Contacts of the helix formed by residues 78 - 106 (chain A) in PDB entry 2D2C
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 PHE 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL 2.3 11.3 + - - -
77A SER* 1.3 74.7 - - - +
79A GLY* 1.3 68.6 + - - +
80A TRP* 3.3 38.5 - + - +
81A LEU* 2.8 23.5 + - + +
82A ILE* 3.1 15.2 + - + +
36D TYR* 5.8 3.4 - + - -
37D PRO* 2.8 51.8 - - + -
40D LYS* 4.1 13.9 - - + -
41D TYR* 3.8 2.5 - - - -
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.2 35.2 - - - -
75A GLU 3.8 1.4 + - - -
76A VAL* 2.8 16.5 + - - -
77A SER 3.6 0.8 - - - -
78A PHE* 1.3 70.3 - - - +
80A TRP* 1.3 66.6 + - - +
81A LEU 2.6 2.8 + - - -
82A ILE* 2.7 12.1 + - - +
83A ARG* 2.9 10.2 + - - -
41D TYR* 3.6 12.9 - - - -
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE 3.8 5.9 + - - -
73A MET* 3.7 46.0 - - + +
75A GLU 5.0 0.9 - - - -
78A PHE* 3.4 46.0 - + - +
79A GLY* 1.3 70.5 - - - +
81A LEU* 1.3 96.9 + - + +
83A ARG* 3.6 0.8 - - - +
84A SER* 2.5 48.3 + - - +
56B VAL* 4.6 14.4 - - + -
59B PRO* 5.7 7.9 - - + -
254C ARG* 3.0 61.7 - - + +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 2.8 23.0 + - + +
79A GLY 2.6 3.8 + - - -
80A TRP* 1.3 110.2 - - + +
82A ILE* 1.3 80.7 + - + +
84A SER* 3.7 1.4 - - - -
85A ILE* 2.9 54.1 + - + +
52B VAL* 5.2 10.3 - - + -
55B SER* 5.0 6.7 - - - -
56B VAL* 4.8 12.3 - - + -
37D PRO* 5.9 6.7 - - + -
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 3.5 40.2 - - + +
53A ALA* 4.3 1.6 - - + -
54A MET* 4.1 6.3 - - + -
78A PHE* 3.3 16.4 - - + +
79A GLY 2.7 5.1 + - - -
81A LEU* 1.3 82.6 - - + +
83A ARG* 1.3 71.2 + - - +
85A ILE* 3.1 7.1 + - + +
86A HIS* 3.0 15.2 + - - +
37D PRO* 5.5 0.4 - - + -
38D LEU* 4.3 20.4 - - + +
41D TYR* 3.0 59.5 - - + +
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 4.6 9.2 - - - -
69A VAL* 3.6 25.5 - - - +
72A ILE* 4.8 8.2 - - + +
73A MET* 3.9 21.1 - - - -
79A GLY 2.9 9.9 + - - +
80A TRP 3.6 6.3 - - - +
82A ILE* 1.3 79.0 - - - +
84A SER* 1.3 70.7 + - - +
86A HIS* 2.6 24.4 + - - +
87A ARG* 2.9 14.2 + - - +
139A PRO* 4.7 5.5 - - - +
141A ASP* 5.6 0.2 + - - -
301A HEM 2.9 57.9 + - - -
60B ALA* 2.9 33.8 - - + +
61B MET 3.1 30.3 + - - +
62B VAL* 4.3 2.4 - - - +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.8 0.9 - - - +
80A TRP* 2.5 32.6 + - - +
81A LEU* 3.7 3.4 - - - -
83A ARG* 1.3 74.4 - - - +
85A ILE* 1.3 65.1 + - - +
87A ARG* 2.9 5.9 + - - +
88A TRP* 2.7 24.9 + - - -
55B SER* 3.5 23.1 - - - -
59B PRO* 3.6 12.3 - - - +
60B ALA* 3.2 33.4 + - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.4 25.4 - - + -
50A THR* 3.8 8.1 - - + -
81A LEU* 2.9 48.4 + - + +
82A ILE* 3.2 8.1 - - - +
83A ARG 2.8 2.6 + - - -
84A SER* 1.3 70.1 - - - +
86A HIS* 1.3 59.5 + - - +
