Contacts of the helix formed by residues 49 - 76 (chain P) in PDB entry 5GSE
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 LEU 49 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J C 5.1 4.7 - - - +
120O MET* 5.7 0.7 - - + -
121O PRO* 3.9 21.0 - - + +
47P SER* 3.2 25.4 - - - +
48P GLY* 1.3 74.3 - - - +
50P ILE* 1.3 62.1 + - - +
51P TYR 3.4 0.4 - - - -
52P GLU* 4.0 7.3 + - - +
53P GLU* 3.5 18.9 + - - +
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Residues in contact with ILE 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O PHE* 4.4 15.0 - - + -
107O THR* 5.2 1.6 - - + -
119O ILE* 3.2 49.8 - - + +
120O MET* 3.4 9.0 - - - +
121O PRO* 3.5 25.5 - - + +
124O ILE* 5.1 6.5 - - + -
34P ILE* 5.0 2.9 - - + -
46P ILE* 5.2 5.2 - - + -
47P SER 3.5 13.4 + - - +
48P GLY 3.1 1.2 - - - -
49P LEU* 1.3 77.3 - - - +
51P TYR* 1.3 64.3 + - + +
52P GLU 3.1 0.4 - - - -
53P GLU* 2.9 6.8 + - + -
54P THR* 2.6 52.6 + - - +
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Residues in contact with TYR 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J C 4.1 0.9 + - - -
31P LYS* 3.5 53.3 - - + -
34P ILE* 3.5 26.0 - - + +
35P ARG* 2.5 40.8 + - + -
46P ILE* 3.1 28.0 - - + +
47P SER 4.0 3.1 - - - -
48P GLY* 3.2 35.0 + - - +
49P LEU 3.4 1.4 - - - -
50P ILE* 1.3 80.9 - - + +
52P GLU* 1.3 60.9 + - - +
54P THR* 3.9 0.8 + - - -
55P ARG* 3.3 46.6 + - - +
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Residues in contact with GLU 52 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ILE* 5.2 1.4 - - - +
27P GLN* 3.4 23.4 + - - +
48P GLY 4.7 1.0 + - - -
49P LEU* 4.0 8.5 + - - +
50P ILE 3.1 0.4 - - - -
51P TYR* 1.3 77.4 - - - +
53P GLU* 1.3 66.6 + - - +
55P ARG* 2.5 53.4 + - - +
56P GLY* 3.0 10.2 + - - -
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Residues in contact with GLU 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121O PRO* 4.2 9.7 - - + +
124O ILE* 4.0 26.8 - - + +
125O GLN* 3.1 34.2 - - - +
128O ARG* 5.7 0.9 - - - -
49P LEU 3.5 13.9 + - - +
50P ILE* 2.9 13.1 + - + +
52P GLU* 1.3 75.9 - - - +
54P THR* 1.3 64.3 + - - +
56P GLY* 3.0 13.5 + - - +
57P VAL* 3.0 19.2 + - - +
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Residues in contact with THR 54 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O LEU* 3.7 31.2 - - + -
104O PHE* 3.8 13.9 - - + -
124O ILE* 4.8 11.3 - - + +
34P ILE* 4.0 26.1 - - + +
50P ILE* 2.6 40.2 + - - +
51P TYR 4.0 4.3 - - - -
53P GLU* 1.3 70.8 - - - +
55P ARG* 1.3 53.2 + - - +
57P VAL* 3.0 9.1 + - + +
58P LEU* 2.7 34.1 + - + +
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Residues in contact with ARG 55 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ILE* 3.2 47.2 - - + +
27P GLN* 3.0 24.5 + - - +
29P ILE* 3.3 24.0 + - + +
31P LYS* 4.1 19.8 - - - +
34P ILE* 3.8 10.6 - - + +
51P TYR* 3.3 30.7 + - - +
52P GLU* 2.5 52.0 + - - +
54P THR* 1.3 77.6 - - - +
56P GLY* 1.3 62.3 - - - +
58P LEU* 3.0 8.5 + - - +
59P LYS* 2.8 23.2 + - - +
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Residues in contact with GLY 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ILE* 5.6 0.4 - - - -
52P GLU* 3.0 8.2 + - - -
53P GLU* 3.0 8.4 + - - -
55P ARG* 1.3 78.0 - - - +
57P VAL* 1.3 64.9 + - - +
59P LYS* 3.0 15.1 + - - +
60P VAL* 3.2 13.0 + - - +
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Residues in contact with VAL 57 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O TYR* 3.5 34.8 - - + +
100O LEU* 4.7 4.0 - - + -
103O LEU* 3.8 11.2 - - + -
124O ILE* 3.9 20.0 - - + -
128O ARG* 3.6 32.5 - - - +
53P GLU* 3.0 16.7 + - - +
54P THR* 3.0 10.6 + - - +
56P GLY* 1.3 71.5 - - - +
58P LEU* 1.3 67.7 + - - +
60P VAL* 2.9 27.1 - - - +
61P PHE* 3.1 5.7 + - - +
