Contacts of the helix formed by residues 4 - 32 (chain A) in PDB entry 6FWF
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 TYR 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 1.3 89.5 - - + +
5A LYS* 1.3 62.9 + - - +
6A LYS* 3.2 10.3 + - + +
7A LEU* 3.5 37.8 + - + +
8A TRP 4.0 1.0 + - - -
447A VAL* 6.0 5.2 - - + -
448A ASP* 3.1 18.9 + - - +
449A LYS* 4.3 1.9 - - - +
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Residues in contact with LYS 5 (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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2A GLY* 4.5 22.2 - - - +
3A GLN 3.7 1.8 - - - +
4A TYR* 1.3 73.2 - - - +
6A LYS* 1.3 76.7 + - + +
7A LEU 3.4 0.2 - - - -
8A TRP* 3.4 13.5 - - + +
9A TYR* 2.8 59.7 + - + +
448A ASP* 3.5 12.0 + - - +
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.2 7.9 - - + +
5A LYS* 1.3 92.7 - - + +
7A LEU* 1.3 55.7 + - + +
9A TYR* 3.1 31.7 + - + +
10A LEU* 2.8 37.2 + - - +
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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
----------------------------------------------------------
4A TYR* 3.5 32.4 + - + +
5A LYS 3.4 0.2 - - - -
6A LYS* 1.3 77.3 - - + +
8A TRP* 1.3 61.6 + - - +
10A LEU* 3.5 36.5 - - + +
11A LEU* 3.9 3.5 + - - +
449A LYS* 3.8 30.9 - - + +
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Residues in contact with TRP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 3.4 22.5 + - + +
7A LEU* 1.3 77.9 - - - +
9A TYR* 1.3 88.8 + + - +
11A LEU* 3.3 6.2 + - + +
12A PHE* 2.8 67.1 + + + +
448A ASP* 4.2 7.2 - - + +
449A LYS* 3.5 37.4 - - + +
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Residues in contact with TYR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 2.8 58.1 + - + +
6A LYS* 3.1 35.0 + - + +
8A TRP* 1.3 96.1 - + - +
10A LEU* 1.3 58.3 + - - +
11A LEU 3.4 0.2 - - - -
12A PHE* 3.7 26.6 - + - -
13A ALA* 2.8 32.7 + - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS 2.8 20.9 + - - +
7A LEU* 3.5 36.8 - - + +
8A TRP 3.2 0.4 - - - -
9A TYR* 1.3 75.6 - - - +
11A LEU* 1.3 61.1 + - - +
13A ALA* 3.9 3.1 - - - +
14A VAL* 3.6 24.1 + - - +
529A ALA* 5.7 2.9 - - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 3.9 3.7 + - - +
8A TRP* 3.3 6.3 + - + +
10A LEU* 1.3 76.2 - - - +
12A PHE* 1.3 57.0 + - - +
14A VAL* 3.2 16.3 - - + +
15A LEU* 2.8 53.8 + - + +
449A LYS* 4.2 15.7 - - - +
454A ILE* 4.1 26.7 - - + -
457A ALA* 5.6 6.3 - - + -
528A ALA* 5.7 4.5 - - + +
529A ALA* 4.9 19.3 - - + +
532A MET* 4.8 19.7 - - + -
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Residues in contact with PHE 12 (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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8A TRP* 2.8 59.0 + + + +
9A TYR* 3.7 29.6 - + + -
10A LEU 3.5 0.2 - - - -
11A LEU* 1.3 73.2 - - - +
13A ALA* 1.3 59.0 + - - +
15A LEU* 4.0 9.4 - - + +
16A ALA* 2.8 46.7 + - + +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR 2.8 22.8 + - - +
