Contacts of the helix formed by residues 76 - 104 (chain A) in PDB entry 3NCF
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 ASN 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN 3.6 2.6 + - - +
75A MET* 1.3 77.1 - - - +
77A GLN* 1.3 64.8 + - - +
78A LYS* 3.3 24.4 + - - +
79A ASP* 2.9 38.6 + - - +
80A PHE* 3.1 18.7 + - - +
192A ARG* 3.5 1.8 - - - +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN* 1.3 76.0 + - - +
78A LYS* 1.3 63.8 + - - +
80A PHE* 3.7 6.1 - - - +
81A LEU* 3.0 29.1 + - - +
137A VAL* 3.3 18.0 - - - +
138A HIS* 3.3 29.2 + - + +
189A LEU* 4.1 10.0 - - + +
192A ARG* 3.3 28.7 + - - +
193A ILE* 3.3 29.5 - - + +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN* 3.2 11.7 + - - +
77A GLN* 1.3 82.2 - - - +
79A ASP* 1.3 66.4 + - - +
81A LEU* 3.3 4.5 + - - +
82A SER* 3.0 24.8 + - - -
138A HIS* 3.8 37.9 - - + +
140A GLU 3.9 10.4 + - - -
141A THR* 3.4 30.9 - - + +
142A LYS* 3.2 36.4 - - - +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 3.7 19.4 - - + +
76A ASN* 2.9 32.1 + - - +
78A LYS* 1.3 82.0 - - - +
80A PHE* 1.3 57.8 - - - +
82A SER* 3.5 7.8 + - - -
83A LEU* 2.9 27.5 + - - +
142A LYS* 4.9 10.2 + - - -
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO* 3.7 25.4 - - + -
72A ALA* 3.8 26.7 - - + -
75A MET* 3.9 21.7 - - + +
76A ASN 3.1 15.6 + - - +
77A GLN 3.7 4.9 - - - +
79A ASP* 1.3 74.9 - - - +
81A LEU* 1.3 64.7 + - - +
83A LEU* 3.2 10.3 + - + +
84A ILE* 3.2 21.1 + - - +
185A TYR* 3.6 46.4 - + + -
188A LEU* 4.3 9.0 - - + -
189A LEU* 3.7 33.9 - - + -
192A ARG* 4.1 13.7 - - - -
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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
----------------------------------------------------------
19A PHE* 4.7 4.7 - - + -
77A GLN 3.0 20.7 + - - +
78A LYS* 3.3 3.8 + - - +
80A PHE* 1.3 75.3 - - - +
82A SER* 1.3 63.7 + - - +
84A ILE* 3.0 6.8 + - + +
85A VAL* 3.0 26.4 + - - +
130A MET* 3.8 27.8 - - + +
133A ILE* 4.4 20.0 - - + -
134A VAL* 4.1 18.8 - - + -
137A VAL* 4.6 4.3 - - + -
138A HIS* 4.0 23.6 - - + +
189A LEU* 3.8 27.4 - - + -
193A ILE* 4.3 15.9 - - + -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS 3.0 18.0 + - - -
79A ASP* 3.6 8.0 + - - -
81A LEU* 1.3 75.5 - - - +
83A LEU* 1.3 58.1 + - - +
85A VAL* 3.2 9.0 + - - +
86A SER* 2.8 37.7 + - - -
134A VAL* 5.2 3.1 - - - +
142A LYS* 5.7 6.7 + - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.7 35.4 - - + -
64A ALA 3.5 23.1 - - - +
65A THR* 4.0 11.2 - - + -
66A PRO* 3.9 21.1 - - + -
75A MET* 4.1 11.9 - - + -
79A ASP 2.9 14.5 + - - +
80A PHE* 3.3 17.3 - - + +
82A SER* 1.3 78.3 + - - +
84A ILE* 1.3 63.4 + - + +
86A SER* 3.2 5.1 + - - -
87A ILE* 2.9 36.4 + - + +
185A TYR* 4.8 4.5 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE 3.4 11.2 - - - +
81A LEU* 3.0 8.4 + - + +
83A LEU* 1.3 77.7 - - - +
85A VAL* 1.3 63.9 + - - +
87A ILE* 3.3 9.2 + - - +
88A LEU* 3.1 40.8 + - + +
130A MET* 4.2 19.5 - - + -
182A ILE* 4.4 17.6 - - + +
185A TYR* 3.8 31.0 - - + -
186A LEU* 4.1 20.6 - - + +
189A LEU* 3.6 28.3 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 3.0 12.6 + - - +
82A SER* 3.6 10.5 - - - +
84A ILE* 1.3 80.5 - - + +
86A SER* 1.3 57.5 + - - +
88A LEU* 3.2 4.6 + - - +
89A ARG* 2.9 68.2 + - - +
127A LEU* 4.2 12.9 - - + +
130A MET* 4.0 28.3 - - + -
131A GLU* 4.7 4.9 - - + +
134A VAL* 4.4 17.3 - - + -
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.8 15.7 - - - -
82A SER* 2.8 26.0 + - - -
83A LEU* 3.6 8.0 - - - -
