Contacts of the helix formed by residues 660 - 682 (chain B) in PDB entry 1QXP
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 ASP 660 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B THR* 4.7 20.2 + - - +
613B PHE* 4.1 1.3 - - - -
622B GLY 3.6 18.4 - - - +
623B SER* 4.5 3.6 - - - +
658B ILE* 4.5 1.5 + - + +
659B ILE* 1.3 73.0 - - - +
661B PHE* 1.4 51.8 - - - +
662B ASP* 3.7 12.3 - - + +
663B ASN* 2.3 44.3 + - - +
664B PHE* 2.4 36.1 + - - -
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Residues in contact with PHE 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B PHE* 3.0 36.1 - + - -
606B ILE* 4.0 14.1 - - + -
609B TYR 3.9 1.3 - - - -
610B LEU* 3.2 52.5 - - + -
613B PHE* 3.5 35.0 - + + -
614B ARG* 5.8 2.2 - - - +
622B GLY 4.0 4.6 + - - +
660B ASP* 1.4 69.1 - - - +
662B ASP* 1.3 67.3 + - - +
664B PHE* 3.5 11.9 - + - -
665B VAL* 2.9 54.6 + - + +
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Residues in contact with ASP 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B THR* 4.3 12.5 + - - +
573B GLY 3.3 19.5 - - - +
574B PHE* 3.2 32.2 - - - +
575B SER* 4.0 15.2 + - - -
578B SER* 4.1 11.1 - - - -
660B ASP* 3.7 13.9 - - - +
661B PHE* 1.3 86.5 - - + +
663B ASN* 1.4 60.5 + - - +
665B VAL* 3.9 4.9 - - - +
666B ARG* 3.4 20.6 + - - +
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Residues in contact with ASN 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B ARG 5.1 1.2 + - - -
652B PHE* 3.8 50.7 + - + +
659B ILE* 5.1 1.1 - - + -
660B ASP* 2.3 46.0 + - - +
662B ASP* 1.4 72.2 - - - +
664B PHE* 1.3 71.3 - - - +
665B VAL 2.9 2.3 + - - -
666B ARG* 3.1 15.1 + - - +
667B CYS* 3.2 11.8 + - - +
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Residues in contact with PHE 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B TYR* 3.2 36.1 - - + -
612B ILE* 4.4 9.0 - - + -
613B PHE* 4.0 26.0 - + + -
616B PHE* 5.9 0.2 - + - -
624B MET* 4.1 20.0 - - + -
629B MET* 3.6 30.8 - - + +
632B ALA* 4.4 16.8 - - + -
659B ILE* 5.3 3.4 - - - +
660B ASP 2.4 25.2 + - - +
661B PHE* 3.4 16.6 - + - +
663B ASN* 1.3 72.7 - - - +
665B VAL* 1.3 75.1 - - + +
667B CYS* 3.2 7.4 - - - +
668B LEU* 3.2 41.1 + - + +
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Residues in contact with VAL 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B PHE* 4.5 12.6 - - + -
578B SER* 6.1 1.8 - - - -
582B MET* 4.2 17.5 - - + +
606B ILE* 5.1 0.9 - - + -
609B TYR* 3.4 43.9 - - + -
661B PHE* 2.9 50.4 + - + +
662B ASP 3.9 5.4 - - - +
663B ASN 2.9 2.6 + - - -
664B PHE* 1.3 79.0 - - + +
666B ARG* 1.3 71.5 + - - +
667B CYS 3.0 1.6 - - - -
668B LEU* 3.6 5.6 - - - +
669B VAL* 3.0 26.9 + - - +
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Residues in contact with ARG 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B SER* 4.2 25.1 - - - +
581B SER* 5.8 3.5 - - - -
582B MET* 6.3 0.2 - - - -
652B PHE* 4.2 14.4 - - + -
662B ASP* 3.4 16.2 + - - +
663B ASN* 3.1 9.6 + - - +
665B VAL* 1.3 79.9 - - - +
667B CYS* 1.3 64.7 + - - +
669B VAL* 4.9 3.4 - - - -
670B ARG* 2.9 25.3 + - - +
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Residues in contact with CYS 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B MET* 5.1 9.0 - - + -
648B ILE* 4.0 24.9 - - - -
652B PHE* 3.5 40.8 - - + -
