Contacts of the helix formed by residues 87 - 116 (chain A) in PDB entry 1NFV
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 ALA 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 6.0 0.4 - - - -
85A GLY 3.7 3.2 + - - -
86A GLN* 1.3 73.9 - - - +
88A VAL* 1.3 66.5 + - - +
89A PRO* 3.4 11.9 - - + -
90A VAL* 3.1 18.7 + - + +
91A ILE* 3.0 18.2 + - - +
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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
----------------------------------------------------------
37A LEU* 4.3 8.3 - - + -
40A MET* 3.7 33.1 - - + +
42A TYR* 4.3 13.0 - - + -
45A LEU* 4.7 5.8 - - + -
86A GLN 3.9 0.4 + - - -
87A ALA* 1.3 70.6 - - - +
89A PRO* 1.3 70.6 - - + +
91A ILE* 3.3 12.5 + - - +
92A TYR* 3.1 28.3 - - + -
146A ILE* 3.4 28.3 - - + -
154A LEU* 4.5 14.6 - - + -
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Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 3.4 13.0 - - + -
88A VAL* 1.3 95.1 - - + +
90A VAL* 1.3 59.7 + - + +
92A TYR* 3.4 3.6 + - + +
93A GLU* 3.0 30.3 + - - +
143A GLY* 5.8 1.4 - - - -
146A ILE* 4.3 26.7 - - + -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.7 28.3 - - + +
87A ALA* 3.1 25.7 + - + +
89A PRO* 1.3 76.5 - - + +
91A ILE* 1.3 59.4 + - - +
93A GLU* 4.4 15.3 - - - +
94A SER* 2.8 38.4 + - - +
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 3.7 36.6 - - + +
36A SER* 5.0 2.2 - - - -
37A LEU* 4.0 24.5 - - + -
40A MET* 4.7 6.7 - - + -
49A MET* 3.6 30.7 - - + -
86A GLN* 3.8 25.1 - - + +
87A ALA 3.0 15.8 + - - +
88A VAL* 3.3 12.5 + - - +
90A VAL* 1.3 77.0 - - - +
92A TYR* 1.3 69.2 + - + +
94A SER* 3.3 4.5 + - - -
95A ASP* 2.9 35.0 + - - +
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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
----------------------------------------------------------
37A LEU* 3.4 26.3 - - + +
45A LEU* 3.4 23.1 + - + +
49A MET* 3.9 10.5 - - + +
88A VAL* 3.1 34.8 - - + -
89A PRO* 3.4 4.5 + - + +
90A VAL 3.3 0.2 - - - -
91A ILE* 1.3 88.5 - - + +
93A GLU* 1.3 67.2 + - - +
95A ASP* 4.1 1.7 - - - +
96A ALA* 3.0 26.0 + - - +
138A TYR* 4.3 4.5 + + - -
139A TYR* 3.6 43.5 - + - +
142A ILE* 3.7 33.2 - - + -
143A GLY* 3.9 16.4 - - - +
146A ILE* 3.8 10.8 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO 3.0 19.4 + - - +
90A VAL* 4.0 15.1 - - - +
92A TYR* 1.3 78.2 - - - +
94A SER* 1.3 72.1 + - - +
96A ALA* 3.4 4.1 + - - +
97A ASP* 3.1 39.3 + - - +
143A GLY* 5.5 1.6 - - - -
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 4.3 0.2 + - - -
86A GLN* 3.1 24.5 + - - -
90A VAL* 2.8 30.4 + - - -
91A ILE* 3.3 4.2 + - - -
93A GLU* 1.3 81.3 - - - +
95A ASP* 1.3 63.7 + - - +
97A ASP* 3.2 11.8 + - - +
98A GLN* 2.8 29.6 + - - +
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 4.5 4.3 - - - +
30A TYR* 3.3 18.2 + - + -
33A GLN* 2.6 40.6 + - - +
49A MET* 3.4 16.1 - - - +
91A ILE 2.9 22.5 + - - +
92A TYR 4.1 0.4 - - - +
93A GLU 3.3 0.2 - - - -
94A SER* 1.3 77.3 + - - +
96A ALA* 1.3 66.8 + - - +
98A GLN* 3.8 7.2 - - - +
99A GLU* 2.9 28.2 + - - +
139A TYR* 3.6 27.5 - - + -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR 3.0 18.6 + - - +
93A GLU* 3.8 4.9 - - - +
95A ASP* 1.3 77.4 - - - +
97A ASP* 1.3 63.4 + - - +
99A GLU 3.3 0.2 + - - -
100A ASP* 3.0 21.9 + - - +
136A LEU* 3.4 14.9 - - + +
139A TYR* 3.9 12.2 - - + +
