Contacts of the helix formed by residues 71 - 103 (chain A) in PDB entry 2EHO
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 GLU 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP* 1.3 93.0 + - - +
73A LEU 3.5 1.1 - - - -
74A LYS* 2.7 30.5 + - - +
75A VAL* 2.9 32.1 + - + +
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Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 1.3 102.8 - - - +
73A LEU* 1.3 65.3 + - - +
75A VAL* 3.0 3.7 + - - +
76A SER* 3.0 22.5 + - - -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU 3.1 1.4 + - - -
72A ASP* 1.3 77.4 + - - +
74A LYS* 1.3 62.7 + - - +
76A SER* 3.4 6.1 + - - -
77A ILE* 3.0 47.8 + - + +
21C PHE* 3.6 38.4 - - + -
23C LEU* 4.1 19.7 - - + -
52C LEU* 4.4 5.6 - - + -
55C ARG* 4.0 26.7 - - - +
57C LYS* 4.3 20.4 - - + -
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 2.7 24.5 + - - +
73A LEU* 1.3 70.5 - - - +
75A VAL* 1.3 69.9 + - + +
77A ILE* 3.1 17.1 + - - +
78A HIS* 3.2 29.2 + - + -
23C LEU* 4.4 18.2 - - + +
24C ASP* 4.5 10.7 + - + +
25C LYS 3.5 9.1 + - - -
26C ILE* 3.1 48.4 - - + +
27C TYR* 4.5 4.1 - - - +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 5.9 0.2 - - - +
65A LEU* 3.7 47.1 - - + +
66A ARG* 5.2 7.9 - - - +
71A GLU* 2.9 40.1 + - + +
72A ASP* 3.5 7.2 - - - +
74A LYS* 1.3 75.2 - - + +
76A SER* 1.3 56.9 + - - +
78A HIS* 2.6 29.1 + - - +
79A GLN* 3.0 25.3 + - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP 3.0 8.9 + - - -
73A LEU* 3.5 12.5 + - - -
75A VAL* 1.3 78.8 - - - +
77A ILE* 1.3 65.3 + - - +
79A GLN* 3.2 17.5 + - - +
80A MSE 3.1 32.2 + - - +
55C ARG* 2.9 32.0 + - - -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.0 28.6 + - + +
74A LYS* 3.4 9.6 - - - +
75A VAL 3.0 0.2 + - - -
76A SER* 1.3 77.8 - - - +
78A HIS* 1.3 60.9 + - - +
80A MSE 3.5 8.7 + - - +
81A GLU* 3.2 20.1 + - - +
23C LEU* 5.3 3.8 - - + -
26C ILE* 3.5 31.9 - - + -
28C LEU* 4.1 13.7 - - + -
47C TRP* 3.9 3.0 - - + -
48C LEU* 3.3 42.2 - - + -
51C ASN* 4.2 10.1 - - - +
52C LEU* 4.2 11.7 - - + -
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MSE 3.6 28.5 - - + +
65A LEU* 3.5 23.6 - - + -
74A LYS* 3.2 40.7 + - + +
75A VAL* 2.6 14.6 + - - +
77A ILE* 1.3 69.9 - - - +
79A GLN* 1.3 64.0 + - - +
81A GLU* 3.3 8.3 + - - +
82A MSE 3.1 26.5 + - - +
26C ILE* 4.5 7.9 - - + +
27C TYR 3.1 31.6 + - - -
28C LEU* 3.2 25.2 - - + +
29C ILE 5.3 0.6 + - - -
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Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.3 24.7 - - + +
66A ARG* 4.1 30.1 + - - +
75A VAL* 3.0 21.5 + - - +
76A SER* 3.2 19.3 + - - +
78A HIS* 1.3 76.0 - - - +
80A MSE 1.3 59.0 + - - +
82A MSE 3.0 10.8 + - + +
83A GLU* 2.9 40.1 + - + +
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Residues in contact with MSE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A SER* 3.1 21.0 + - - +
77A ILE* 3.7 8.1 - - - +
79A GLN* 1.3 74.3 - - + +
81A GLU* 1.3 66.1 + - - +
82A MSE 3.2 0.7 + - - -
83A GLU* 3.3 22.2 + - - +
84A ARG* 3.1 20.3 + - - +
145B SER* 3.4 35.0 - - - +
