU* 2.9 49.2 + - - +
98P LEU* 3.6 20.9 - - + -
143P THR* 4.0 3.8 - - - +
146P LYS* 3.4 30.5 - - - +
147P LEU* 3.4 29.2 - - + +
150P LEU* 3.9 18.0 - - + +
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Residues in contact with ILE 53 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P VAL* 2.9 24.0 + - + +
50P ASN* 3.5 26.5 - - - +
51P GLU 3.2 0.2 - - - -
52P GLN* 1.3 77.8 - - - +
54P ASN* 1.3 59.3 + - - +
56P GLU* 3.4 4.0 + - - +
57P TYR* 3.0 30.1 + - + +
95P ALA* 4.0 10.0 - - + +
98P LEU* 3.6 29.4 - - + +
99P MET* 3.7 37.7 - - + +
102P GLN* 4.7 0.4 - - + -
109P VAL* 4.3 8.5 - - + -
110P LYS 5.8 1.3 - - - +
111P LEU* 3.8 28.7 - - + -
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Residues in contact with ASN 54 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ILE* 3.9 3.4 + - + +
15K PHE* 3.9 18.0 + - - +
50P ASN 3.2 5.2 + - - +
51P GLU 3.1 10.1 + - - +
53P ILE* 1.3 77.8 - - - +
55P VAL* 1.3 60.1 + - + +
57P TYR* 4.4 3.1 - - - +
58P ASN* 2.9 54.2 + - - +
111P LEU* 6.5 0.2 - - - -
112P GLN* 3.4 46.7 + - + +
113P SER 3.1 26.2 + - - +
114P ILE* 4.4 2.4 - - - +
61T TYR* 4.2 6.8 + - - -
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Residues in contact with VAL 55 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ILE* 6.3 0.2 - - + -
15K PHE* 4.1 35.8 - - + -
51P GLU* 3.0 21.4 + - + +
52P GLN* 3.1 33.2 + - - +
54P ASN* 1.3 77.4 - - - +
56P GLU* 1.3 63.0 + - - +
58P ASN* 3.7 2.3 - - - +
59P VAL* 3.0 23.5 + - + +
143P THR* 4.4 16.6 - - + +
146P LYS* 4.2 29.8 - - + -
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Residues in contact with GLU 56 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P GLN* 2.9 42.2 + - - +
53P ILE 3.8 3.6 - - - +
55P VAL* 1.3 75.4 - - - +
57P TYR* 1.3 57.7 + - - +
59P VAL* 3.3 4.8 + - - +
60P SER* 2.9 27.7 + - - -
91P GLU* 3.0 17.1 - - - +
94P HIS* 3.7 14.0 - - + +
95P ALA* 3.8 19.3 - - + +
98P LEU* 3.9 16.6 - - + -
143P THR* 3.8 12.2 - - - +
147P LEU* 3.8 10.2 - - - +
170P TYR* 4.2 7.2 - - - -
214P CA 2.4 27.8 - - - -
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Residues in contact with TYR 57 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P ILE* 3.0 22.4 + - + +
54P ASN* 3.9 7.0 - - - +
56P GLU* 1.3 76.8 - - - +
58P ASN* 1.3 62.3 + - - +
60P SER* 3.2 11.8 + - - -
61P TYR* 3.0 22.6 + + + +
92P ARG* 3.7 23.9 + - + -
95P ALA* 3.8 23.0 - - + +
99P MET* 4.4 7.0 - - - -
111P LEU* 4.6 3.1 - - + -
114P ILE* 3.6 22.3 - - + +
57T TYR* 5.4 11.2 - + - -
60T SER* 5.0 2.6 + - - -
61T TYR* 3.6 40.1 - + - +
64T HIS* 2.6 41.5 + + - +
88T SER* 4.6 1.4 + - - -
114T ILE* 6.3 0.2 - - + -
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Residues in contact with ASN 58 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 3.9 20.4 + - + -
17K PRO* 3.8 15.2 - - + +
54P ASN* 2.9 52.1 + - - +
55P VAL 3.7 4.3 - - - +
57P TYR* 1.3 78.4 - - - +
59P VAL* 1.3 56.9 + - - +
61P TYR* 3.1 7.0 + - - +
62P VAL* 2.9 33.5 + - - +
113P SER 4.1 5.9 + - - -
114P ILE* 3.4 10.7 - - - +
115P VAL* 3.4 33.6 + - - +