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Residues in contact with LEU 58 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62O ILE* 5.3 5.4 - - + -
67O PHE* 5.3 0.9 - - + -
70O LEU* 4.4 12.6 - - + -
96O CYS* 3.6 37.7 - - + +
99O TYR* 5.4 1.1 - - + -
100O LEU* 4.1 29.4 - - + -
26P ILE* 4.6 2.9 - - + -
29P ILE* 3.8 41.3 - - + -
54P THR* 2.7 17.1 + - + +
55P ARG* 3.0 9.6 + - - +
57P VAL* 1.3 76.3 - - - +
59P LYS* 1.3 66.2 - - - +
61P PHE* 3.0 8.7 + - + +
62P LEU* 2.8 24.0 + - + +
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Residues in contact with LYS 59 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O LEU* 4.8 1.5 - - + +
73O GLU* 5.5 4.8 + - - +
74O ILE* 3.9 25.6 - - + +
77O ASP* 5.4 3.0 + - - -
26P ILE* 3.6 40.6 - - + -
55P ARG 2.8 12.6 + - - +
56P GLY* 3.4 11.2 - - - +
58P LEU* 1.3 74.1 - - - +
60P VAL* 1.3 52.7 + - - +
62P LEU* 3.0 5.5 + - - +
63P GLU* 2.6 76.0 + - - +
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Residues in contact with VAL 60 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128O ARG* 4.3 16.4 - - - +
56P GLY 3.2 8.8 + - - +
57P VAL* 2.9 24.2 - - + +
59P LYS* 1.3 77.9 - - - +
61P PHE* 1.3 67.2 + - + +
63P GLU* 3.0 18.1 + - - +
64P ASN* 3.0 36.1 + - - +
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Residues in contact with PHE 61 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O LEU* 6.5 0.2 - - + -
95O ALA* 4.3 9.9 - - + -
96O CYS* 3.9 35.0 - - - -
99O TYR* 3.5 61.2 - + + +
57P VAL 3.1 10.8 + - - +
58P LEU* 3.0 9.2 + - + +
60P VAL* 1.3 81.2 - - - +
62P LEU* 1.3 66.6 + - + +
64P ASN* 3.0 14.8 + - - +
65P VAL* 3.0 40.2 + - + +
90P LEU* 4.6 5.4 - - + -
93P GLN* 4.8 5.3 - - - +
95P ARG* 3.7 24.5 - - - -
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Residues in contact with LEU 62 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67O PHE* 3.7 31.4 - - + -
70O LEU* 4.0 19.3 - - + -
71O VAL* 4.0 10.3 - - + -
74O ILE* 3.9 16.6 - - + -
92O LEU* 4.2 19.1 - - + -
96O CYS* 3.5 21.1 - - - -
58P LEU* 2.8 18.3 + - + +
59P LYS 3.5 5.6 - - - +
61P PHE* 1.3 76.2 - - + +
63P GLU* 1.3 64.2 + - - +
64P ASN 3.0 0.3 + - - -
65P VAL* 3.0 4.6 + - + +
66P ILE* 2.9 47.9 + - + +
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Residues in contact with GLU 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74O ILE* 3.7 26.4 - - + +
77O ASP* 4.9 7.5 - - - +
78O PHE* 3.6 15.1 - - + -
59P LYS* 2.6 50.5 + - - +
60P VAL* 3.4 24.4 + - - +
62P LEU* 1.3 72.8 - - - +
64P ASN* 1.3 61.6 + - - +
67P ARG* 3.1 36.0 + - - +
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Residues in contact with ASN 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P VAL* 3.0 34.2 + - - +
61P PHE* 3.0 7.5 + - - +
63P GLU* 1.3 76.9 - - - +
65P VAL* 1.3 67.4 + - - +
67P ARG* 2.7 41.1 + - + +
68P ASP* 2.9 26.8 + - - +
93P GLN* 3.4 19.2 + - - +
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Residues in contact with VAL 65 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O LEU* 3.5 26.5 - - + -
95O ALA* 5.7 0.7 - - + -
61P PHE* 3.0 40.7 + - + +
62P LEU* 3.0 7.5 + - + +
64P ASN* 1.3 74.5 - - - +
66P ILE* 1.3 63.4 + - - +
68P ASP* 4.7 1.3 - - - -
69P ALA* 3.0 22.5 + - - +
86P VAL* 4.6 2.2 - - + -
89P ALA* 3.6 11.0 - - + +
90P LEU* 3.5 35.7 - - + -
93P GLN* 3.9 17.7 - - - +
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Residues in contact with ILE 66 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O VAL* 3.7 38.4 - - + +
74O ILE* 3.9 19.1 - - + -
75O ALA* 3.9 25.6 - - + +
78O PHE* 4.3 11.0 - - + -
84O PHE* 4.9 5.2 - - + -
92O LEU* 4.0 19.3 - - + -
62P LEU* 2.9 30.6 + - + +
63P GLU 4.3 2.2 - - - +
65P VAL* 1.3 76.0 - - - +
67P ARG* 1.3 64.2 + - - +
69P ALA* 3.0 9.3 + - + +
70P VAL* 2.8 28.4 + - + +
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Residues in contact with ARG 67 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O PHE* 3.3 51.9 - - + +