85A VAL* 1.3 73.7 - - - +
87A ILE* 1.3 57.8 + - - +
89A ARG* 3.4 6.4 + - - +
90A SER* 2.9 26.0 + - - -
146A ILE* 3.9 14.4 + - - +
147A TYR* 3.4 26.8 - - - +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 5.0 4.5 - - + -
63A LEU* 3.8 18.8 - - + -
65A THR* 4.2 22.9 - - + -
83A LEU* 2.9 22.4 + - + +
84A ILE* 3.7 8.3 - - - +
86A SER* 1.3 73.8 - - - +
88A LEU* 1.3 64.9 + - - +
90A SER* 2.9 23.1 + - - +
91A TRP* 3.2 23.7 - - + -
178A ASP* 4.2 15.9 - - + +
181A LYS* 4.7 8.3 - - + -
182A ILE* 3.6 27.4 - - + -
185A TYR* 4.6 13.7 - - + -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 5.9 0.2 - - + -
84A ILE* 3.1 27.5 + - + +
85A VAL* 3.2 6.3 + - - +
87A ILE* 1.3 76.5 - - - +
89A ARG* 1.3 62.6 + - - +
91A TRP* 3.0 16.2 + - + +
92A ASN* 3.1 18.1 - - - +
123A THR* 4.0 27.7 - - + +
126A LEU* 4.0 26.5 - - + -
127A LEU* 4.1 20.6 - - + -
130A MET* 3.7 31.0 - - + -
182A ILE* 3.9 21.8 - - + -
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 2.9 41.3 + - - +
86A SER* 3.8 6.3 + - - +
88A LEU* 1.3 75.6 - - - +
90A SER* 1.3 62.5 + - - +
91A TRP 3.1 1.2 + - - -
92A ASN* 3.3 17.8 + - - +
93A GLU 4.6 1.7 + - - -
127A LEU* 4.0 18.8 - - + +
131A GLU* 2.9 33.3 + - - +
144A ASN 4.6 3.6 + - - -
145A GLU* 3.5 46.8 + - - +
146A ILE 5.3 0.6 - - - +
147A TYR* 3.6 36.4 + - + -
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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
----------------------------------------------------------
59A HIS* 3.1 29.5 + - - -
60A THR* 3.3 13.2 - - - +
86A SER 2.9 16.1 + - - -
87A ILE 2.9 13.0 + - - -
89A ARG* 1.3 77.4 - - - +
91A TRP* 1.3 58.4 + - - +
92A ASN 3.5 0.2 - - - -
93A GLU* 4.5 2.6 + - - +
94A PRO* 3.5 12.5 - - - +
147A TYR* 3.4 14.0 - - - -
148A PRO* 3.5 30.3 - - - +
150A TRP* 4.6 1.9 + - - +
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Residues in contact with TRP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A CYS* 5.9 0.2 - - + -
59A HIS* 3.4 21.8 - + - -
87A ILE* 3.2 30.1 + - + +
88A LEU* 3.0 12.3 + - + +
90A SER* 1.3 79.4 + - - +
92A ASN* 1.3 67.6 + - - +
93A GLU 3.2 2.9 - - - -
94A PRO* 3.5 27.0 - - + +
95A LEU* 3.1 45.2 + - + +
123A THR* 5.1 2.9 - - + -
150A TRP* 5.9 0.9 - + - -
171A LEU* 3.7 28.3 - - + -
174A CYS* 3.6 27.6 - - + -
175A LEU* 3.5 39.9 - - + -
178A ASP* 2.7 37.2 + - + +
182A ILE* 5.4 2.5 - - + -
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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
----------------------------------------------------------
88A LEU 3.1 16.2 - - - +
89A ARG* 3.3 11.3 + - - +
91A TRP* 1.3 79.5 - - - +
93A GLU* 1.3 61.5 + - - +
95A LEU* 4.3 4.0 - - - +
96A TYR* 3.2 23.0 + - - +
120A GLU* 5.2 1.4 - - - +
123A THR* 3.5 22.1 - - - +
124A LYS* 4.9 16.8 - - - +
127A LEU* 3.8 22.7 - - - +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG 4.6 1.8 + - - +
90A SER 4.5 2.6 + - - +
92A ASN* 1.3 75.7 - - - +
94A PRO* 1.3 75.5 - - + +
96A TYR* 3.2 7.3 + - - +
97A HIS* 2.7 55.2 + - - -
147A TYR* 6.5 0.9 - - + -
150A TRP* 3.8 28.2 - - + +
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Residues in contact with PRO 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 4.2 1.6 - - + -
90A SER 3.5 17.7 - - - +
91A TRP* 3.5 35.0 - - + +
93A GLU* 1.3 96.3 - - + +
95A LEU* 1.3 55.7 + - - +
97A HIS* 3.4 1.1 + - - +
98A LEU* 2.9 30.0 + - - +
150A TRP* 3.6 52.1 - - + +
171A LEU* 4.6 8.7 - - + +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 5.6 0.2 - - + -