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Residues in contact with VAL 59 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 5.0 8.5 - - + -
17K PRO* 5.7 0.4 - - + -
55P VAL* 3.0 19.9 + - + +
56P GLU* 3.7 3.4 - - - +
58P ASN* 1.3 73.1 - - - +
60P SER* 1.3 65.9 + - - +
62P VAL* 3.3 8.0 + - - +
63P TYR* 3.0 48.9 + - + -
91P GLU* 3.5 24.5 - - - +
139P LEU* 4.7 22.4 - - + +
140P GLU* 4.4 4.3 - - - +
143P THR* 3.5 24.0 - - - +
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Residues in contact with SER 60 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P GLU 2.9 11.0 + - - -
57P TYR* 3.2 16.6 + - - -
59P VAL* 1.3 77.1 - - - +
61P TYR* 1.3 56.7 + - - +
63P TYR 3.4 0.5 + - - -
64P HIS 3.0 14.2 + - - -
88P SER* 2.8 44.0 + - - +
91P GLU* 3.5 24.5 - - - +
92P ARG* 3.7 19.1 - - - +
57T TYR* 4.9 2.6 + - - -
92T ARG* 4.5 4.3 + - - -
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Residues in contact with TYR 61 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P TYR* 3.0 14.1 + + + +
58P ASN 3.1 7.8 + - - +
60P SER* 1.3 74.8 - - - +
62P VAL* 1.3 66.2 + - + +
64P HIS* 3.1 6.1 + - - +
65P ALA* 3.0 20.8 + - - +
114P ILE* 3.4 31.0 - - + -
115P VAL 3.8 3.1 - - - -
117P PRO* 3.6 31.1 - - + +
54T ASN* 4.1 5.2 + - - -
57T TYR* 3.5 50.9 - + - +
111T LEU* 3.6 20.7 - - + +
112T GLN 2.7 37.1 + - - -
114T ILE* 3.8 18.1 - - + +
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Residues in contact with VAL 62 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K PRO* 4.0 20.9 - - + -
18K PHE* 3.6 40.4 - - + -
58P ASN* 2.9 20.5 + - - +
59P VAL* 3.8 5.8 - - - +
61P TYR* 1.3 77.6 - - + +
63P TYR* 1.3 57.5 + - - +
65P ALA* 3.1 4.2 + - - +
66P MET* 2.9 37.2 + - + +
117P PRO* 4.2 11.9 - - + -
121P PHE* 5.1 0.4 - - + -
139P LEU* 3.5 28.7 - - + -
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Residues in contact with TYR 63 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P VAL* 3.0 28.4 + - + +
60P SER 3.7 4.0 - - - +
62P VAL* 1.3 76.4 - - - +
64P HIS* 1.3 57.4 + - - +
66P MET* 3.2 11.1 + - - +
67P PHE* 2.9 25.8 + - - +
83P PHE* 6.0 1.3 - + - -
84P PHE* 3.6 41.5 - + - +
87P SER* 3.6 22.0 - - - -
88P SER 3.7 5.2 - - - +
91P GLU* 3.6 23.8 - - + -
136P ALA* 3.7 28.4 + - + +
139P LEU* 4.2 15.0 - - + +
140P GLU* 2.5 41.9 + - - +
181P ILE* 4.2 4.0 - - + +
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Residues in contact with HIS 64 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P SER 3.0 8.8 + - - +
61P TYR 3.1 9.6 + - - +
63P TYR* 1.3 77.6 - - - +
65P ALA* 1.3 57.7 + - - +
67P PHE* 3.3 25.1 + + + +
68P ALA* 3.0 28.4 + - - +
85P LYS* 5.2 2.2 - - + -
88P SER* 3.5 16.4 - - - +
57T TYR* 2.6 35.6 + + - +
92T ARG* 3.5 23.5 + - + -
96T GLU* 2.8 38.7 + - + +
99T MET* 3.7 22.8 - - + +
111T LEU* 4.1 9.4 - - + -
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Residues in contact with ALA 65 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P TYR 3.0 11.6 + - - +
62P VAL 3.3 8.7 - - - +
64P HIS* 1.3 77.6 - - - +
66P MET* 1.3 61.7 + - - +