10A LEU* 3.9 4.9 - - - +
12A PHE* 1.3 74.2 - - - +
14A VAL* 1.3 58.4 + - + +
16A ALA* 3.3 3.5 + - - +
17A VAL* 2.8 45.6 + - + +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.6 14.1 + - - +
11A LEU* 3.2 26.2 - - + +
13A ALA* 1.3 79.1 - - + +
15A LEU* 1.3 56.8 + - - +
17A VAL* 3.3 10.0 - - + +
18A CYS* 2.8 38.5 + - - +
529A ALA* 4.2 20.4 - - + +
532A MET* 5.2 2.2 - - + -
533A LEU* 3.7 40.2 - - + +
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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
----------------------------------------------------------
11A LEU* 2.8 33.6 + - + +
12A PHE* 4.0 9.9 - - + +
14A VAL* 1.3 72.7 - - - +
16A ALA* 1.3 59.7 + - - +
18A CYS* 3.3 11.2 - - - -
19A PHE* 2.8 74.2 + - + +
532A MET* 4.2 26.2 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 2.8 41.9 + - + +
13A ALA* 3.8 3.4 - - - +
15A LEU* 1.3 72.2 - - - +
17A VAL* 1.3 56.4 + - + +
19A PHE* 3.7 4.9 - - - +
20A THR* 2.7 39.6 + - - +
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 2.8 29.6 + - + +
14A VAL* 3.3 14.6 - - + +
16A ALA* 1.3 72.2 - - + +
18A CYS* 1.3 62.1 + - - +
20A THR* 3.7 6.0 - - - -
21A ILE* 2.8 45.4 + - + +
533A LEU* 4.1 14.1 - - + -
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Residues in contact with CYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL 2.8 22.9 + - - +
15A LEU* 3.3 22.2 - - - -
17A VAL* 1.3 75.0 - - + +
19A PHE* 1.3 66.9 + - - +
21A ILE* 3.8 8.9 - - - +
22A LEU* 2.8 33.1 + - - +
532A MET 3.6 18.4 - - - +
533A LEU* 4.9 3.8 - - + +
536A VAL* 3.4 24.6 - - + +
537A PRO* 3.9 20.8 - - + +
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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 59.5 + - + +
16A ALA* 4.0 4.5 - - - +
18A CYS* 1.3 78.5 - - - +
20A THR* 1.3 60.8 + - - +
22A LEU* 4.7 1.1 - - + -
23A GLY* 2.8 28.4 + - - +
465A PHE* 3.6 38.8 - + - -
487A TRP* 4.4 19.5 - + - -
491A LEU* 6.1 0.7 - - + -
532A MET* 6.4 0.7 - - - -
536A VAL* 4.2 17.9 - - + -
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Residues in contact with THR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 2.7 29.7 + - - +
17A VAL* 3.7 7.7 - - - -
18A CYS 3.3 0.2 - - - -
19A PHE* 1.3 70.4 - - - +
21A ILE* 1.3 62.3 + - + +
24A TYR* 2.8 45.8 + - + +
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Residues in contact with ILE 21 (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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17A VAL* 2.8 38.0 + - + +
18A CYS* 3.8 7.2 - - - +
20A THR* 1.3 73.7 - - + +
22A LEU* 1.3 58.0 + - - +
24A TYR* 5.2 0.9 - - - -
25A MET* 2.8 44.0 + - + +
533A LEU* 6.2 0.4 - - + -
537A PRO* 3.8 10.3 - - + -
540A LEU* 5.9 0.2 - - + -
555A ILE* 3.4 44.2 - - + -
559A PHE* 3.7 28.5 - - + -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A CYS 2.8 21.5 + - - +
19A PHE* 4.7 2.5 - - + +
21A ILE* 1.3 75.4 - - - +
23A GLY* 1.3 56.8 + - - +
25A MET* 4.9 2.2 - - - -