91A TRP* 3.1 44.5 + - + +
92A ASN* 4.3 3.8 - - - +
94A PRO* 1.3 73.0 - - - +
96A TYR* 1.3 66.1 + - - +
98A LEU* 3.8 14.9 - - + +
99A VAL* 3.2 30.0 + - - +
116A ALA 4.9 3.8 - - - +
119A ILE* 3.8 26.2 - - + -
120A GLU* 4.3 20.8 - - + +
123A THR* 4.0 30.5 - - + +
175A LEU* 4.0 23.1 - - + -
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN 3.2 13.9 + - - +
93A GLU* 3.2 12.0 + - - +
95A LEU* 1.3 80.6 - - - +
97A HIS* 1.3 90.5 + + - +
99A VAL* 3.5 2.1 + - - +
100A THR* 2.9 55.7 + - + +
120A GLU* 3.5 21.7 + - - +
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Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 2.7 55.1 + - - +
94A PRO 4.2 2.0 - - - +
96A TYR* 1.3 100.0 - + - +
98A LEU* 1.3 66.7 + - - +
100A THR* 4.3 5.2 + - - +
101A GLU* 2.9 34.7 + - + +
150A TRP* 4.1 18.4 - + + -
153A LEU* 3.7 42.2 - - + +
156A LEU* 4.9 1.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 4.0 18.2 - - + -
94A PRO 2.9 18.0 + - - +
95A LEU* 3.8 19.3 - - + +
97A HIS* 1.3 75.3 - - - +
99A VAL* 1.3 63.3 + - + +
101A GLU* 3.9 3.2 - - - +
102A VAL* 3.1 31.6 + - + +
112A ILE* 5.8 4.3 - - + -
116A ALA* 4.4 15.5 - - + -
156A LEU* 4.8 6.8 - - - +
168A TYR* 4.0 28.0 - - + -
171A LEU* 4.4 16.4 - - + -
172A LEU* 3.7 29.2 - - + -
175A LEU* 4.8 0.7 - - + -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.2 18.1 + - + +
96A TYR 3.9 2.7 - - - +
98A LEU* 1.3 78.3 - - + +
100A THR* 1.3 65.0 + - - +
102A VAL* 3.9 0.9 - - - +
103A ARG* 2.9 37.6 + - - +
113A LEU* 4.3 9.0 - - + +
116A ALA* 3.7 38.1 - - + +
117A VAL* 3.9 22.4 - - + +
120A GLU* 4.0 21.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 2.9 48.4 + - + +
97A HIS* 3.2 8.5 + - - +
99A VAL* 1.3 76.5 - - - +
101A GLU* 1.3 70.6 + - - +
103A ARG* 3.9 4.8 - - - +
104A GLY* 3.0 21.3 + - - -
----------------------------------------------------------
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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 HIS* 2.9 25.4 + - - +
98A LEU* 3.9 3.6 - - - +
100A THR* 1.3 84.1 - - - +
102A VAL* 1.3 62.7 + - - +
104A GLY* 3.3 9.9 + - - -
105A MET* 3.5 15.8 + - + +
153A LEU* 3.9 14.3 - - + +
156A LEU* 4.5 9.5 - - + +
157A GLN* 3.3 41.0 + - - +
168A TYR* 3.4 24.7 + - - +
----------------------------------------------------------
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.1 33.5 + - + +
99A VAL* 4.1 1.3 - - - +
101A GLU* 1.3 79.9 - - - +
103A ARG* 1.3 62.7 + - - +
105A MET* 3.3 28.2 + - + +
108A ALA* 3.3 20.5 - - + +
109A PRO* 4.6 11.4 - - + -
112A ILE* 5.3 9.0 - - + -
113A LEU* 3.6 38.1 - - + +
168A TYR* 4.4 13.7 - - + -
----------------------------------------------------------
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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
----------------------------------------------------------
99A VAL* 2.9 31.5 + - - +
100A THR* 3.9 4.5 - - - +
102A VAL* 1.3 78.1 - - - +
104A GLY* 1.3 60.2 + - - +
105A MET 3.4 8.5 + - - +
108A ALA* 4.9 2.5 - - - +
113A LEU* 4.2 26.3 - - + +
117A VAL* 5.3 5.2 - - - +
----------------------------------------------------------
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR 3.0 16.7 + - - -
101A GLU 3.7 4.5 - - - -
102A VAL 3.2 0.4 - - - -
103A ARG* 1.3 74.1 - - - +
105A MET* 1.3 61.4 + - - -
106A GLN 4.0 0.7 + - - -
----------------------------------------------------------
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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