663B ASN 3.2 9.5 + - - +
664B PHE* 3.2 13.2 - - - +
666B ARG* 1.3 75.0 - - - +
668B LEU* 1.3 86.4 - - + +
669B VAL 2.8 0.5 + - - -
670B ARG* 2.9 2.8 + - - -
671B LEU* 2.8 23.2 + - - +
891B MET* 3.7 13.7 - - - -
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Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B TYR* 3.2 40.2 - - + -
612B ILE* 6.0 0.4 - - + -
629B MET* 5.0 1.1 - - + -
632B ALA 4.8 0.2 - - - +
633B ILE* 3.8 44.2 - - + -
636B ALA* 3.2 30.1 - - + -
638B PHE* 4.3 7.4 - - + -
664B PHE* 3.2 37.5 + - + +
665B VAL* 3.6 2.8 - - - +
666B ARG 3.4 0.2 - - - -
667B CYS* 1.3 96.7 - - + +
669B VAL* 1.4 53.0 + - - +
671B LEU* 2.8 29.4 + - + +
672B GLU* 3.2 13.4 + - - +
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Residues in contact with VAL 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B SER* 4.8 14.4 - - - +
582B MET* 4.7 22.0 - - + +
585B LEU* 4.4 18.1 - - + +
609B TYR* 3.8 15.0 + - + +
665B VAL 3.0 22.1 + - - +
666B ARG* 4.3 2.9 - - - +
667B CYS 2.8 1.0 + - - -
668B LEU* 1.4 70.0 - - - +
670B ARG* 1.3 64.5 + - - +
671B LEU 3.2 0.2 + - - -
672B GLU* 3.5 5.4 - - - +
673B ILE* 2.9 25.8 + - + +
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Residues in contact with ARG 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B SER* 4.5 18.2 - - - +
651B ARG* 2.2 77.6 - - - +
652B PHE* 3.8 11.3 - - - -
666B ARG 2.9 20.0 + - - +
667B CYS* 2.9 7.1 + - - +
669B VAL* 1.3 71.7 - - - +
671B LEU* 1.3 60.0 + - - +
673B ILE* 3.0 24.6 - - - +
674B LEU* 2.4 42.8 - - + +
702B LEU* 4.3 24.8 - - - +
860B ARG* 4.6 0.6 - - - +
890B THR 3.3 6.9 + - - +
891B MET* 3.9 2.2 - - - -
893B SER* 2.8 14.3 + - - -
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Residues in contact with LEU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ILE* 4.0 13.5 - - + -
638B PHE* 3.7 40.2 - - + -
640B LEU* 3.7 33.0 - - + -
644B LEU* 5.5 1.1 - - + -
648B ILE* 4.7 7.4 - - + -
667B CYS* 2.8 16.0 + - - +
668B LEU* 2.8 17.3 + - + +
670B ARG* 1.3 68.7 - - - +
672B GLU* 1.3 55.3 + - - +
674B LEU* 3.1 12.7 - - - +
675B PHE* 2.7 47.4 + - + -
887B LEU* 4.4 15.0 - - + -
891B MET* 4.4 18.3 - - + -
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Residues in contact with GLU 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B LEU* 3.9 11.3 - - + +
585B LEU* 3.3 33.0 - - + +
586B MET* 4.2 2.9 - - - +
605B ARG* 2.3 55.2 + - - -
609B TYR* 3.3 6.6 + - - +
638B PHE* 3.5 21.6 - - + -
668B LEU 3.2 8.1 + - - +
669B VAL* 3.5 8.5 - - - +
671B LEU* 1.3 75.9 - - - +
673B ILE* 1.3 70.3 + - - +
675B PHE* 2.8 6.8 + - - +
676B LYS* 2.8 20.6 + - + +
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Residues in contact with ILE 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B SER* 4.3 25.8 - - - +
584B ASN* 5.3 8.5 - - + +
585B LEU* 3.7 29.6 - - + +
669B VAL 2.9 24.3 + - - +
670B ARG* 3.0 22.4 + - + +
672B GLU* 1.3 73.7 - - - +
674B LEU* 1.4 53.7 + - + +
676B LYS* 2.5 29.4 + - - +
677B ILE* 2.5 44.2 + - + +
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Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670B ARG* 2.4 62.0 + - + +
671B LEU* 3.1 12.1 - - - +
673B ILE* 1.4 78.4 - - + +
675B PHE* 1.3 61.6 + - - +
677B ILE* 3.3 13.6 + - + -
678B PHE* 2.8 25.3 + - - +
699B PHE 5.8 1.6 - - - +