26A GLY* 2.8 24.0 + - - +
483A TYR* 3.7 10.5 + - + -
487A TRP* 3.3 32.8 - - + +
491A LEU* 3.5 27.8 - - + -
536A VAL* 3.1 37.9 - - + +
537A PRO* 4.4 5.6 - - + -
539A THR* 4.1 4.7 - - + -
540A LEU* 4.1 24.9 - - + -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE 2.8 26.0 + - - -
20A THR* 5.0 0.2 - - - -
22A LEU* 1.3 74.5 - - - +
24A TYR* 1.3 52.0 + - - +
26A GLY* 3.5 1.6 - - - -
27A SER* 2.8 28.6 + - - -
483A TYR* 4.3 8.3 + - - -
487A TRP* 5.2 5.3 - - - -
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 2.8 32.6 + - + +
21A ILE* 4.4 0.9 - - - +
23A GLY* 1.3 69.4 - - - +
25A MET* 1.3 66.0 + - + +
26A GLY 3.1 0.9 - - - -
27A SER* 3.2 17.1 + - - +
28A GLU* 2.8 37.8 + - + +
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.8 30.7 + - + +
22A LEU 4.7 0.2 - - - +
24A TYR* 1.3 76.5 - - + +
26A GLY* 1.3 52.0 + - - +
28A GLU* 3.3 18.5 - - - +
29A VAL* 2.8 38.1 + - - +
540A LEU* 4.4 15.0 - - + -
551A ALA* 3.8 29.6 - - + -
552A SER* 3.7 13.0 - - - +
555A ILE* 4.0 35.4 - - + -
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.8 23.8 + - - +
23A GLY 3.5 3.4 - - - -
24A TYR 3.1 0.2 - - - -
25A MET* 1.3 75.1 - - - +
27A SER* 1.3 53.9 + - - +
29A VAL* 3.5 5.3 - - - +
30A TYR* 2.8 33.3 + - - +
483A TYR* 3.3 29.7 - - - -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 2.8 16.3 + - - -
24A TYR* 3.2 25.1 + - - -
26A GLY* 1.3 72.6 - - - +
28A GLU* 1.3 54.5 - - - +
30A TYR* 3.6 11.6 - - - +
31A LYS* 2.8 42.8 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 2.8 27.8 + - + +
25A MET* 3.3 26.7 - - - +
26A GLY 3.3 0.2 - - - -
27A SER* 1.3 76.2 - - - +
29A VAL* 1.3 57.4 + - - +
31A LYS* 4.6 11.6 + - - +
32A LYS* 2.8 68.0 + - - +
549A THR* 3.6 25.4 + - + +
551A ALA* 4.9 4.7 - - - +
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET 2.8 22.9 + - - +
26A GLY 3.5 12.1 - - - +
28A GLU* 1.3 72.5 - - - +
30A TYR* 1.3 59.9 + - - +
32A LYS 4.0 11.4 - - - +
479A ALA* 4.0 18.8 - - + +
480A VAL* 4.0 11.0 + - - +
483A TYR* 3.6 36.3 - - + -
540A LEU* 5.6 4.0 - - + -
543A LEU* 5.0 7.9 - - + -
547A GLY 5.1 2.0 - - - +
548A SER* 3.7 32.3 - - - +
549A THR 4.8 1.6 - - - +
552A SER* 3.7 14.8 - - - +
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLY 2.8 18.7 + - - +
27A SER* 3.6 13.0 - - - +
28A GLU 3.3 0.2 - - - -
29A VAL* 1.3 76.8 - - - +
31A LYS* 1.3 64.5 + - + +
480A VAL* 3.7 42.3 - - + +
483A TYR* 5.8 3.1 - + + -
484A TRP* 5.4 3.6 - - - -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 2.8 24.3 + - - +
28A GLU* 4.1 9.4 + - - +
30A TYR* 1.3 82.4 - - + +
32A LYS* 1.3 78.1 + - + +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 2.8 58.4 + - - +
29A VAL* 4.0 11.6 - - - +
31A LYS* 1.3 93.0 - - + +
35A PRO* 6.5 1.1 - - - -
204A ARG* 5.8 8.5 - - - +
211A TYR* 6.1 5.2 - - - -
479A ALA* 5.5 3.4 - - - +
547A GLY 3.0 24.8 - - - +
549A THR* 4.1 26.6 + - - +
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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