Contacts of the helix formed by residues 14 - 45 (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 MET 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 1.3 66.0 + - - +
16A ARG* 3.2 30.1 + - + -
17A ASP* 3.0 62.9 + - + +
18A LEU* 3.1 30.5 + - - +
21A ARG* 4.9 3.2 + - - +
136A GLN* 4.6 16.4 - - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 1.3 74.0 - - - +
16A ARG* 1.3 59.5 + - + +
18A LEU* 3.5 8.6 - - + +
19A PHE* 2.8 44.9 + - + +
133A ILE* 5.0 4.5 - - + -
136A GLN* 4.3 19.3 - - + +
137A VAL* 3.8 31.6 - - + -
193A ILE* 4.2 18.8 - - + -
194A ILE* 4.3 13.2 - - + -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.2 20.9 - - + -
15A LEU* 1.3 78.9 - - + +
17A ASP* 1.3 60.1 + - - +
19A PHE* 4.2 0.3 - - - +
20A ASP* 3.0 37.2 + - - +
194A ILE* 3.8 44.2 + - + +
195A HIS* 4.0 20.6 + - - -
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.0 43.3 - - + +
16A ARG* 1.3 74.1 - - - +
18A LEU* 1.3 66.5 + - - +
20A ASP* 3.5 8.2 + - - +
21A ARG* 3.0 51.9 + - - +
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET 3.1 20.8 + - - +
15A LEU* 3.5 11.7 - - + +
17A ASP* 1.3 78.1 - - - +
19A PHE* 1.3 57.8 + - - +
21A ARG* 3.1 22.0 + - - +
22A ALA* 2.9 26.6 + - - +
129A ARG* 4.1 38.4 - - + +
132A LEU* 4.0 31.4 - - + +
133A ILE* 4.2 22.9 - - + +
136A GLN* 4.6 12.3 - - + -
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 2.8 31.5 + - + +
16A ARG 4.3 1.1 - - - +
18A LEU* 1.3 68.8 - - - +
20A ASP* 1.3 67.7 + - - +
22A ALA* 3.2 4.1 + - + +
23A VAL* 2.9 27.2 + - - +
81A LEU* 4.7 3.1 - - + -
133A ILE* 3.9 35.2 - - + -
137A VAL* 5.2 0.2 - - + -
186A LEU* 3.8 29.4 - - + -
189A LEU* 4.3 4.9 - - + -
190A LYS* 3.7 42.0 - - + -
193A ILE* 3.9 41.1 - - + -
194A ILE* 3.5 23.8 - - + -
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.0 25.6 + - - +
17A ASP* 3.8 8.6 - - - +
18A LEU 3.3 0.2 - - - -
19A PHE* 1.3 76.9 - - - +
21A ARG* 1.3 62.7 + - + +
23A VAL* 3.3 4.1 + - - +
24A VAL* 3.0 32.6 + - + +
190A LYS* 3.5 23.6 - - - +
194A ILE* 5.9 0.3 - - - +
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 4.9 3.8 + - - +
17A ASP* 3.0 50.0 + - - +
18A LEU* 3.7 34.7 - - - +
20A ASP* 1.3 73.8 - - + +
22A ALA* 1.3 65.9 + - - +
24A VAL* 3.1 9.4 + - - +
25A LEU* 3.0 27.4 + - + +
129A ARG* 4.3 29.1 - - + +
132A LEU* 6.1 1.2 - - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 2.9 15.8 + - - +
19A PHE* 3.7 5.2 - - - +
21A ARG* 1.3 78.4 - - - +
23A VAL* 1.3 56.6 + - - +
25A LEU* 3.3 0.4 + - - -
26A SER* 2.9 26.5 + - - -
126A LEU* 3.3 23.3 - - + +
129A ARG* 4.2 14.0 - - + +
130A MET* 4.2 10.8 - - - -
133A ILE* 4.3 9.4 - - + -
186A LEU* 3.5 18.6 - - + +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 2.9 19.6 + - + +
20A ASP* 4.1 3.6 - - - +
22A ALA* 1.3 73.7 - - - +
24A VAL* 1.3 67.8 + - + +
26A SER* 3.4 6.1 - - - +
27A HIS* 3.0 23.4 + - + +
186A LEU* 3.9 22.7 - - + +
187A LYS* 3.9 41.7 - - + +
190A LYS* 4.0 25.6 - - + +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP* 3.0 25.3 + - + +
21A ARG* 3.5 7.6 - - - +
23A VAL* 1.3 79.5 - - + +
25A LEU* 1.3 66.9 + - + +
27A HIS* 3.9 3.9 - - - +
28A TYR* 3.1 24.7 + - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.0 15.7 + - + +
22A ALA 3.5 6.5 - - - +
24A VAL* 1.3 81.6 - - + +
26A SER* 1.3 64.6 + - - +
28A TYR* 3.1 10.0 + - + +
29A ILE* 2.9 27.2 + - + +
