Contacts of the helix formed by residues 1 - 33 (chain A) in PDB entry 3PCV
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 1 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 1.3 69.2 + - - +
3A ASP* 2.9 7.3 + - + +
4A GLU* 3.3 15.6 + - + +
5A VAL* 3.7 14.8 + - + +
208A LMT 4.9 14.1 - - - +
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Residues in contact with LYS 2 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 1.3 72.0 - - - +
3A ASP* 1.3 63.9 + - - +
4A GLU 3.1 0.9 + - - -
5A VAL* 3.2 7.7 + - - -
6A ALA* 3.1 31.2 + - + +
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Residues in contact with ASP 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 2.9 4.2 + - + +
2A LYS* 1.3 80.1 - - - +
4A GLU* 1.3 59.9 + - + +
5A VAL 3.7 0.3 + - - -
6A ALA* 4.4 6.2 + - - +
76A GLU* 4.4 5.0 - - - +
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Residues in contact with GLU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 12.2 + - + +
3A ASP* 1.3 79.6 - - + +
5A VAL* 1.3 64.8 + - - +
8A LEU* 4.7 0.9 - - - +
71A GLY 5.1 1.7 - - - +
72A ILE* 5.8 0.3 - - - +
76A GLU* 3.2 25.5 - - - +
208A LMT 4.1 23.7 - - - +
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Residues in contact with VAL 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 3.7 17.3 - - - +
2A LYS* 3.2 7.4 + - - +
4A GLU* 1.3 86.6 - - - +
6A ALA* 1.3 58.6 + - - +
8A LEU* 3.2 11.8 + - + +
9A ALA* 2.9 28.7 + - + +
68A TRP* 3.4 33.0 - - + -
72A ILE* 4.5 3.4 - - + -
76A GLU* 2.9 11.0 - - - -
208A LMT 4.4 26.2 - - - -
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 3.1 17.5 + - + +
3A ASP* 4.4 6.3 + - - +
4A GLU 3.8 0.2 - - - -
5A VAL* 1.3 78.9 - - - +
7A LEU* 1.3 60.0 + - + +
9A ALA* 3.7 7.3 - - - +
10A ALA* 2.9 28.2 + - - +
76A GLU* 3.1 1.4 + - - -
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA* 1.3 76.6 - - + +
8A LEU* 1.3 61.1 + - - +
10A ALA* 3.3 4.7 + - - +
11A VAL* 3.0 34.0 + - - +
76A GLU* 2.8 25.7 + - - +
77A GLY* 4.1 24.0 - - - +
80A ALA* 3.9 13.0 - - + -
203A LMT 3.6 43.7 - - + -
207A LMT 4.1 27.1 - - + +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU 4.7 0.4 - - - +
5A VAL* 3.5 11.9 - - + +
7A LEU* 1.3 79.0 - - - +
9A ALA* 1.3 52.1 + - - +
11A VAL* 3.5 1.4 + - - -
12A THR* 2.7 37.5 + - - -
67A LEU* 3.7 37.4 - - + +
68A TRP* 3.8 41.7 - - + +
71A GLY* 3.8 31.0 - - - -
72A ILE* 4.3 5.4 - - + +
76A GLU* 3.2 34.5 + - + +
79A ALA* 4.0 1.8 - - + -
80A ALA 4.2 2.0 - - - +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 2.9 19.0 + - + +
6A ALA* 3.7 9.0 - - - +
7A LEU 3.2 0.2 - - - -
8A LEU* 1.3 77.4 - - - +
10A ALA* 1.3 56.3 + - - +
12A THR* 3.3 4.8 + - - -
13A LEU* 2.9 28.6 + - - +
68A TRP* 3.7 17.0 - - + -
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA 2.9 17.0 + - - +
7A LEU* 3.7 7.9 - - - +
8A LEU 3.3 0.2 - - - -
9A ALA* 1.3 73.9 - - - +
11A VAL* 1.3 60.2 + - - +
13A LEU* 3.3 6.9 + - - +
14A LEU 3.0 22.7 + - - -
203A LMT 4.0 24.7 - - + -
207A LMT 3.2 35.5 - - + +
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 3.0 20.1 + - - +
8A LEU 4.0 3.1 - - - +
10A ALA* 1.3 75.5 - - - +
12A THR* 1.3 57.3 + - - +
14A LEU* 3.3 5.7 + - - +
15A GLY* 2.9 24.4 + - - -
63A PHE* 3.8 27.9 - - + -
67A LEU* 3.9 11.4 - - + -
80A ALA* 3.6 29.4 - - + +
83A GLY* 3.9 17.3 - - - -
84A LEU* 4.0 9.2 - - + +
87A LEU* 3.5 10.6 - - + +
207A LMT 4.0 17.0 - - + -
