Contacts of the helix formed by residues 90 - 122 (chain A) in PDB entry 3MQ6
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 ASP 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 1.3 75.7 - - - +
91A SER* 1.3 70.6 + - - +
92A ASN* 2.8 38.8 + - - +
93A ALA* 3.0 24.2 + - - +
94A LYS* 3.3 7.6 + - - +
90B ASP* 5.2 4.9 - - - +
91B SER* 4.5 9.0 + - - -
11L G 4.2 19.5 - - - +
12L T 4.2 18.7 + - - +
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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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89A VAL 3.8 1.4 + - - -
90A ASP* 1.3 76.5 + - - +
92A ASN* 1.3 60.5 + - - +
94A LYS* 3.5 16.7 + - - +
95A ALA* 2.9 28.9 + - - +
90B ASP* 3.9 17.5 + - - -
91B SER* 5.7 0.3 + - - -
92B ASN* 4.1 6.5 + - - -
10K G 4.3 12.4 - - - +
11K G 3.9 32.8 - - - -
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Residues in contact with ASN 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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90A ASP* 2.8 15.0 + - - +
91A SER* 1.3 80.8 + - - +
93A ALA* 1.3 57.2 + - - +
95A ALA* 3.8 5.6 - - - +
96A LYS* 3.0 15.9 + - - +
91B SER* 3.8 12.7 + - - -
92B ASN* 3.5 20.6 + - - +
9K C 4.9 0.2 - - - +
10K G 4.6 1.7 + - - +
10L G 3.2 39.6 + - - -
11L G 2.8 63.8 + - - +
12L T 4.3 1.5 + - - +
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Residues in contact with ALA 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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33A THR* 6.3 0.2 - - + -
35A PHE 5.8 1.3 - - - +
37A LEU* 3.8 16.8 - - + -
89A VAL* 4.6 4.7 - - + -
90A ASP* 3.0 18.3 + - - +
92A ASN* 1.3 74.6 - - - +
94A LYS* 1.3 67.1 + - - +
95A ALA 3.1 1.1 - - - -
96A LYS* 3.2 2.9 + - - +
97A VAL* 2.9 28.2 + - - +
12L T 3.6 40.3 - - - +
13L G 4.5 3.6 - - - +
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Residues in contact with LYS 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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37A LEU* 3.8 13.2 - - + -
72A VAL* 3.9 28.3 - - + +
76A VAL* 4.9 9.5 - - + +
89A VAL* 3.7 36.5 + - + -
90A ASP 3.3 1.5 + - - +
91A SER* 3.8 18.2 - - - +
93A ALA* 1.3 79.5 - - - +
95A ALA* 1.3 57.5 + - - +
97A VAL 4.7 0.2 - - - +
98A ALA* 2.9 34.2 + - - +
85G ASP* 5.2 7.2 + - - -
10K G 5.2 2.7 - - - -
11K G 5.8 2.8 + - - -
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Residues in contact with ALA 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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91A SER 2.9 19.1 + - - +
92A ASN* 3.8 9.0 - - - +
93A ALA 3.1 0.2 - - - -
94A LYS* 1.3 75.3 - - - +
96A LYS* 1.3 65.8 + - - +
98A ALA* 3.9 0.5 - - - +
99A GLY 3.2 17.7 + - - -
9K C 3.2 38.0 - - - +
10K G 3.6 32.0 - - - +
11L G 5.0 1.6 - - - +
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Residues in contact with LYS 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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39A GLN* 2.8 20.0 + - - +
92A ASN 3.0 18.5 + - - +
93A ALA 3.2 3.6 + - - +
95A ALA* 1.3 79.8 - - - +
97A VAL* 1.3 65.2 + - + +
99A GLY* 3.5 1.0 + - - -
100A ASP* 2.7 47.4 + - - +
152A ARG* 3.9 10.0 - - - +
7K A 4.5 1.1 - - + -
8K C 3.3 31.0 + - + +
