Contacts of the helix formed by residues 77 - 104 (chain A) in PDB entry 3H90
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 LYS 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS 3.2 0.9 + - - -
76A GLY* 1.3 70.4 - - - +
78A ALA* 1.3 66.4 + - - +
79A GLU 3.0 0.4 - - - -
80A SER* 2.9 13.4 + - - +
81A LEU* 2.9 23.0 + - - +
204A SER* 3.4 21.1 - - - +
205A LEU* 4.0 15.1 + - + +
207A ASP* 3.2 16.4 + - - -
237A ARG* 5.1 1.3 - - - +
238A GLN 4.6 1.8 - - - -
239A SER* 3.8 29.6 + - - +
240A GLY 4.8 0.7 - - - +
77C LYS* 3.0 25.4 - - - +
205C LEU 3.5 21.3 + - - +
206C LEU* 4.1 17.0 - - + -
207C ASP* 2.9 31.4 + - + +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.7 16.4 - - + +
62A TYR* 4.0 19.1 - - + -
63A SER* 3.8 18.8 - - - -
75A HIS 3.0 16.8 + - - +
76A GLY 2.8 4.8 + - - -
77A LYS* 1.3 73.0 - - - +
79A GLU* 1.3 55.4 + - - +
81A LEU* 3.4 7.1 + - - +
82A ALA* 2.8 30.1 + - - +
206C LEU* 3.9 14.0 - - + +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 3.3 35.3 + - - -
14A ILE* 4.4 7.9 - - + +
59A VAL* 5.3 0.7 - - - -
60A VAL* 5.1 1.8 - - + -
63A SER* 3.3 24.9 + - - +
64A LEU* 5.1 1.6 - - - +
76A GLY 2.8 10.3 + - - +
78A ALA* 1.3 77.8 - - - +
80A SER* 1.3 52.2 + - - +
82A ALA* 3.0 6.0 + - - +
83A ALA* 2.7 35.5 + - - +
144A SER* 2.8 28.7 + - - -
145A GLN* 3.6 8.7 + - + +
146A ALA* 3.2 28.2 + - + +
240A GLY* 4.2 6.9 - - - -
241A PRO* 3.9 11.4 - - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 2.9 18.3 + - - +
79A GLU* 1.3 72.7 - - - +
81A LEU* 1.3 55.6 - - - +
83A ALA* 3.4 8.0 + - - +
84A LEU* 2.8 35.5 + - - +
145A GLN* 3.3 27.4 + - - +
201A ALA* 3.5 13.0 - - - +
204A SER* 3.7 12.2 - - - -
205A LEU* 3.8 18.6 - - - -
240A GLY* 4.9 7.8 + - - -
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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
----------------------------------------------------------
59A VAL* 5.9 0.7 - - + -
77A LYS 2.9 8.0 + - - +
78A ALA* 3.4 9.0 - - - +
80A SER* 1.3 75.2 - - - +
82A ALA* 1.3 54.6 + - - +
84A LEU* 2.9 6.5 + - + +
85A ALA* 2.7 35.6 + - - +
205A LEU* 3.5 37.7 - - + -
84C LEU* 5.0 9.2 - - + -
202C VAL* 3.9 27.4 - - + +
205C LEU* 3.8 22.2 - - + -
206C LEU* 3.5 29.8 - - + -
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 3.9 18.8 - - - +
59A VAL* 3.6 23.5 - - + +
60A VAL* 5.9 0.4 - - + -
78A ALA 2.8 17.7 + - - +
79A GLU* 3.3 11.0 - - - +
81A LEU* 1.3 72.5 - - - +
83A ALA* 1.3 61.2 + - - +
85A ALA* 3.5 7.3 - - - +
86A GLN* 3.1 32.4 + - - +
146A ALA* 4.7 4.3 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU 2.7 15.6 + - - +
80A SER* 3.4 12.1 - - - +
82A ALA* 1.3 70.4 - - - +
84A LEU* 1.3 53.8 + - - +
86A GLN* 2.7 8.5 + - - +
87A SER* 2.7 36.1 + - - -
145A GLN* 3.9 22.7 - - - +
146A ALA* 4.9 1.3 - - - +
149A ALA* 3.8 16.1 - - + +
197A MET* 4.3 9.4 - - + -
201A ALA* 4.0 12.1 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER 2.8 20.8 + - - +
81A LEU* 3.5 4.9 - - + +
83A ALA* 1.3 72.0 - - - +
85A ALA* 1.3 63.0 + - - +
87A SER* 3.0 26.3 + - - +
88A MET* 3.3 38.0 + - + +
198A GLY* 4.2 5.8 - - - +
201A ALA* 3.7 9.1 - - + +
202A VAL* 3.8 28.0 - - + -
205A LEU* 4.0 20.4 - - + -
81C LEU* 4.9 10.3 - - + -