88A TRP 2.7 3.6 + - - -
89A SER 2.4 33.1 + - - -
48B PHE* 4.7 20.4 - - + -
51B ILE* 3.3 23.8 - - + +
52B VAL* 4.8 6.3 - - + -
55B SER* 3.2 18.1 + - - +
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 2.6 35.7 + - + -
50A THR* 2.7 19.6 + - - +
51A GLY* 3.3 12.6 + - - -
54A MET* 3.4 16.6 - - + -
82A ILE 3.0 5.9 + - - +
83A ARG* 2.6 18.1 + - - +
85A ILE* 1.3 76.4 - - - +
87A ARG* 1.3 55.9 + - - -
90A ALA* 2.8 33.3 + - - +
301A HEM 2.2 84.5 + + + -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 2.9 12.7 + - - +
84A SER* 2.9 12.3 + - - +
86A HIS* 1.3 82.3 - - - +
88A TRP* 1.3 94.8 + - - +
90A ALA* 3.1 4.6 - - - +
91A SER* 3.1 26.2 + - - +
301A HEM 3.9 33.3 - - + +
58B ASP* 3.6 17.4 + - - -
59B PRO 3.8 5.9 + - - -
60B ALA* 3.2 26.0 - - + +
61B MET 4.3 1.6 - - - +
146C LYS* 2.9 25.9 - - - +
3E LEU* 6.0 2.6 - - - +
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Residues in contact with TRP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 2.7 22.9 + - - -
85A ILE 2.7 9.1 + - - +
87A ARG* 1.3 91.0 - - - +
89A SER* 1.3 69.8 + - - +
90A ALA 2.7 2.5 + - - -
91A SER* 2.9 6.4 + - - -
92A MET* 2.6 36.9 + - + +
51B ILE* 4.0 14.4 - - + +
54B LEU* 3.7 35.4 - - + -
55B SER* 3.7 17.9 - - - +
58B ASP* 2.7 56.0 + - + -
59B PRO 4.4 0.2 + - - -
2E ILE* 4.9 6.3 - - + -
3E LEU* 4.0 42.2 - - + -
6E VAL* 4.8 10.1 - - + -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A CYS* 2.8 33.7 + - - +
46A ILE* 3.0 20.2 - - - +
47A GLN* 2.8 16.0 + - - -
85A ILE 2.4 22.8 + - - -
88A TRP* 1.3 72.3 - - - +
90A ALA* 1.3 50.0 + - - +
92A MET* 3.1 6.2 - - - +
93A MET* 2.6 37.6 + - - +
51B ILE* 3.2 22.6 - - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 2.3 19.9 - - - +
86A HIS 2.8 20.0 + - - +
87A ARG 3.1 6.1 - - - +
88A TRP 2.7 3.0 + - - -
89A SER* 1.3 67.1 - - - +
91A SER* 1.3 55.4 + - - +
92A MET 2.4 16.7 + - - -
93A MET* 2.7 11.7 + - - +
94A VAL* 3.1 16.0 + - - +
301A HEM 3.6 45.3 - - + -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.1 14.9 + - - +
88A TRP* 2.9 5.9 + - - -
90A ALA* 1.3 76.4 - - - +
92A MET* 1.3 58.3 + - - +
94A VAL* 4.0 11.0 - - - -
95A LEU 4.0 0.7 + - - -
301A HEM 5.1 4.3 - - - +
78B GLU* 4.3 14.5 + - - -
79B TRP* 5.3 4.7 - - - +
80B TYR* 2.6 40.4 + - - -
3E LEU* 4.1 24.0 - - - +
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A CYS* 5.0 3.4 - - - -
88A TRP* 2.6 41.6 + - + +
89A SER* 3.1 10.5 - - - +
90A ALA 2.4 12.9 + - - -
91A SER* 1.3 70.9 - - - +
93A MET* 1.3 65.3 + - - +
94A VAL 3.1 1.3 - - - -
95A LEU* 2.9 26.6 + - + +
96A MET* 2.9 45.6 + - + +
50B CYS* 5.3 4.5 - - + -
51B ILE* 4.5 16.6 - - + -
54B LEU* 4.0 21.8 - - + -
3E LEU* 5.2 8.3 - - + -
6E VAL* 5.9 5.6 - - + +
101E BCR 6.1 2.9 - - + -