122A GLN* 3.3 38.1 - - + +
125A ARG* 4.0 11.0 - - + +
126A LEU* 3.6 39.0 - - + +
129A ARG* 4.3 19.7 - - + +
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 2.9 14.4 + - - -
23A VAL* 3.2 13.3 + - - +
25A LEU* 1.3 77.1 - - - +
27A HIS* 1.3 52.4 + - - +
29A ILE* 3.7 4.3 - - - +
30A ALA* 2.8 35.3 + - - +
126A LEU* 3.8 22.4 - - - +
179A SER* 4.5 1.4 - - - +
182A ILE* 4.3 4.7 - - - -
183A ASP* 2.9 35.9 + - - +
186A LEU* 3.5 12.1 - - - +
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Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.0 20.3 + - + +
24A VAL* 3.9 3.8 - - - +
26A SER* 1.3 73.5 + - - +
28A TYR* 1.3 64.4 + - - +
30A ALA* 3.6 1.7 + - - +
31A ASN* 2.9 34.3 + - + +
183A ASP* 3.4 14.6 + - - +
187A LYS* 3.3 21.8 + - - +
141B THR* 5.7 2.7 - - + +
143B LEU* 5.1 12.6 - - + +
187B ASP* 3.7 32.4 - - + +
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.1 13.9 + - + +
25A LEU* 3.1 13.9 + - + +
27A HIS* 1.3 82.1 - - + +
29A ILE* 1.3 60.2 + - - +
31A ASN* 3.2 4.8 + - + +
32A LEU* 2.9 59.6 + - + +
118A GLU* 2.9 37.3 + - - +
122A GLN* 3.8 22.9 - - + -
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 2.9 21.9 + - + +
26A SER* 3.7 4.0 - - - +
28A TYR* 1.3 75.9 - - + +
30A ALA* 1.3 64.7 + - - +
32A LEU* 3.1 10.2 + - - +
33A SER* 2.9 25.2 + - - +
88A LEU* 5.9 0.7 - - + -
119A ILE* 3.9 26.9 - - + +
122A GLN* 3.8 35.7 - - + +
123A THR* 3.8 19.7 - - - +
126A LEU* 4.0 24.5 - - + -
175A LEU* 5.9 0.2 - - + -
179A SER* 3.9 18.8 - - - -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 2.8 18.5 + - - +
27A HIS 3.8 4.0 - - - +
29A ILE* 1.3 76.9 - - - +
31A ASN* 1.3 65.8 + - - +
33A SER* 3.3 2.3 + - - -
34A SER* 3.1 20.6 + - - -
176A ARG* 5.7 0.5 - - - +
179A SER* 3.8 32.7 - - - +
180A HIS* 4.2 11.9 - - + +
183A ASP* 4.2 12.3 - - + +
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Residues in contact with ASN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 2.9 28.1 + - + +
28A TYR* 3.2 5.1 + - + +
30A ALA* 1.3 76.9 - - - +
32A LEU* 1.3 67.3 + - - +
34A SER* 3.0 12.0 + - - -
35A GLU* 3.0 48.5 + - - +
187B ASP 5.3 7.7 + - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 2.9 51.6 + - + +
29A ILE* 3.5 8.1 - - - +
31A ASN* 1.3 79.3 + - - +
33A SER* 1.3 57.0 + - - +
35A GLU* 3.1 18.2 + - - +
36A MET* 2.8 31.5 + - - +
115A LYS* 4.1 21.7 - - + +
118A GLU* 3.6 30.5 - - + -
119A ILE* 3.9 21.1 - - + +
122A GLN* 5.5 0.2 - - + -
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 2.9 11.9 + - - +
30A ALA 3.5 7.2 - - - -
31A ASN 3.2 0.2 - - - -
32A LEU* 1.3 77.4 - - - +
34A SER* 1.3 57.9 + - - +
36A MET* 3.7 3.4 - - - +
37A PHE* 2.9 30.8 + - - +
119A ILE* 3.6 19.0 - - - +
172A LEU 5.0 1.0 - - - +
175A LEU* 3.8 11.0 - - - +
176A ARG* 3.9 19.7 - - - +
179A SER* 3.1 28.5 + - - -
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.1 8.1 + - - -
31A ASN* 3.0 15.4 + - - -
33A SER* 1.3 75.1 - - - +
35A GLU* 1.3 68.9 + - - +
36A MET 3.2 0.2 + - - -
37A PHE* 3.2 3.1 + - - +
38A SER* 3.0 25.7 + - - -
176A ARG* 3.6 28.6 + - - +
180A HIS* 6.1 0.7 - - - -
99B TYR* 4.7 6.2 - - - -
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASN* 3.0 40.7 + - - +
32A LEU* 3.1 13.7 + - - +
34A SER* 1.3 77.5 - - - +
36A MET* 1.3 59.1 + - - +
38A SER* 3.5 6.7 - - - -
39A GLU* 3.0 32.8 + - - +
115A LYS* 3.6 27.0 - - - -