11L G 3.6 2.5 - - - +
12L T 3.2 22.2 - - + +
13L G 3.0 55.7 + - + +
14L G 4.6 2.2 + - - -
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Residues in contact with VAL 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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37A LEU* 3.8 19.7 - - + -
39A GLN* 3.7 33.2 - - + +
42A MET* 4.0 14.4 - - + -
72A VAL* 4.2 4.5 - - + -
93A ALA 2.9 19.0 + - - +
94A LYS 4.2 1.1 - - - +
96A LYS* 1.3 74.1 - - + +
98A ALA* 1.3 62.8 + - - +
100A ASP* 3.2 1.0 + - - +
101A ILE* 2.8 52.9 + - + +
13L G 3.7 25.8 - - - -
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Residues in contact with ALA 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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68A ILE* 4.1 8.8 - - + +
69A GLY* 6.6 0.2 - - - -
72A VAL* 4.6 10.9 - - + +
94A LYS 2.9 21.0 + - - +
95A ALA 3.9 2.7 - - - +
97A VAL* 1.3 78.3 - - - +
99A GLY* 1.3 57.4 + - - +
101A ILE* 3.5 6.7 + - - +
102A PHE* 2.9 29.3 + - - +
243A ARG* 4.2 19.9 - - - -
10K G 4.3 8.5 - - - +
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Residues in contact with GLY 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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95A ALA 3.2 7.7 + - - -
96A LYS 3.9 1.8 - - - -
97A VAL 3.2 0.6 - - - -
98A ALA* 1.3 77.1 - - - +
100A ASP* 1.3 65.9 + - - +
102A PHE* 3.1 6.6 + - - +
103A GLU* 3.0 22.4 + - - +
241A PHE* 5.9 0.2 - - - +
243A ARG* 4.7 0.7 - - - -
8K C 3.3 25.5 - - - +
9K C 3.4 19.1 + - - -
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Residues in contact with ASP 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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39A GLN* 2.9 28.5 + - - +
96A LYS* 2.7 36.7 + - - +
97A VAL 3.2 2.6 + - - +
99A GLY* 1.3 74.2 - - - +
101A ILE* 1.3 52.2 + - - +
103A GLU* 3.2 13.2 + - - +
104A ILE* 2.7 47.1 + - + +
152A ARG* 3.0 36.5 + - - -
8K C 3.5 13.2 - - - +
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Residues in contact with ILE 101 (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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39A GLN* 4.9 5.2 - - + -
42A MET* 4.1 8.3 - - + -
43A LEU* 4.0 22.0 - - + -
47A PHE* 5.0 0.2 - - + -
68A ILE* 3.7 27.1 - - + +
71A PRO* 3.7 33.0 - - + -
72A VAL* 4.8 4.5 - - + -
97A VAL* 2.8 41.9 + - + +
98A ALA* 3.7 4.5 - - - +
100A ASP* 1.3 77.4 - - - +
102A PHE* 1.3 62.8 + - - +
104A ILE* 4.6 4.9 - - + -
105A VAL* 2.9 39.9 + - + +
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Residues in contact with PHE 102 (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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64A TYR* 3.9 6.7 - + - -
68A ILE* 3.7 29.6 - - + -
98A ALA 2.9 18.4 + - - +
99A GLY 3.5 4.5 - - - +
101A ILE* 1.3 75.5 - - - +
103A GLU* 1.3 62.0 + - - +
105A VAL* 4.5 0.5 - - - +
106A SER* 3.2 45.6 + - - -
241A PHE* 3.9 15.8 - + + -
242A LYS 3.7 6.3 - - - -
243A ARG* 3.4 37.7 - - + -
278A HIS* 3.5 40.8 - - + -
279A THR* 4.2 0.9 - - - -
280A LEU* 3.6 31.6 - - + -
316A PRO* 4.6 3.4 - - + -
9K C 4.6 1.1 - - - -
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Residues in contact with GLU 103 (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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99A GLY 3.0 12.4 + - - +