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Residues in contact with MET 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.0 34.3 - - + +
41A LEU* 4.9 0.7 - - - -
43A CYS* 3.5 15.9 - - + +
44A PHE* 3.4 40.8 - - + -
47A GLN* 5.5 0.2 - - - +
89A SER 2.6 18.6 + - - +
90A ALA* 2.7 5.5 + - - +
92A MET* 1.3 73.5 - - - +
94A VAL* 1.3 54.1 + - + +
95A LEU 2.9 0.3 + - - -
96A MET* 3.0 3.5 + - - +
97A MET* 2.6 37.7 + - - +
128A THR* 3.7 32.1 - - + +
195A ILE* 4.6 6.5 - - + -
199A MET* 6.4 0.4 - - + -
301A HEM 3.5 26.5 - - + -
302A HEM 5.5 3.8 - - + -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA 3.1 23.1 - - - +
91A SER* 4.0 7.0 - - - +
92A MET 3.1 0.2 - - - -
93A MET* 1.3 76.3 - - + +
95A LEU* 1.3 57.3 + - - +
97A MET* 4.0 22.9 - - + +
98A ILE* 2.9 30.7 + - + +
128A THR* 4.5 16.8 - - + +
129A VAL* 5.2 12.1 - - + -
301A HEM 4.8 8.3 - - + -
80B TYR* 3.8 28.5 - - + -
81B LEU* 5.8 2.5 - - + -
201B CLA 5.6 3.4 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A SER 4.1 0.4 - - - +
92A MET* 2.9 31.6 + - + +
94A VAL* 1.3 76.6 - - - +
96A MET* 1.3 72.1 + - + +
97A MET 2.8 2.3 + - - -
98A ILE* 2.9 15.7 + - + +
99A LEU* 3.1 45.6 - - + +
80B TYR* 3.1 26.6 + - + +
3E LEU* 5.6 0.7 - - + -
6E VAL 4.3 2.0 - - - +
7E PHE* 3.2 32.3 - - + -
10E VAL* 3.9 24.0 - - + +
11E PHE* 4.0 4.3 - - + -
101E BCR 6.2 1.1 - - + -
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.7 12.4 - - + +
39A ILE* 3.6 29.6 - - + -
40A THR* 3.1 25.1 + - - +
43A CYS* 4.3 8.7 - - - -
92A MET* 2.9 35.9 + - + +
93A MET 3.4 6.3 - - - +
95A LEU* 1.3 80.7 - - - +
97A MET* 1.3 61.5 + - - +
99A LEU* 3.5 7.1 + - - +
100A HIS* 3.1 16.5 + - - +
47B THR* 4.2 9.0 - - + -
51B ILE* 6.3 2.2 - - + -
101E BCR 4.0 48.9 - - + -
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.3 16.3 + - + -
93A MET 2.6 21.2 + - - +
94A VAL* 4.0 19.1 - - + +
95A LEU 2.8 0.6 + - - -
96A MET* 1.3 69.4 - - - +
98A ILE* 1.3 65.5 + - + +
100A HIS* 2.6 31.7 + - + +
101A VAL* 3.1 12.3 + - + +
125A ALA* 4.0 26.0 - - + +
128A THR* 3.8 26.5 - - + -
129A VAL* 4.7 1.1 - - + -
302A HEM 3.5 46.9 - - + -
201B CLA 4.4 15.3 - - + +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 2.9 23.1 - - + +
95A LEU* 2.9 10.8 + - + +
97A MET* 1.3 79.5 - - + +
99A LEU* 1.3 65.9 + - + +
101A VAL* 3.0 26.3 + - - +
102A PHE* 3.2 33.5 + - + -
80B TYR* 3.6 26.7 - - + -
201B CLA 4.3 40.8 - - + +
11E PHE* 5.5 1.8 - - + -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.4 11.7 - - + -
95A LEU* 3.1 42.4 - - + +
96A MET* 3.7 10.5 - - - +
97A MET 3.1 0.4 - - - -
98A ILE* 1.3 74.7 - - + +
100A HIS* 1.3 53.1 + - - +
101A VAL 2.9 5.2 - - - -
102A PHE* 2.7 38.8 + - + +
103A ARG* 2.8 19.0 + - - +
10E VAL 4.7 0.2 - - - +
11E PHE* 3.6 19.1 - - + -
14E LEU* 3.6 27.7 - - + +