140A GLU* 3.9 30.1 - - + +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 3.1 31.7 + - - +
94A SER* 3.4 13.6 - - - +
96A ALA* 1.3 79.7 - - - +
98A GLN* 1.3 58.3 + - - +
100A ASP* 3.4 5.9 + - - +
101A ALA* 3.0 28.8 + - - +
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A MET 4.8 2.2 + - - -
25A HIS* 3.4 37.2 + - - -
26A ALA* 3.7 26.3 - - - +
29A GLN* 3.9 12.5 - - - +
30A TYR* 3.9 15.7 + - - +
94A SER 2.8 16.9 + - - +
95A ASP* 3.8 8.3 - - - +
97A ASP* 1.3 76.8 - - - +
99A GLU* 1.3 56.6 + - - +
101A ALA* 3.2 7.9 + - + +
102A THR* 2.8 40.7 + - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 2.8 22.6 + - - +
56A GLU* 3.2 2.6 - - - +
95A ASP 2.9 20.9 + - - +
96A ALA 3.8 2.0 - - - +
98A GLN* 1.3 75.2 - - - +
100A ASP* 1.3 62.6 + - - +
102A THR* 3.1 7.5 + - - -
103A ILE* 3.0 29.9 + - - +
132A GLU* 3.1 21.9 - - - +
135A HIS* 3.4 17.8 + - + +
136A LEU* 3.8 20.4 - - + +
139A TYR* 3.7 19.1 - - + -
201A FE 2.2 30.6 - - - -
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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
----------------------------------------------------------
96A ALA 3.0 17.4 + - - +
97A ASP* 3.8 6.0 - - - +
99A GLU* 1.3 78.1 - - - +
101A ALA* 1.3 62.8 + - - +
103A ILE* 3.5 5.4 + - - +
104A GLU* 3.1 32.5 + - - +
136A LEU* 4.2 22.9 - - + +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A MET* 4.9 2.2 - - + -
97A ASP 3.0 17.9 + - - +
98A GLN* 3.2 7.8 + - + +
100A ASP* 1.3 80.7 + - - +
102A THR* 1.3 60.8 + - - +
104A GLU* 3.3 8.2 + - - +
105A ALA* 2.9 24.1 + - - +
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A MET* 3.7 19.6 - - + +
23A GLU* 4.9 0.7 - - - +
98A GLN* 2.8 28.5 + - - +
99A GLU* 3.1 14.9 + - - -
101A ALA* 1.3 73.0 - - - +
103A ILE* 1.3 58.0 + - - +
105A ALA* 3.3 1.0 + - - +
106A TYR* 2.8 70.2 + - + +
132A GLU* 4.3 14.4 - - + +
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Residues in contact with ILE 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 GLU 3.0 19.9 + - - +
100A ASP* 3.8 5.6 - - - +
102A THR* 1.3 74.2 - - - +
104A GLU* 1.3 63.9 + - + +
106A TYR* 4.1 4.2 - - - +
107A SER* 2.6 41.5 + - - +
129A ILE* 4.3 19.7 - - + +
132A GLU* 3.5 24.9 - - + +
133A GLN* 3.8 35.7 - - + +
136A LEU* 4.0 20.0 - - + -
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Residues in contact with GLU 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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100A ASP* 3.1 28.5 + - - +
101A ALA* 3.6 10.1 - - - +
103A ILE* 1.3 81.8 - - + +
105A ALA* 1.3 63.1 + - - +
107A SER* 3.4 7.7 + - - -
108A GLN* 3.2 42.7 + - - +
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Residues in contact with ALA 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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22A MET* 3.8 25.4 - - + -
101A ALA 2.9 16.7 + - - +
102A THR 3.7 3.4 - - - +
104A GLU* 1.3 77.6 - - - +
106A TYR* 1.3 59.2 + - - +
108A GLN* 2.9 17.3 + - - +
109A PHE* 2.9 39.2 + - + -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.3 35.0 + - + -
22A MET* 3.8 15.5 - - + +
23A GLU* 2.5 37.4 + - - +
63A PHE* 4.0 4.0 - + - -
102A THR* 2.8 47.2 + - + +
103A ILE 4.1 0.7 - - - +
105A ALA* 1.3 72.2 - - - +
107A SER* 1.3 52.5 + - - +
109A PHE* 3.1 21.3 + + - +
110A LEU* 2.8 35.2 + - - +
125A PHE* 3.9 14.9 - + + -
128A ILE* 3.8 19.1 - - + -