100A ASP* 3.5 19.3 - - - +
102A PHE* 1.3 76.6 - - - +
104A ILE* 1.3 68.2 + - - +
106A SER* 4.1 0.7 - - - -
107A SER* 2.8 34.3 + - - +
149A ASN* 3.2 11.3 - - - +
152A ARG* 5.7 1.4 + - - -
188A ASP* 3.5 28.5 - - + +
241A PHE* 3.7 34.4 - - + +
340A CA 2.5 29.3 - - - -
8K C 5.5 6.5 - - - +
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Residues in contact with ILE 104 (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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39A GLN* 4.3 17.5 - - + +
40A GLN* 6.1 2.0 - - + -
43A LEU* 3.6 34.1 - - + -
100A ASP* 2.7 30.5 + - + +
101A ILE 4.1 1.8 - - - +
103A GLU* 1.3 79.0 - - - +
105A VAL* 1.3 61.7 + - - +
107A SER* 3.4 3.3 + - - -
108A ALA* 3.1 20.4 + - - +
149A ASN* 4.3 22.0 - - - +
211A LEU* 4.0 19.1 - - + -
216A GLN* 5.5 5.6 - - + +
219A LEU* 5.4 3.9 - - + +
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Residues in contact with VAL 105 (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* 3.8 25.8 - - + -
47A PHE* 3.8 20.2 - - + -
52A PRO* 3.9 31.8 - - + +
64A TYR* 3.8 7.0 - - - +
68A ILE* 3.7 21.1 - - + -
101A ILE* 2.9 23.1 + - + +
104A ILE* 1.3 74.1 - - - +
106A SER* 1.3 66.2 + - - +
108A ALA* 2.9 16.8 + - + +
109A VAL* 3.0 12.4 + - + +
211A LEU* 4.1 8.1 - - + -
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 2.6 35.6 + - - -
102A PHE* 3.2 25.9 + - - -
105A VAL* 1.3 77.6 - - - +
107A SER* 1.3 59.0 + - - +
109A VAL* 3.2 5.1 + - - +
110A MET* 3.0 31.6 + - - +
241A PHE* 3.5 25.0 - - - -
278A HIS* 5.4 0.5 + - - -
316A PRO* 5.7 0.2 - - - +
322A LEU* 3.8 13.6 - - - +
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Residues in contact with SER 107 (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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103A GLU* 2.8 27.0 + - - +
104A ILE 3.7 4.9 - - - -
105A VAL 3.2 0.4 - - - -
106A SER* 1.3 76.1 - - - +
108A ALA* 1.3 57.2 + - - +
110A MET* 3.5 2.5 + - - +
111A TRP* 2.9 25.5 + - - +
147A VAL* 3.9 6.4 - - - +
149A ASN* 4.2 23.5 - - - +
189A LEU* 3.3 32.5 - - - +
219A LEU* 4.6 5.3 - - - +
241A PHE* 3.7 8.1 - - - -
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Residues in contact with ALA 108 (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 ILE* 4.1 20.5 - - + +
52A PRO* 6.3 0.2 - - + -
104A ILE 3.1 11.4 + - - +
105A VAL* 2.9 12.1 + - - +
107A SER* 1.3 74.9 - - - +
109A VAL* 1.3 69.2 + - - +
110A MET 3.1 0.7 - - - -
111A TRP* 3.1 2.8 + - - +
112A ASN* 3.0 23.0 + - - +
208A ILE* 4.6 1.0 - - + +
211A LEU* 4.1 16.8 - - + -
219A LEU* 3.8 24.7 - - + -
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Residues in contact with VAL 109 (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 ILE* 4.1 11.1 - - + +
52A PRO* 3.3 34.8 - - + +
54A PHE* 3.7 12.7 - - + -
64A TYR* 4.2 14.6 - - - +
105A VAL 3.0 18.3 + - - +
106A SER* 3.5 7.9 - - - +
108A ALA* 1.3 76.9 - - - +
110A MET* 1.3 64.6 + - + +
112A ASN* 3.1 1.7 + - - -
113A CYS* 3.0 23.3 + - - -
319A ALA* 4.3 7.6 - - + +
322A LEU* 4.1 15.3 - - + -
323A ALA* 4.1 22.7 - - + -