84C LEU* 5.5 11.4 - - + -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 2.7 19.4 + - - +
82A ALA* 3.5 10.8 - - - +
84A LEU* 1.3 75.4 - - - +
86A GLN* 1.3 64.5 + - + +
88A MET* 3.3 7.4 + - - +
89A PHE* 3.3 25.9 + - + -
88C MET* 5.7 11.2 - - + -
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 5.6 6.8 - - + +
53A SER* 5.6 0.9 - - - -
56A ASN* 3.4 39.3 + - - +
82A ALA* 3.1 15.0 + - - +
83A ALA 2.7 12.3 + - - +
85A ALA* 1.3 72.9 - - + +
87A SER* 1.3 53.5 + - - +
89A PHE* 3.0 6.8 + - - +
90A ILE* 2.7 51.3 + - + +
146A ALA 3.7 5.3 + - - -
149A ALA* 3.9 12.1 - - + +
150A ASP* 3.4 37.4 - - - +
153A HIS* 5.5 2.1 - - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 2.7 14.7 + - - -
84A LEU* 3.0 18.0 + - - +
86A GLN* 1.3 73.2 - - - +
88A MET* 1.3 58.6 + - - +
90A ILE* 4.5 6.7 - - - +
91A SER* 2.8 31.7 + - - -
149A ALA* 5.0 1.0 - - - +
152A LEU* 6.0 0.2 - - - -
194A ALA* 3.4 26.0 - - - +
197A MET* 4.0 10.5 - - - -
198A GLY* 3.2 25.7 - - - -
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.3 40.7 + - + +
85A ALA* 3.6 9.2 - - - +
86A GLN 3.2 0.6 - - - -
87A SER* 1.3 83.8 + - - +
89A PHE* 1.3 65.3 + - + +
91A SER* 3.3 6.4 + - - -
92A GLY* 2.9 24.9 + - - -
84C LEU* 6.5 0.4 - - + -
85C ALA* 5.7 11.2 - - + -
88C MET* 5.1 23.1 - - + +
89C PHE* 6.0 6.5 - - - -
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 3.3 14.3 + - + +
86A GLN* 3.0 9.5 + - - +
88A MET* 1.3 83.8 - - + +
90A ILE* 1.3 62.0 + - + +
92A GLY* 3.4 2.0 + - - -
93A SER* 3.2 29.8 + - - -
88C MET* 5.9 7.4 - - - -
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 2.7 41.6 + - + +
87A SER* 4.6 1.3 - - - +
89A PHE* 1.3 70.8 - - + +
91A SER* 1.3 63.8 + - - +
92A GLY 3.1 1.8 - - - -
93A SER* 3.6 7.0 + - - +
94A ALA* 3.2 23.4 + - - +
149A ALA* 3.5 26.2 - - - +
152A LEU* 4.1 13.9 - - + -
153A HIS* 3.7 35.4 - - + +
156A SER* 5.2 1.6 - - - +
190A ILE* 4.0 19.0 - - + +
194A ALA* 3.8 19.1 - - + -
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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 SER 2.8 23.1 + - - -
88A MET* 3.5 8.3 - - - -
90A ILE* 1.3 75.9 - - - +
92A GLY* 1.3 60.3 + - - +
94A ALA* 4.1 2.7 - - - -
95A LEU* 3.6 10.4 + - - +
191A LEU* 3.4 35.4 + - - +
194A ALA* 3.7 13.6 - - - +
195A LEU* 4.2 14.1 - - - +
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET 2.9 14.5 + - - -
89A PHE* 3.4 3.5 + - - -
90A ILE 3.1 0.4 - - - -
91A SER* 1.3 75.1 - - - +
93A SER* 1.3 57.2 + - - +
94A ALA 3.0 4.4 + - - -
95A LEU* 3.1 6.2 + - - +
96A PHE* 2.9 28.5 + - - +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE 3.2 16.8 + - - -
90A ILE* 3.6 7.3 + - - -
92A GLY* 1.3 73.9 - - - +
94A ALA* 1.3 56.7 + - - +
96A PHE* 3.5 12.2 - - - +
97A LEU* 3.1 27.5 + - - +
153A HIS* 5.9 5.5 + - - -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE 3.2 17.6 + - - +
91A SER 4.2 1.6 - - - +
92A GLY 3.0 1.2 - - - -
93A SER* 1.3 76.8 - - - +
95A LEU* 1.3 60.9 + - - +
96A PHE 3.3 0.2 - - - -
97A LEU* 3.8 4.0 - - - +
98A PHE* 3.1 26.2 + - - +
187A GLY* 3.5 13.4 - - - +
190A ILE* 4.0 14.1 - - + -
191A LEU* 3.5 35.7 - - + +
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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 3.6 12.0 + - - +