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Residues in contact with THR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU 2.7 24.3 + - - -
9A ALA* 3.4 10.1 - - - +
10A ALA 3.2 0.2 - - - -
11A VAL* 1.3 77.1 - - - +
13A LEU* 1.3 63.3 + - - +
15A GLY* 3.1 3.9 + - - -
16A VAL* 3.0 29.0 + - + +
60A PHE* 4.4 1.9 - - - -
63A PHE* 5.6 0.9 - - - -
64A LEU* 3.7 26.0 - - + +
67A LEU* 3.5 7.4 - - - +
68A TRP* 2.8 26.5 + - + +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA 2.9 16.4 + - - +
10A ALA* 3.3 7.4 + - - +
12A THR* 1.3 73.9 - - - +
14A LEU* 1.3 66.3 + - - +
16A VAL* 3.1 19.0 + - + +
17A LEU* 2.9 40.0 + - + +
203A LMT 4.7 21.1 - - + -
207A LMT 5.2 2.9 - - + -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 3.0 14.1 + - - +
11A VAL* 3.5 8.5 - - - +
12A THR 3.3 0.2 - - - -
13A LEU* 1.3 75.6 - - - +
15A GLY* 1.3 58.6 + - - +
17A LEU* 3.3 8.6 + - + +
18A LEU* 3.0 27.0 + - - +
84A LEU* 3.6 31.6 - - + +
87A LEU* 4.0 10.5 - - + -
205A LMT 4.0 21.3 - - + -
207A LMT 3.7 23.9 - - + +
211A LMT 4.5 25.4 - - + -
213A LMT 3.9 23.6 - - + -
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL 2.9 12.4 + - - -
12A THR* 3.1 4.4 + - - -
14A LEU* 1.3 73.6 - - - +
16A VAL* 1.3 57.8 + - - +
18A LEU* 3.3 3.5 + - - +
19A GLN* 3.0 32.9 + - - +
60A PHE* 3.5 20.9 - - - -
63A PHE* 5.1 0.4 - - - -
87A LEU* 3.5 23.0 - - - +
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.0 26.8 + - + +
13A LEU* 3.1 20.8 + - + +
15A GLY* 1.3 75.0 - - - +
17A LEU* 1.3 61.4 + - + +
19A GLN* 3.2 6.0 + - + +
20A ALA* 2.9 27.0 + - - +
60A PHE* 4.1 17.9 - - + -
64A LEU* 6.1 0.2 - - + -
204A LMT 4.6 17.9 - - + -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 2.9 37.3 + - + +
14A LEU* 3.6 19.3 - - + +
16A VAL* 1.3 77.9 - - + +
18A LEU* 1.3 58.7 + - - +
20A ALA* 3.2 11.0 + - + +
21A TYR* 3.0 26.9 + - - +
203A LMT 6.5 0.2 - - + -
204A LMT 6.0 3.1 - - + -
205A LMT 4.0 15.2 - - + +
207A LMT 5.1 7.4 - - + -
211A LMT 5.4 7.6 - - + -
219A UNL 4.0 4.5 - - - +
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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 LEU 3.0 17.4 + - - +
15A GLY* 3.6 5.4 - - - +
16A VAL 3.2 0.2 - - - -
17A LEU* 1.3 74.1 - - - +
19A GLN* 1.3 61.5 + - + +
21A TYR* 3.1 6.9 + - + +
22A PHE* 2.9 70.3 + - + -
87A LEU* 3.4 45.8 - - + +
90A ARG* 4.2 4.5 - - + -
91A LEU* 3.9 24.2 - - + +
205A LMT 4.0 22.8 - - + +
213A LMT 4.8 7.9 - - + -
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 3.0 18.8 + - - +
16A VAL* 3.2 9.2 + - - +
18A LEU* 1.3 79.3 - - - +
20A ALA* 1.3 62.4 + - - +
22A PHE* 3.3 21.1 + - - +
23A SER* 3.0 26.5 + - - -
53A GLN* 4.3 1.4 - - - +
56A CYS* 3.4 36.0 + - - +
57A SER* 3.2 28.1 + - - -
60A PHE* 3.8 30.8 - - + -
87A LEU* 6.2 1.0 - - - +
90A ARG* 6.0 1.8 - - - +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL 2.9 13.7 + - - +
17A LEU* 3.5 14.8 - - + +
18A LEU 3.2 0.2 - - - -
19A GLN* 1.3 77.6 - - - +
21A TYR* 1.3 56.6 + - - +
23A SER* 3.3 5.9 + - - -
24A LEU* 2.9 37.5 + - + +
204A LMT 3.7 38.3 - - + +
219A UNL 4.7 8.1 - - + -
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.0 13.2 + - - +
18A LEU* 3.3 7.6 - - + +
20A ALA* 1.3 76.4 - - - +
22A PHE* 1.3 82.3 + + - +
24A LEU* 3.2 9.7 + - + +
25A GLN* 2.9 61.1 + - + +
91A LEU* 4.0 20.0 - - + -
94A PHE* 4.5 6.7 - + - -
95A GLN* 4.8 5.6 + - + +
205A LMT 3.8 65.5 + - + +
219A UNL 4.4 8.7 - - + +
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Residues in contact with PHE 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 59.4 + - + -