68P ALA* 3.2 7.0 + - - +
69P TYR* 3.0 22.0 + - - +
117P PRO* 3.9 16.8 - - + -
118P LEU 3.4 25.8 - - - +
119P SER* 4.6 4.3 - - - +
121P PHE* 3.8 6.2 - - + -
111T LEU* 3.7 11.3 - - + +
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Residues in contact with MET 66 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62P VAL* 2.9 25.8 + - + +
63P TYR* 3.2 31.6 + - - +
65P ALA* 1.3 73.8 - - - +
67P PHE* 1.3 65.3 + - - +
69P TYR* 3.1 1.6 + - - +
70P PHE* 3.0 32.0 + - + -
84P PHE* 3.3 24.0 - - + -
121P PHE* 3.5 33.7 - - + -
132P ALA* 3.2 50.9 - - + +
135P LEU* 4.8 4.0 - - + -
136P ALA* 4.7 2.0 - - - +
139P LEU* 4.8 4.0 - - - -
----------------------------------------------------------
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Residues in contact with PHE 67 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P TYR 2.9 13.3 + - - +
64P HIS* 3.5 24.9 - + - +
65P ALA 3.3 0.2 - - - -
66P MET* 1.3 76.4 - - - +
68P ALA* 1.3 63.7 + - - +
70P PHE* 3.2 1.9 + - - +
71P ASP* 2.9 57.6 + - + +
81P ALA* 3.4 27.0 - - + +
82P LYS* 5.9 0.2 - - - -
84P PHE* 3.6 7.7 - - - +
85P LYS* 3.7 44.4 - - + +
96T GLU* 4.4 15.0 - - + -
99T MET* 4.1 16.6 - - + -
100T GLU* 3.9 26.2 - - + -
103T ASN* 5.5 0.2 - - - -
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Residues in contact with ALA 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P HIS 3.0 14.5 + - - +
65P ALA* 3.2 11.2 + - - +
67P PHE* 1.3 82.4 - - + +
69P TYR* 1.3 62.5 + - - +
72P ARG* 3.7 5.6 + - - +
99T MET* 3.9 10.1 - - + -
103T ASN* 2.9 32.2 + - - +
109T VAL* 3.7 38.3 - - + +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P ALA 3.0 8.0 + - - +
66P MET 3.6 6.5 - - - +
67P PHE 3.1 0.2 - - - -
68P ALA* 1.3 79.3 - - - +
70P PHE* 1.3 89.0 + + - +
72P ARG* 3.2 60.3 + - - +
75P VAL* 3.6 32.4 - - + +
119P SER 3.7 6.9 + - - +
120P ASP* 3.9 2.9 - - - -
121P PHE* 3.6 42.6 - + + -
122P ASP* 3.4 33.1 - - - +
128P ASP* 4.1 12.7 + - + +
33T GLN* 5.9 1.2 - - - +
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Residues in contact with PHE 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P MET* 3.0 30.3 + - + +
69P TYR* 1.3 92.1 - + - +
71P ASP* 1.3 58.5 + - - +
72P ARG 3.2 1.9 + - - -
75P VAL* 3.6 17.0 - - + -
76P ALA* 3.8 5.5 + - - -
77P LEU* 3.5 46.7 + - + +
78P ARG* 5.3 0.3 - - - -
80P LEU* 3.6 19.7 - - + -
81P ALA* 3.9 25.4 - - - +
84P PHE* 3.8 18.4 - + - -
121P PHE* 4.6 5.8 - - + -
128P ASP* 3.6 26.5 - - + -
132P ALA* 3.4 34.8 - - + -
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Residues in contact with ASP 71 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L LYS* 2.9 36.7 + - - -
183L GLU* 4.6 2.0 - - - +
67P PHE* 2.9 45.6 + - + +
69P TYR 3.2 0.4 - - - -
70P PHE* 1.3 75.0 - - - +
72P ARG* 1.3 64.0 + - - +
76P ALA* 5.8 0.2 - - - -
81P ALA* 4.0 7.5 - - + +
100T GLU* 4.1 13.2 - - - +
103T ASN* 2.9 33.5 + - - +
----------------------------------------------------------
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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