92A GLY* 3.1 7.9 + - - +
94A ALA* 1.3 76.2 - - - +
96A PHE* 1.3 61.8 + - - +
97A LEU 3.2 0.2 - - - -
98A PHE* 4.3 6.5 - - + +
99A LEU* 3.0 54.6 + - + +
191A LEU* 4.4 21.9 - - + +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLY 2.9 18.0 + - - +
93A SER* 3.5 12.1 - - - +
95A LEU* 1.3 79.9 - - - +
97A LEU* 1.3 60.7 + - + +
99A LEU* 3.7 3.6 + - - +
100A THR* 2.4 48.5 + - + -
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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
----------------------------------------------------------
93A SER 3.1 18.0 + - - +
94A ALA* 3.6 6.3 + - - +
95A LEU 3.2 0.2 - - - -
96A PHE* 1.3 83.8 - - + +
98A PHE* 1.3 60.8 + - - +
100A THR* 3.8 12.8 - - + +
101A GLY 3.1 14.4 + - - -
183A ALA* 3.0 43.1 - - + +
186A ILE* 4.7 22.9 - - + -
187A GLY* 4.7 3.8 - - - +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 3.1 18.4 + - - +
95A LEU* 3.3 7.6 + - + +
97A LEU* 1.3 74.8 - - - +
99A LEU* 1.3 79.7 + - + +
100A THR 3.3 0.2 - - - -
101A GLY* 3.1 13.3 + - - -
102A ILE* 3.2 29.7 + - + +
183A ALA 4.5 1.8 - - - -
184A LEU* 3.8 30.1 - - + -
187A GLY* 4.1 12.8 - - - -
188A ILE* 3.7 29.8 - - + -
191A LEU* 6.2 4.9 - - + -
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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
----------------------------------------------------------
95A LEU* 3.0 43.8 + - + +
96A PHE* 4.2 4.0 - - - +
98A PHE* 1.3 93.7 - - + +
100A THR* 1.3 59.6 + - - +
101A GLY 3.2 0.4 - - - -
102A ILE* 3.7 23.7 + - + +
103A GLN* 3.0 27.0 + - - +
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Residues in contact with THR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 2.4 42.7 + - + -
97A LEU* 3.8 17.0 - - + +
98A PHE 3.3 0.2 - - - -
99A LEU* 1.3 75.9 - - - +
101A GLY* 1.3 62.7 + - - +
103A GLN* 3.6 16.7 - - - +
104A HIS* 3.2 52.1 + - + +
183A ALA* 5.7 2.5 - - + -
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 3.1 12.8 + - - -
98A PHE 3.1 10.5 + - - -
100A THR* 1.3 79.2 - - - +
102A ILE* 1.3 56.5 + - - +
104A HIS 4.3 0.2 - - - -
105A LEU* 3.8 6.2 + - - +
180A ALA* 3.7 28.2 - - - +
183A ALA* 4.4 5.8 - - - -
184A LEU* 3.8 28.9 - - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.2 31.1 + - + +
99A LEU* 3.8 31.0 - - + +
101A GLY* 1.3 72.9 - - - +
103A GLN* 1.3 66.5 + - - +
105A LEU* 3.5 29.2 - - + +
107A SER* 4.1 3.3 + - - -
184A LEU* 3.6 20.9 - - + -
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU 3.0 21.1 + - - +
100A THR* 3.3 17.5 + - - +
102A ILE* 1.3 77.2 - - - +
104A HIS* 1.3 76.0 + - - +
105A LEU 3.1 0.2 + - - -
107A SER* 2.8 31.7 + - - -
108A PRO* 4.4 7.8 - - + +
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 3.2 38.7 + - + +
101A GLY 4.3 2.9 - - - -
103A GLN* 1.3 84.3 + - - +
105A LEU* 1.3 50.2 + - - +
106A ILE* 2.7 18.8 + - - +
108A PRO* 3.7 25.6 - - + -
109A THR 4.9 10.6 - - - +
110A PRO* 6.4 1.6 - - + -
178A ALA* 4.9 3.0 - - + +
179A ASP* 4.4 21.0 + - + +
180A ALA* 3.8 20.0 + - - +
183A ALA* 4.9 9.0 - - + +
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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