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Residues in contact with MET 110 (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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106A SER 3.0 19.2 + - - +
107A SER 3.9 4.5 - - - +
109A VAL* 1.3 79.7 - - + +
111A TRP* 1.3 61.7 + - - +
113A CYS* 3.3 2.0 + - - -
114A ALA* 2.9 20.6 + - - +
147A VAL* 3.8 8.5 - - + -
189A LEU* 3.8 36.1 - - + -
191A VAL* 3.9 17.7 - - + -
237A LEU* 4.6 3.1 - - + -
239A VAL* 4.4 11.2 - - + -
241A PHE* 4.4 13.0 - - - -
276A GLU* 6.0 0.2 - - - +
278A HIS* 4.8 11.2 - - - -
322A LEU* 4.9 13.9 - - + -
326A PHE* 3.4 45.3 - - + -
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Residues in contact with TRP 111 (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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107A SER 2.9 15.8 + - - +
108A ALA 3.4 7.4 - - - +
110A MET* 1.3 75.5 - - - +
112A ASN* 1.3 73.6 + - - +
114A ALA* 3.1 5.9 + - + +
115A ALA* 2.9 24.6 + - - +
147A VAL* 3.4 40.1 - - + +
203A MET* 3.9 32.7 + - + -
204A TRP* 3.9 17.2 - + - -
206A GLU 3.7 18.3 + - - -
208A ILE* 4.1 11.6 - - + +
218A LEU* 4.2 11.6 - - + +
219A LEU* 3.6 45.4 - - + +
222A ALA* 3.6 26.9 - - + -
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Residues in contact with ASN 112 (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 ILE* 3.8 19.4 - - - +
54A PHE* 3.5 36.3 - - + +
108A ALA 3.0 12.6 + - - +
109A VAL 3.8 1.1 - - - +
111A TRP* 1.3 81.6 - - - +
113A CYS* 1.3 66.2 + - - +
115A ALA* 3.3 4.9 + - - +
116A ARG* 3.0 25.1 + - - +
207A GLU* 3.3 14.8 + - + +
208A ILE* 2.9 50.9 + - - +
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Residues in contact with CYS 113 (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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54A PHE* 3.4 12.8 - - - -
109A VAL* 3.0 22.4 + - - -
110A MET* 3.6 1.8 - - - +
112A ASN* 1.3 75.0 - - - +
114A ALA* 1.3 57.7 + - - +
116A ARG 3.3 0.7 + - - -
117A TRP* 2.8 32.2 + - - +
323A ALA* 3.7 35.0 - - - -
326A PHE* 3.5 26.5 - - + -
327A PHE* 3.4 30.7 - - + -
330A LEU* 5.1 0.7 - - - -
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Residues in contact with ALA 114 (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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110A MET 2.9 14.3 + - - +
111A TRP* 3.3 10.8 - - + +
113A CYS* 1.3 77.6 - - - +
115A ALA* 1.3 52.1 + - - +
117A TRP* 3.7 5.2 - - - +
118A ASN* 2.8 43.7 + - - +
145A VAL* 4.0 25.6 - - + +
146A ALA* 5.3 0.2 - - - -
147A VAL* 3.7 22.2 - - + +
204A TRP 5.6 0.2 - - - +
326A PHE* 4.3 3.8 - - + -
330A LEU* 5.0 0.7 - - - -
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Residues in contact with ALA 115 (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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111A TRP* 2.9 14.1 + - + +
112A ASN* 3.7 3.1 - - - +
114A ALA* 1.3 75.3 - - - +
116A ARG* 1.3 57.4 + - - +
118A ASN* 3.3 0.9 + - - +
119A SER* 2.9 31.2 + - - -
127A ARG* 4.0 0.2 - - - -
204A TRP 3.5 14.1 + - - +
205A ARG 3.5 10.3 - - - +
206A GLU 3.5 35.4 - - - +
207A GLU* 3.6 13.2 - - + -
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Residues in contact with ARG 116 (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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54A PHE* 3.5 19.8 - - - -