63P GLU* 3.1 23.6 + - - +
64P ASN* 2.7 53.6 + - + +
66P ILE* 1.3 75.0 - - - +
68P ASP* 1.3 75.2 + - - +
70P VAL* 3.0 14.3 + - - +
71P THR* 3.3 16.6 + - - +
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Residues in contact with ASP 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P ASN* 2.9 15.7 + - - +
65P VAL 3.7 0.7 - - - +
67P ARG* 1.3 82.1 - - - +
69P ALA* 1.3 65.4 + - - +
71P THR* 2.5 29.1 + - - +
72P TYR* 3.2 9.1 + - + -
89P ALA* 3.5 23.1 - - + +
92P ARG* 5.1 8.6 - - - +
93P GLN* 3.3 31.3 + - - +
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Residues in contact with ALA 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O LEU* 5.8 0.9 - - + -
65P VAL 3.0 14.6 + - - +
66P ILE* 3.0 14.2 + - + +
68P ASP* 1.3 74.8 - - - +
70P VAL* 1.3 65.6 + - + +
72P TYR* 2.9 7.9 + - - +
73P THR* 2.8 24.1 + - - +
81P VAL* 5.2 7.2 - - + -
85P ASP* 3.7 33.9 - - + +
86P VAL* 4.3 11.7 - - + +
89P ALA* 3.6 1.5 - - + +
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Residues in contact with VAL 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75O ALA* 5.4 0.4 - - + +
78O PHE* 4.4 20.6 - - + -
79O LYS* 4.7 2.5 - - + -
82O LEU* 3.5 33.4 - - + -
84O PHE* 5.9 0.7 - - + -
66P ILE* 2.8 28.1 + - + +
67P ARG* 3.0 10.0 + - - +
69P ALA* 1.3 75.7 - - + +
71P THR* 1.3 56.6 + - + +
73P THR* 3.0 8.2 + - - -
74P GLU* 2.5 63.2 + - + +
81P VAL* 4.4 8.1 - - + -
----------------------------------------------------------
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Residues in contact with THR 71 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P ARG* 3.6 12.8 - - + +
68P ASP* 2.5 24.3 + - - +
70P VAL* 1.3 79.5 - - + +
72P TYR* 1.3 59.9 + - - +
74P GLU* 3.7 15.8 - - - +
75P HIS* 2.8 29.5 + - - +
----------------------------------------------------------
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Residues in contact with TYR 72 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P ASP* 3.9 12.8 - - + -
69P ALA 2.9 6.9 + - - +
71P THR* 1.3 84.8 + - - +
73P THR* 1.3 62.8 + - - +
75P HIS* 3.0 13.4 + + + +
76P ALA* 2.9 22.3 + - - +
85P ASP* 3.9 21.3 - - + +
88P TYR* 3.5 52.0 + + + +
89P ALA* 3.9 10.8 - - - -
92P ARG* 4.6 20.2 + - + +
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Residues in contact with THR 73 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O LEU* 5.0 4.3 - - + -
69P ALA 2.8 12.6 + - - -
70P VAL* 3.4 7.0 - - - -
72P TYR* 1.3 73.6 - - - +
74P GLU* 1.3 64.9 + - + +
76P ALA* 2.9 15.4 + - - +
77P LYS 2.9 8.8 + - - -
78P ARG* 3.5 25.0 + - + +
79P LYS 4.9 1.3 - - - -
80P THR 3.5 26.0 - - - +
81P VAL* 3.2 28.8 - - + +
85P ASP* 2.1 32.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 74 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O PHE 4.3 2.9 - - - +
79O LYS* 3.3 42.8 - - + +
82O LEU* 6.2 1.1 - - + -
70P VAL* 2.5 37.1 + - + +
71P THR* 3.9 16.3 - - - +
73P THR* 1.3 74.8 - - + +
75P HIS* 1.3 61.6 + - - +
77P LYS* 3.1 20.1 + - - +
78P ARG 5.0 4.7 - - - +
----------------------------------------------------------
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Residues in contact with HIS 75 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G ALA* 5.9 7.4 - - + -
71P THR 2.8 19.4 + - - +
72P TYR* 3.0 15.2 + + + +
74P GLU* 1.3 73.8 - - - +
76P ALA* 1.3 60.9 + - + +
77P LYS* 3.0 19.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 76 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P TYR 2.9 9.7 + - - +
73P THR 2.9 4.2 + - - +
75P HIS* 1.3 76.9 - - + +
77P LYS* 1.3 70.1 + - - +
78P ARG* 3.2 45.2 + - - +
85P ASP* 5.6 0.2 - - - +
----------------------------------------------------------
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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