19A GLN* 3.3 22.4 + - - +
21A TYR* 1.3 82.0 - + - +
23A SER* 1.3 64.4 + - - +
25A GLN* 3.2 3.5 + - - +
26A VAL* 3.0 26.9 + - - +
53A GLN* 3.9 13.7 - - + -
56A CYS* 3.5 36.1 - - + -
90A ARG* 3.7 18.4 - - + -
91A LEU* 4.0 5.6 - - + -
94A PHE* 3.3 48.9 - + + -
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN 3.0 14.6 + - - -
20A ALA* 3.3 11.5 + - - -
22A PHE* 1.3 76.4 - - - +
24A LEU* 1.3 62.0 + - - +
26A VAL* 3.3 6.5 + - - +
27A ILE* 3.1 29.3 + - - +
53A GLN* 4.2 17.3 + - - +
57A SER* 5.7 0.2 + - - -
204A LMT 4.4 17.0 - - - -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 2.9 27.0 + - + +
21A TYR* 3.2 9.2 + - + +
23A SER* 1.3 74.6 - - - +
25A GLN* 1.3 61.3 + - - +
27A ILE* 3.3 12.4 + - + +
28A SER* 3.0 27.5 + - - -
204A LMT 4.0 40.8 - - + -
219A UNL 4.5 17.3 - - + -
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 2.9 55.5 + - + +
22A PHE 3.2 7.6 + - - +
24A LEU* 1.3 77.1 - - - +
26A VAL* 1.3 59.3 + - - +
28A SER* 3.3 12.6 + - - -
29A ALA* 2.9 29.3 + - - +
49A VAL* 3.9 5.2 - - + +
94A PHE* 3.6 25.6 - - + -
205A LMT 5.7 2.2 + - - -
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE 3.0 12.3 + - - +
23A SER* 3.6 7.9 - - - +
25A GLN* 1.3 75.6 - - - +
27A ILE* 1.3 60.6 + - + +
29A ALA* 3.2 2.5 + - - +
30A ARG* 2.8 48.9 + - + +
46A PHE* 4.8 4.3 - - + -
49A VAL* 3.7 23.6 - - + +
50A TYR* 4.1 20.0 - - + -
53A GLN* 3.4 45.5 - - + +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 3.1 17.6 + - - +
24A LEU* 3.6 13.0 - - + +
26A VAL* 1.3 78.0 - - + +
28A SER* 1.3 64.4 + - - +
30A ARG* 3.2 13.9 + - - +
31A ARG* 3.1 23.3 + - + +
204A LMT 4.1 43.7 - - + -
217A EDO 3.8 35.9 + - - +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.0 14.1 + - - -
25A GLN* 3.5 20.5 + - - -
27A ILE* 1.3 78.1 - - - +
29A ALA* 1.3 56.8 + - - +
31A ARG* 3.3 7.8 + - - +
32A ALA* 3.0 29.7 + - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN 2.9 17.5 + - - +
26A VAL* 3.2 5.1 + - - +
28A SER* 1.3 73.6 + - - +
30A ARG* 1.3 60.0 + - - +
32A ALA* 4.4 3.1 - - - -
33A PHE* 2.9 49.4 + - + +
46A PHE* 3.9 17.2 - - + -
49A VAL* 4.1 25.6 - - + -
----------------------------------------------------------
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 2.8 32.4 + - + +
27A ILE* 3.4 17.0 - - - +
29A ALA* 1.3 72.9 - - - +
31A ARG* 1.3 58.7 + - - +
34A ARG* 2.8 24.8 + - - -
35A VAL* 2.8 43.1 + - - +
37A PRO* 3.5 35.5 - - + +
38A PRO 5.3 0.6 - - - -
39A LEU 2.9 29.1 + - - -
40A THR* 3.8 16.6 - - - +
46A PHE* 3.5 21.9 - - + -
50A TYR* 4.6 8.7 - - - -
217A EDO 5.0 9.9 - - - +
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.1 13.2 + - + +
28A SER* 3.6 10.8 - - - +
29A ALA 3.2 0.2 - - - -
30A ARG* 1.3 74.9 - - - +
32A ALA* 1.3 65.4 + - - +
34A ARG* 3.2 18.6 + - - +
217A EDO 6.4 1.8 - - - -
----------------------------------------------------------
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.0 17.9 + - - +
29A ALA* 3.4 5.1 + - - +
31A ARG* 1.3 77.3 - - - +
33A PHE* 1.3 72.5 + - + +
34A ARG* 3.3 4.0 + - - +
251A SO4 4.4 14.4 + - - -
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 2.9 36.3 + - + +
32A ALA* 1.3 87.2 - - + +
34A ARG* 1.3 73.1 + - - +
35A VAL* 3.3 20.2 + - + +
43A PRO* 3.7 28.6 - - + +
45A GLU* 3.5 45.5 - - + -
46A PHE* 4.0 21.3 - - + -
49A VAL* 6.0 0.9 - - + -
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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