101E BCR 3.5 32.3 - - + -
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.0 11.2 - - + +
37A GLY* 3.1 23.2 + - - -
40A THR* 3.9 7.2 - - - +
96A MET 3.1 11.3 + - - +
97A MET 2.6 19.6 + - - +
99A LEU* 1.3 74.1 - - - +
101A VAL* 1.3 58.5 + - + -
103A ARG* 3.3 30.2 + - - +
104A VAL* 3.2 23.3 + - + +
302A HEM 2.3 89.2 + + + -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 3.5 15.3 - - + +
98A ILE* 3.1 17.0 - - - +
99A LEU 2.9 0.2 - - - -
100A HIS* 1.3 79.1 - - + +
102A PHE* 1.3 68.7 + - + +
104A VAL* 2.9 7.2 + - + +
105A TYR* 2.8 30.6 + - + +
118A TRP* 5.7 0.2 - - - +
302A HEM 4.0 42.4 - - + -
108B LEU* 6.2 2.0 - - + -
201B CLA 3.4 38.8 - - + -
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 3.5 28.7 - - + -
99A LEU* 2.7 32.0 + - + +
101A VAL* 1.3 70.4 - - + +
103A ARG* 1.3 70.0 + - - +
104A VAL 2.7 0.9 + - - -
105A TYR* 4.9 1.3 - - + -
106A LEU* 2.6 44.4 + - + +
133B PHE* 4.1 20.4 - + - -
137B THR* 5.3 6.1 - - + -
201B CLA 4.5 12.6 - + + -
11E PHE* 3.3 22.4 - + - -
14E LEU* 4.3 6.7 - - + -
15E PHE* 3.0 41.7 - + + -
18E ILE* 4.1 7.6 - - + -
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.6 28.0 - - + -
34A TYR* 2.6 89.8 - - - +
35A CYS 3.3 8.3 - - - +
36A LEU* 3.9 10.2 - - + +
37A GLY 4.6 0.2 - - - +
99A LEU 2.8 13.6 + - - +
100A HIS* 3.3 40.5 + - - +
102A PHE* 1.3 72.8 - - - +
104A VAL* 1.3 65.0 + - - +
106A LEU* 3.6 4.8 - - - +
107A THR* 2.4 33.3 + - - +
302A HEM 3.7 25.9 + - - +
18E ILE* 4.4 1.0 - - - +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A HIS* 3.2 15.2 + - + +
101A VAL* 2.9 11.6 + - + +
102A PHE 2.7 3.6 + - - -
103A ARG* 1.3 88.4 - - - +
105A TYR* 1.3 58.2 + - - +
106A LEU 2.9 0.7 - - - -
107A THR* 2.2 45.0 + - - -
108A GLY 2.8 22.2 - - - +
110A PHE* 3.8 1.8 - - + -
118A TRP* 3.7 26.7 - - + +
302A HEM 3.7 37.2 - - + +
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 2.8 15.7 + - + +
102A PHE* 4.2 1.3 - - + +
104A VAL* 1.3 79.0 - - + +
106A LEU* 1.3 65.5 + - + +
107A THR 2.9 15.6 + - - +
110A PHE* 3.3 37.8 - + + -
118A TRP* 5.9 1.6 - - - +
111B VAL* 5.2 10.8 - - + -
115B GLU* 5.9 2.2 - - + -
123B PRO* 4.1 12.3 - - + +
129B ALA* 2.9 44.5 + - + +
130B THR* 3.2 8.3 + - - -
133B PHE* 3.4 42.2 - + + -
201B CLA 4.3 26.7 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 2.6 44.7 + - + +
103A ARG* 3.6 5.4 - - - +
104A VAL 2.6 0.6 + - - -
105A TYR* 1.3 74.1 - - + +
107A THR* 1.3 61.2 + - + +
122B ASN* 4.9 7.8 + - - -
124B PHE* 5.3 3.3 - - - +
133B PHE* 3.3 34.1 - - + -
134B LEU* 5.6 0.2 - - + -
15E PHE* 5.0 1.1 - - + -
18E ILE* 3.1 30.7 - - + -
19E ALA* 3.7 35.7 - - + +
23E ILE* 4.2 18.9 - - + +
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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