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Residues in contact with MET 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 2.8 17.1 + - - +
33A SER* 3.7 2.9 - - - +
35A GLU* 1.3 75.0 - - - +
37A PHE* 1.3 65.6 + - - +
39A GLU* 3.2 4.3 + - - +
40A PHE* 3.0 23.0 + - - +
95A LEU* 5.6 0.2 - - + -
98A LEU* 4.0 17.0 - - + -
112A ILE* 3.7 40.0 - - + +
115A LYS* 3.8 16.3 - - + +
116A ALA* 3.8 20.0 - - - -
119A ILE* 3.6 12.1 - - + -
172A LEU* 4.1 16.6 - - + -
175A LEU* 3.4 32.5 - - + -
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Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER 2.9 18.5 + - - +
34A SER 3.8 2.2 - - - +
36A MET* 1.3 78.1 - - - +
38A SER* 1.3 62.4 + - - +
40A PHE* 3.5 5.0 + + - +
41A ASP* 3.0 36.8 + - + +
51A ILE* 5.9 1.6 - - + -
169A TYR* 3.9 44.0 - + - -
172A LEU* 3.7 25.1 - - + +
173A HIS* 3.7 37.2 - - + -
176A ARG* 3.5 46.7 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.0 14.2 + - - -
35A GLU* 3.5 11.4 - - - -
37A PHE* 1.3 80.2 - - - +
39A GLU* 1.3 62.6 + - - +
41A ASP* 2.9 6.8 + - - +
42A LYS* 2.8 33.5 + - - +
176A ARG* 5.7 1.6 + - - -
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.0 16.4 + - - +
36A MET 3.2 3.8 + - - +
38A SER* 1.3 81.2 - - - +
40A PHE* 1.3 59.6 + - - +
42A LYS* 3.9 23.0 - - - +
43A ARG* 3.4 23.4 + - - +
111A ALA* 3.2 23.8 - - + +
112A ILE* 4.0 14.4 + - + +
115A LYS* 3.0 33.2 + - - +
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET 3.0 16.3 + - - +
37A PHE* 3.7 6.3 - + - +
39A GLU* 1.3 77.4 - - - +
41A ASP* 1.3 62.6 + - - +
44A TYR* 3.0 56.9 + + + +
45A THR* 3.8 27.6 - - + -
112A ILE* 3.8 17.2 - - + +
165A LEU* 3.9 17.3 - - + -
168A TYR* 3.7 30.7 - + + -
169A TYR* 3.9 25.6 - + + -
172A LEU* 3.8 24.5 - - + -
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.0 27.5 + - + +
38A SER* 2.9 7.4 + - - +
40A PHE* 1.3 77.7 - - + +
42A LYS* 1.3 63.2 + - - +
45A THR* 2.9 30.1 + - - +
46A HIS* 2.6 53.6 + - - -
169A TYR* 3.9 18.4 + - + -
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER 2.8 13.0 + - - +
39A GLU* 3.9 28.5 - - - +
41A ASP* 1.3 77.9 + - - +
43A ARG* 1.3 69.4 + - - +
44A TYR 5.2 0.2 - - - -
46A HIS* 3.8 22.5 + - + +
----------------------------------------------------------
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU 3.4 17.9 + - - +
40A PHE 3.7 0.8 + - - -
41A ASP 3.2 0.8 - - - -
42A LYS* 1.3 86.0 - - + +
44A TYR* 1.3 104.0 + - + +
107A GLU 4.9 4.9 + - - -
109A PRO* 3.4 30.2 - - - +
112A ILE* 5.1 2.0 - - - -
----------------------------------------------------------
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.0 45.1 + + + +
42A LYS 5.2 0.2 - - - -
43A ARG* 1.3 130.0 + - + +
45A THR* 1.3 64.9 + - + +
46A HIS 3.7 1.3 - - - -
47A GLY 5.5 1.0 - - - +
50A PHE* 5.2 1.7 - - - -
105A MET* 5.7 2.9 - - - +
107A GLU 5.5 0.5 + - - -
109A PRO* 3.6 14.1 - - + +
112A ILE* 4.0 15.7 - - + -
165A LEU* 4.3 32.2 - - + +
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.8 25.0 + - + -
41A ASP* 2.9 33.6 + - - -
44A TYR* 1.3 80.8 - - + +
46A HIS* 1.3 67.7 + - - +
47A GLY 2.8 16.7 + - - +
48A ARG* 3.4 11.1 + - - +
50A PHE* 3.4 36.5 - - + -
165A LEU* 4.7 7.0 - - + +
169A TYR* 3.7 17.8 - - + -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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