129A ILE* 3.6 26.0 - - + +
132A GLU* 3.7 9.9 - - + -
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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
----------------------------------------------------------
103A ILE* 2.6 28.9 + - - +
104A GLU* 3.6 9.1 + - - -
106A TYR* 1.3 78.7 - - - +
108A GLN* 1.3 61.5 + - - +
110A LEU* 3.6 6.2 + - - +
111A LYS* 3.4 19.9 + - - +
129A ILE* 3.7 18.0 - - - +
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 3.2 34.7 + - - +
105A ALA* 2.9 14.1 + - - +
107A SER* 1.3 77.0 - - - +
109A PHE* 1.3 70.0 + - + +
111A LYS* 3.4 23.1 + - - +
112A VAL* 3.2 23.7 + - - +
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.6 35.1 - - + +
18A LYS* 3.7 33.4 - - + -
19A ALA* 3.8 18.8 - - + -
22A MET* 4.1 9.2 - - - -
105A ALA* 2.9 30.6 + - + -
106A TYR* 3.1 30.7 + + - +
108A GLN* 1.3 81.7 - - + +
110A LEU* 1.3 62.6 + - - +
112A VAL* 3.0 7.4 + - + +
113A CYS* 3.0 25.2 + - - -
125A PHE* 3.6 19.7 - + + -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR 2.8 14.9 + - - +
107A SER* 3.7 8.3 - - - +
109A PHE* 1.3 77.1 - - - +
111A LYS* 1.3 57.2 + - - +
113A CYS* 3.1 11.2 + - - +
114A LYS* 2.9 60.4 + - + +
122A ALA* 3.9 16.8 - - + +
125A PHE* 3.8 11.4 - - + -
126A GLU* 3.3 42.8 - - + +
129A ILE* 3.9 14.4 - - + -
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER 3.4 10.3 + - - +
108A GLN* 3.4 25.7 + - - +
109A PHE 3.3 0.2 - - - -
110A LEU* 1.3 82.2 - - + +
112A VAL* 1.3 59.5 + - - +
114A LYS* 3.3 12.2 + - + +
115A GLU* 2.9 55.1 + - + +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 4.3 14.6 - - + +
12A VAL* 5.0 0.9 - - - +
15A VAL* 4.1 28.0 - - + -
108A GLN 3.2 12.0 + - - +
109A PHE* 3.0 11.2 + - + +
111A LYS* 1.3 75.5 - - + +
113A CYS* 1.3 61.9 + - - +
115A GLU* 3.1 16.4 + - - +
116A GLN* 2.8 50.8 + - + +
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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
----------------------------------------------------------
12A VAL* 4.0 18.8 - - - -
15A VAL* 4.3 4.5 - - - -
109A PHE 3.0 17.5 + - - -
110A LEU 3.1 8.5 + - - +
112A VAL* 1.3 77.8 - - - +
114A LYS* 1.3 60.3 + - - +
116A GLN 3.2 2.3 + - - -
117A GLY 3.2 4.3 + - - -
118A ASP* 2.9 43.1 + - + +
121A THR* 3.4 33.2 - - - -
122A ALA* 3.9 9.0 - - + -
125A PHE* 3.8 17.0 - - - -
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 2.9 41.2 + - + +
111A LYS* 3.6 14.0 - - + +
112A VAL 3.2 0.2 - - - -
113A CYS* 1.3 76.0 - - - +
115A GLU* 1.3 63.9 + - + +
117A GLY* 3.3 12.7 + - - -
118A ASP 4.9 2.5 - - - +
119A ILE* 5.5 9.0 - - + +
122A ALA* 4.3 9.9 - - + -
126A GLU* 4.7 9.0 - - - -
1004A SO4 5.1 14.1 + - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 2.9 45.0 + - + +
112A VAL* 3.1 18.8 + - - +
114A LYS* 1.3 78.1 - - + +
116A GLN* 1.3 69.1 + - - +
117A GLY 3.2 2.9 + - - -
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP* 4.5 0.3 - - - -
8A ARG* 3.2 59.9 + - - +
11A LYS* 3.6 38.0 + - + +
12A VAL* 3.8 19.7 - - + -
112A VAL* 2.8 35.5 + - + +
113A CYS 3.2 1.5 + - - +
115A GLU* 1.3 87.2 + - - +
117A GLY* 1.3 62.4 + - - +
118A ASP* 3.4 2.4 + - - +
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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
------------------------------------------------------------
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