47C TRP* 3.5 31.9 - - + +
51C ASN* 3.0 53.6 - - + +
55C ARG* 5.1 0.4 - - - -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MSE 5.3 0.9 - - - +
77A ILE 3.2 11.8 + - - +
78A HIS* 3.7 11.7 + - - +
79A GLN 3.3 0.2 - - - -
80A MSE 1.3 78.6 - - - +
82A MSE 1.3 57.2 + - - +
84A ARG* 3.5 7.7 + - - +
85A ILE* 2.9 38.9 + - + +
28C LEU* 3.5 21.1 - - + +
29C ILE* 2.9 38.9 + - - +
30C GLY* 2.8 32.6 + - - -
47C TRP* 3.9 22.4 - - + -
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Residues in contact with MSE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.6 18.8 - - + +
61A MSE 3.5 33.7 - - + -
62A GLU* 4.1 21.1 - - + +
65A LEU* 4.1 15.9 - - + -
78A HIS 3.1 16.0 + - - +
79A GLN* 3.0 12.0 + - + +
81A GLU* 1.3 77.4 - - - +
83A GLU* 1.3 52.2 + - - +
84A ARG 2.9 5.4 - - - -
85A ILE* 3.5 5.2 - - - +
86A ARG* 2.7 78.8 + - - +
29C ILE* 4.8 4.5 - - + -
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLN* 2.9 27.9 + - + +
80A MSE 3.3 21.4 + - - +
82A MSE 1.3 75.7 - - - +
84A ARG* 1.3 58.2 + - + +
86A ARG* 4.0 10.4 - - - +
87A TYR* 3.1 25.5 + - - +
139B ASP* 4.9 4.9 - - - +
143B PRO* 3.6 27.3 - - + +
145B SER 4.2 16.1 - - - +
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 5.7 0.2 + - - -
80A MSE 3.1 18.6 - - - +
81A GLU* 3.7 7.2 - - - +
82A MSE 2.9 0.4 - - - -
83A GLU* 1.3 77.2 - - + +
85A ILE* 1.3 69.2 + - + +
86A ARG 3.1 1.3 - - - -
87A TYR* 3.2 2.8 + - - +
88A VAL* 3.1 28.2 + - - +
143B PRO* 5.0 7.3 - - + +
8C PHE* 3.0 66.5 + - + -
11C GLU* 3.1 32.9 + - - +
12C LYS* 3.5 23.4 - - - +
47C TRP* 3.6 46.1 - - - +
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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
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27A ILE* 3.4 50.7 - - + -
30A LEU* 4.3 5.4 - - + +
54A VAL* 4.9 9.0 - - + +
57A GLN* 6.5 0.4 - - + -
58A LEU* 3.3 38.8 - - + -
81A GLU* 2.9 36.6 - - + +
82A MSE 3.0 3.8 + - - +
84A ARG* 1.3 79.5 - - + +
86A ARG* 1.3 64.4 + - - +
88A VAL* 3.7 4.0 + - - +
89A LEU* 3.3 19.1 + - - +
29C ILE* 4.6 7.6 - - + -
30C GLY* 6.0 0.4 - - - +
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.4 33.3 - - + +
59A GLU* 5.8 2.0 - - - +
62A GLU* 3.5 24.0 + - - +
82A MSE 2.7 51.9 + - - +
83A GLU* 4.0 9.2 - - - +
85A ILE* 1.3 70.7 - - - +
87A TYR* 1.3 68.3 + - - +
89A LEU* 2.9 8.2 + - + +
90A SER* 2.9 27.3 + - - +
134B LEU* 4.7 23.4 - - + +
139B ASP* 3.6 18.8 - - - +
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Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TRP* 4.0 22.4 - + - -
83A GLU 3.1 19.9 + - - +
84A ARG* 3.2 5.6 + - - +
86A ARG* 1.3 78.2 - - - +
88A VAL* 1.3 57.6 + - + +
90A SER* 3.5 1.3 + - - -
91A SER* 2.8 40.0 + - - -
94A ARG* 4.1 9.3 + - - -
139B ASP* 3.7 30.0 + - + -
140B MSE 4.2 2.0 + - - -
141B LYS 3.6 5.2 - - - -
142B PRO* 3.2 47.0 - - + +
143B PRO* 4.0 7.4 - - + -
5C GLU* 3.1 36.4 + - + +
8C PHE* 3.8 24.7 - + + -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.2 18.8 - - + +
31A GLU* 4.4 14.1 - - + +
34A TRP* 3.3 44.9 - - + +
84A ARG 3.1 15.2 + - - +