112A ASN 3.0 14.5 + - - +
113A CYS 3.8 2.7 - - - +
115A ALA* 1.3 76.7 - - - +
117A TRP* 1.3 60.4 + - - +
119A SER* 3.8 3.8 + - - -
120A LEU* 3.5 14.0 + - - +
125A GLY 4.9 1.2 - - - +
126A TRP* 3.6 37.9 - - + -
127A ARG* 3.7 42.6 + - + +
129A GLN 2.9 25.4 + - - -
130A PRO* 3.0 29.5 + - - +
132A TYR* 4.1 7.2 - - - +
207A GLU* 2.8 44.2 + - - +
327A PHE* 4.3 11.4 - - + -
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Residues in contact with TRP 117 (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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113A CYS 2.8 18.4 + - - +
114A ALA 3.7 1.8 - - - +
116A ARG* 1.3 75.9 - - - +
118A ASN* 1.3 80.0 + - - +
120A LEU* 3.2 4.9 + - + +
121A MET* 3.0 49.5 + - + +
126A TRP* 4.2 6.9 - - - -
135A PRO* 3.7 37.0 - - + -
137A LEU* 3.8 13.9 - - + -
143A ARG* 2.8 21.7 + - + -
145A VAL* 4.2 13.0 - - + +
327A PHE* 4.5 9.0 - + + -
330A LEU* 3.8 40.3 - - + +
331A ASN* 3.7 20.0 - - + -
334A MET* 3.7 25.6 - - + +
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Residues in contact with ASN 118 (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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114A ALA* 2.8 26.6 + - - +
115A ALA 3.3 1.3 + - - +
117A TRP* 1.3 76.6 - - - +
119A SER* 1.3 66.1 + - - +
121A MET* 2.9 13.9 + - - +
122A VAL* 3.0 15.2 + - - +
144A GLN* 3.1 28.7 - - - +
145A VAL 2.8 46.8 + - - -
204A TRP* 2.8 36.6 + - - +
205A ARG* 3.9 6.3 - - + -
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA 2.9 16.8 + - - -
116A ARG 3.8 5.8 - - - -
117A TRP 3.4 0.2 - - - -
118A ASN* 1.3 75.7 - - - +
120A LEU* 1.3 56.2 + - - +
122A VAL 3.8 0.7 + - - -
123A GLY 3.6 2.4 + - - -
124A GLU* 2.8 60.6 + - - +
125A GLY 4.1 6.3 + - - -
127A ARG* 3.4 30.8 + - - +
205A ARG* 3.9 11.3 - - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG 3.5 9.6 + - - +
117A TRP* 3.2 7.3 + - + +
118A ASN 3.0 1.0 - - - -
119A SER* 1.3 74.6 - - - +
121A MET* 1.3 84.2 + - + +
122A VAL 3.0 2.1 + - - -
123A GLY* 3.2 10.7 + - - -
125A GLY* 3.4 25.1 - - - +
126A TRP* 3.6 21.8 - - + -
134A ARG* 3.6 35.2 - - + +
135A PRO* 3.8 30.3 - - + +
137A LEU 5.7 1.3 - - - +
139A PRO* 3.4 22.3 - - + +
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TRP* 3.0 58.6 + - + +
118A ASN* 2.9 8.2 + - - +
120A LEU* 1.3 102.6 - - + +
122A VAL* 1.3 58.6 + - - +
123A GLY 3.4 0.4 + - - -
135A PRO* 5.4 0.4 - - + -
137A LEU* 4.9 6.5 - - + +
138A SER 4.6 0.9 - - - +
139A PRO* 3.8 15.2 - - + +
140A SER* 2.9 58.1 + - - +
141A PRO* 3.2 3.3 - - - +
143A ARG* 3.7 25.4 - - - +
144A GLN* 4.0 10.8 - - + +
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASN 3.0 11.0 + - - +
119A SER 4.2 0.9 - - - +
120A LEU 3.0 1.0 - - - -
121A MET* 1.3 78.4 - - - +
123A GLY* 1.3 58.6 + - - +
124A GLU* 4.0 17.9 - - + +
141A PRO* 4.4 17.6 - - + +
144A GLN* 3.9 23.8 - - - +
199A GLN 4.2 4.0 - - - +
200A ASN* 5.3 4.7 - - - +
205A ARG* 3.8 42.8 - - - +
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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) + - + + + + + -
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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