886B TRP* 3.0 18.4 + - + +
887B LEU* 3.7 20.0 - - + -
890B THR* 2.9 43.7 - - + +
891B MET* 4.4 6.1 - - - -
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Residues in contact with PHE 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ILE* 4.5 2.2 - - + -
518B GLN* 3.8 16.2 - - - -
519B ALA* 3.2 48.5 - - + -
521B LEU* 6.3 0.4 - - + -
638B PHE* 3.3 23.3 - + + -
640B LEU* 4.8 4.3 - - + -
671B LEU* 2.7 29.0 + - + -
672B GLU* 2.8 8.9 + - - +
674B LEU* 1.3 74.4 - - - +
676B LYS* 1.4 53.9 + - - +
678B PHE* 2.9 8.7 - + + +
679B LYS* 2.6 35.2 + - - +
883B ILE* 3.7 26.9 - - + -
887B LEU* 4.1 21.3 - - + -
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Residues in contact with LYS 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B LEU* 5.6 3.8 - - + -
672B GLU* 2.8 14.3 + - + +
673B ILE* 2.5 17.8 + - - +
675B PHE* 1.4 74.4 - - - +
677B ILE* 1.3 64.3 + - + +
679B LYS* 2.6 18.5 + - - +
680B GLN* 2.7 16.9 + - + +
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Residues in contact with ILE 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B ILE* 2.5 50.5 + - + +
674B LEU* 4.0 15.7 - - + +
676B LYS* 1.3 70.4 - - + +
678B PHE* 1.4 53.4 + - - +
680B GLN* 3.1 9.8 + - + +
681B LEU* 2.4 72.6 + - + +
699B PHE* 3.7 41.7 - - + +
886B TRP* 3.8 16.4 - - + -
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Residues in contact with PHE 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B LEU 2.8 14.7 + - - +
675B PHE* 2.9 18.6 - + + +
677B ILE* 1.4 79.9 - - - +
679B LYS* 1.3 64.8 + - - -
681B LEU* 2.8 9.3 + - - +
682B ASP* 2.7 48.6 + - + +
687B GLY* 4.1 10.8 - - - -
689B ILE* 3.8 24.0 - - + +
882B ASN* 3.6 12.8 - - - -
883B ILE* 3.4 50.5 - - + -
886B TRP* 3.2 33.0 - + + +
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Residues in contact with LYS 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675B PHE 2.6 18.7 + - - +
676B LYS* 2.6 11.9 + - - +
678B PHE* 1.3 74.7 - - - +
680B GLN* 1.4 55.9 + - - +
682B ASP* 2.7 40.8 + - - +
683B PRO* 3.6 3.4 - - + +
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Residues in contact with GLN 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B LYS* 2.7 21.3 + - + +
677B ILE* 3.3 13.9 - - + +
679B LYS* 1.4 71.9 - - - +
681B LEU* 1.4 60.3 + - + +
683B PRO* 3.9 9.5 - - - +
699B PHE* 6.2 2.2 - - + -
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Residues in contact with LEU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B ILE* 2.4 60.2 + - + +
678B PHE 2.8 5.8 + - - +
680B GLN* 1.4 69.6 - - + +
682B ASP* 1.3 55.4 + - - +
683B PRO* 2.9 14.9 - - - +
684B GLU* 4.5 2.3 - - - +
689B ILE* 3.6 40.1 - - + +
690B GLN* 4.6 12.4 + - - +
691B LEU* 4.7 14.4 - - + -
699B PHE* 4.3 24.7 - - + -
886B TRP* 4.7 1.3 - - + -
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Residues in contact with ASP 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B PHE* 2.7 30.0 + - + +
679B LYS* 2.7 18.0 + - - +
681B LEU* 1.3 72.3 - - - +
683B PRO* 1.3 65.6 - - - +
684B GLU* 3.4 5.0 - - - +
685B ASN* 3.0 18.6 + - - +
686B THR* 2.8 34.7 + - - -
687B GLY* 3.1 25.7 + - - -
688B THR 4.1 5.9 - - - +
689B ILE* 4.1 7.6 - - + -
690B GLN* 6.1 0.4 - - - +
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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