85A ILE* 4.2 3.1 - - - +
87A TYR* 1.3 79.4 - - + +
89A LEU* 1.3 68.7 + - - +
91A SER* 4.3 3.8 - - - -
92A TYR* 2.8 26.0 + - - +
8C PHE* 3.8 27.8 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.1 19.2 - - + +
51A VAL* 4.2 22.2 - - + -
54A VAL* 3.6 27.4 - - + -
55A MSE 3.5 34.1 - - + -
58A LEU* 4.7 12.1 - - + -
85A ILE 3.3 12.4 + - - +
86A ARG* 2.9 9.5 + - - +
88A VAL* 1.3 77.2 - - - +
90A SER* 1.3 58.7 + - - +
92A TYR* 3.0 9.7 - - + +
93A LEU* 3.0 40.9 + - + +
134B LEU* 4.3 14.8 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 2.9 18.0 + - - +
87A TYR* 3.7 4.5 - - - -
89A LEU* 1.3 72.0 - - - +
91A SER* 1.3 66.0 + - - +
92A TYR 2.7 5.7 + - - -
93A LEU 3.0 1.3 + - - +
94A ARG* 2.7 43.1 + - - +
134B LEU* 3.5 22.9 - - - +
135B ASP 4.1 2.3 + - - -
136B ILE* 3.8 22.8 - - - +
138B GLN 4.6 3.9 + - - -
139B ASP* 4.4 7.6 + - - -
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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
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34A TRP* 2.9 28.9 + - - -
38A LYS* 3.8 5.9 + - - -
87A TYR* 2.8 33.1 + - - -
90A SER* 1.3 73.1 - - - +
92A TYR* 1.3 61.8 + - - +
94A ARG* 3.2 27.3 + - - +
95A CYS* 3.3 19.9 + - - +
5C GLU* 3.5 19.4 + - - -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.4 15.5 - - + -
33A ALA* 2.9 34.6 - - + +
34A TRP* 3.4 22.6 - - + -
37A GLU* 3.3 30.2 + - + -
45A GLU 4.7 0.9 + - - -
47A LYS* 4.0 29.2 + - + +
50A ILE* 6.1 0.2 - - + -
51A VAL* 3.5 27.6 - - + +
88A VAL* 2.8 20.6 + - + +
89A LEU* 3.0 7.4 - - + +
90A SER 2.7 1.0 + - - -
91A SER* 1.3 72.6 - - - +
93A LEU* 1.3 80.0 + - + +
94A ARG 3.1 0.7 - - - -
95A CYS* 2.8 27.5 + - - +
96A ARG* 3.2 18.4 + - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.3 22.2 - - + -
55A MSE 6.5 0.7 - - + -
89A LEU* 3.0 25.0 + - + +
90A SER 4.1 1.6 - - - +
92A TYR* 1.3 101.6 - - + +
94A ARG* 1.3 56.9 + - - +
96A ARG* 3.0 18.1 + - - +
97A LEU* 2.9 32.2 + - - +
126A GLU* 5.0 1.1 - - - +
124B TYR* 4.4 16.3 + - + +
128B LEU* 3.4 35.7 - - + -
134B LEU* 5.4 0.2 - - + -
136B ILE* 4.2 19.1 - - + -
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.1 3.6 + - - -
90A SER* 2.7 25.3 + - - +
91A SER* 3.2 37.1 + - - +
93A LEU* 1.3 74.7 - - - +
95A CYS* 1.3 61.3 + - - +
97A LEU* 3.8 4.2 + - - +
98A MSE 3.3 21.1 + - - +
88B ARG* 5.2 1.6 + - - -
92B TRP* 3.8 22.3 - - + -
136B ILE* 3.0 26.8 + - + +
138B GLN 3.2 15.4 + - - -
139B ASP 2.9 30.9 + - - -
140B MSE 3.4 40.2 + - + +
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Residues in contact with CYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TRP* 5.8 1.1 - - + +
37A GLU* 3.2 34.5 - - + -
38A LYS* 4.0 24.0 - - - +
91A SER 3.3 11.7 + - - +
92A TYR* 2.8 14.4 + - - +
94A ARG* 1.3 79.5 - - - +
96A ARG* 1.3 62.0 + - - +
98A MSE 3.5 19.1 + - - +
99A LYS* 3.1 33.5 + - - +
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 2.5 31.6 + - + +
43A LEU* 4.0 16.0 - - + +
44A LEU 2.6 31.5 + - - -
45A GLU 3.4 3.2 + - - -
46A SER* 3.4 30.4 + - - +
47A LYS 5.3 0.2 - - - +
92A TYR* 3.2 28.3 + - + +
93A LEU* 3.0 16.0 + - - +
95A CYS* 1.3 74.7 - - - +
97A LEU* 1.3 60.8 + - - +
99A LYS* 2.9 8.5 + - - +
100A ILE* 2.9 32.4 + - - +
121A SER 3.2 13.4 + - - -
126A GLU* 2.3 50.4 + - - +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU 2.9 17.8 + - - +
94A ARG 4.1 4.5 - - - +
96A ARG* 1.3 76.4 - - + +
98A MSE 1.3 63.5 + - - +
100A ILE* 3.0 15.7 - - + +
101A GLU* 3.0 34.2 + - - +
126A GLU* 5.2 4.9 - - + +
129A PHE* 3.6 25.8 - - + -
88B ARG* 4.7 0.9 - - - +
92B TRP* 3.8 12.3 - - + -
121B LEU* 3.5 26.9 - - + -
124B TYR* 3.5 28.7 - - + +
136B ILE* 3.5 27.4 - - + -
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Residues in contact with MSE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ARG 3.3 16.7 + - - +
95A CYS* 3.6 19.1 - - - +
96A ARG 3.2 0.2 - - - -
97A LEU* 1.3 79.8 - - - +
99A LYS* 1.3 72.9 + - + +
102A LYS* 3.0 45.0 + - - +
88B ARG* 3.8 16.8 - - - +
3D GLU 6.1 0.4 - - - +
6D PHE* 3.5 32.6 - - + -
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 2.7 51.8 + - + +
38A LYS 5.8 0.2 - - - -
40A ALA* 2.8 27.5 + - - +
41A PRO 4.7 2.0 - - - +
42A GLU* 3.2 16.9 + - - +
43A LEU* 3.7 31.0 - - + +
44A LEU 4.2 0.2 - - - +
95A CYS* 3.1 16.9 + - - +
96A ARG* 2.9 8.3 + - - +
98A MSE 1.3 86.2 - - - +
100A ILE* 1.3 65.9 + - - +
102A LYS* 3.1 4.1 + - - -
103A PHE* 3.0 39.0 + - + +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.5 30.7 - - + -
96A ARG* 2.9 22.5 + - + +
97A LEU* 3.0 26.2 - - + +
99A LYS* 1.3 71.8 - - - +
101A GLU* 1.3 67.0 + - + +
103A PHE 3.0 1.2 - - - -
104A PHE* 2.4 41.5 + - - -
107A VAL* 4.5 11.4 - - + -
122A LEU* 4.0 11.7 - - + -
126A GLU* 4.4 9.9 - - + +
129A PHE* 3.3 35.9 - - + -
130A ALA* 4.4 21.1 - - + -
133A PHE* 6.5 0.2 - - + -
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.0 20.7 + - - +
98A MSE 4.0 2.5 - - - +
100A ILE* 1.3 83.2 - - + +
102A LYS* 1.3 62.6 + - - +
103A PHE 3.0 6.4 + - - -
104A PHE* 3.4 19.1 - - - -
129A PHE* 3.6 14.6 - - + -
133A PHE* 3.8 35.9 - - + -
81B TYR* 4.3 4.5 + - - -
85B LEU* 5.9 1.6 - - - +
88B ARG* 2.5 39.8 + - - +
92B TRP* 4.7 1.0 - - - -
117B TYR* 2.6 37.2 + - - -
6D PHE* 3.8 7.5 - - + -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A MSE 3.0 31.1 + - - +
99A LYS* 3.1 6.2 + - - +
101A GLU* 1.3 76.8 - - - +
103A PHE* 1.3 97.0 + - + +
162A VAL* 3.7 14.3 - - - +
163A PRO* 4.2 2.5 - - + +
81B TYR* 5.2 2.8 + - - -
85B LEU* 6.2 0.9 - - - -
6D PHE* 3.7 31.6 - - + +
7D ARG 4.8 7.6 - - - +
9D GLU* 2.9 34.3 + - - -
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PRO 4.0 10.3 - - - -
42A GLU* 5.3 0.9 - - - -
43A LEU* 5.6 4.5 - - + -
99A LYS* 3.0 31.3 + - + +
100A ILE 3.0 5.3 + - - -
101A GLU 3.0 0.2 - - - -
102A LYS* 1.3 125.1 - - + +
104A PHE* 1.3 65.0 + - - +
105A PRO* 2.8 12.7 - - - -
106A HIS* 3.0 15.9 + - + -
107A VAL* 3.3 19.6 - - + +
162A VAL* 4.4 2.0 - - - -
163A PRO* 3.2 23.6 - - + -
164A LYS* 3.5 5.8 - - - -
165A PRO* 3.2 54.7 - - + -
9D GLU* 6.0 0.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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