Contacts of the helix formed by residues 633 - 658 (chain B) in PDB entry 3VF1
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 633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LYS* 3.4 30.0 + - - +
119B ALA* 3.0 24.3 + - - +
494B ILE* 5.7 1.6 - - + -
495B TYR* 2.7 34.5 + - + +
631B PHE* 3.7 1.5 - - - +
632B GLY* 1.3 78.7 + - - +
634B ALA* 1.3 65.8 + - - +
635B ALA* 4.3 9.2 - - + +
636B ALA* 3.0 18.9 + - + +
637B HIS* 3.3 12.0 + - - -
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A ALA 4.5 1.9 - - - +
644A LYS* 4.2 7.6 - - + +
645A SER* 3.6 21.8 - - - +
648A ALA* 3.8 28.5 - - + -
632B GLY 3.3 4.9 + - - +
633B ASP* 1.3 71.0 - - - +
635B ALA* 1.3 61.2 + - - +
637B HIS* 3.4 16.7 + - - +
638B ALA 3.1 17.0 + - - -
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Residues in contact with ALA 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A SER* 3.4 16.9 + - - +
649A ASN* 6.0 2.5 - - - +
494B ILE* 3.4 36.4 - - + +
633B ASP* 3.1 5.1 - - + +
634B ALA* 1.3 76.9 - - - +
636B ALA* 1.3 64.1 + - - +
638B ALA* 3.3 5.2 + - - +
639B ALA* 3.2 16.5 + - - +
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Residues in contact with ALA 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ILE* 4.1 9.5 - - + +
494B ILE* 3.8 10.8 - - + +
495B TYR* 3.9 10.1 - - + +
631B PHE* 3.5 41.7 - - + -
633B ASP* 3.0 12.0 + - - +
635B ALA* 1.3 77.5 - - - +
637B HIS* 1.3 59.2 + - - +
639B ALA* 3.1 4.3 + - - +
640B MET* 2.9 33.2 + - - +
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Residues in contact with HIS 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A ALA* 4.1 8.5 - - + +
629B ASN* 3.0 23.3 + - - -
631B PHE* 2.9 28.8 + - + -
632B GLY* 3.7 18.4 - - - -
633B ASP 3.3 6.7 + - - -
634B ALA* 3.5 14.9 - - - +
635B ALA 3.3 0.6 - - - -
636B ALA* 1.3 77.9 - - - +
638B ALA* 1.3 57.9 + - - +
640B MET* 3.4 13.5 + - + +
641B ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ALA 5.2 2.3 - - - +
641A ALA* 4.0 24.6 - - - +
642A LYS* 4.1 11.7 - - + +
645A SER* 4.0 11.2 - - - +
634B ALA 3.1 12.9 + - - +
635B ALA 3.5 10.3 - - - +
636B ALA 3.2 0.2 - - - -
637B HIS* 1.3 77.5 - - - +
639B ALA* 1.3 61.0 + - - +
641B ALA* 3.4 2.1 + - - +
642B LYS* 3.0 24.8 + - - +
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Residues in contact with ALA 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B PHE* 3.7 8.0 - - + -
490B ASP* 4.0 27.3 - - + +
491B ILE* 3.6 22.7 - - + -
494B ILE* 4.5 4.5 - - + -
635B ALA 3.2 8.9 + - - +
636B ALA 3.1 9.1 + - - +
638B ALA* 1.3 79.0 - - - +
640B MET* 1.3 57.3 + - - +
642B LYS* 3.3 9.1 + - - +
643B PHE* 3.0 26.5 + - - +
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Residues in contact with MET 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B PHE* 3.6 28.3 - - + -
491B ILE* 5.1 0.9 - - + -
626B TYR* 3.9 34.3 - - + +
629B ASN* 3.6 40.8 - - + +
631B PHE* 4.1 15.9 - - - -
636B ALA 2.9 23.1 + - - +
637B HIS* 3.7 10.1 - - + +
639B ALA* 1.3 78.2 - - - +
641B ALA* 1.3 57.6 + - - +
643B PHE* 3.1 6.0 - - - +
644B LYS* 3.0 34.8 + - + +
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Residues in contact with ALA 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA 4.6 1.9 - - - +
637A HIS* 4.1 5.6 - - + +
638A ALA* 3.8 18.0 - - - +
641A ALA* 3.6 24.9 - - + -
637B HIS 2.9 18.3 + - - +
638B ALA 3.7 2.0 - - - +
639B ALA 3.3 0.2 - - - -
640B MET* 1.3 73.2 - - - +
642B LYS* 1.3 66.7 + - - +
644B LYS* 3.3 12.8 + - - +
645B SER* 3.0 22.2 + - - -
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Residues in contact with LYS 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ALA* 4.2 12.7 - - + +
486B GLN* 3.4 27.3 - - - +
490B ASP* 2.9 30.6 + - - +
638B ALA 3.0 17.1 + - - +
639B ALA* 3.6 5.8 - - - +
641B ALA* 1.3 72.7 - - - +
643B PHE* 1.3 61.3 + - - +
645B SER* 3.2 4.4 + - - -
646B ASN* 2.9 48.7 + - - +
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Residues in contact with PHE 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B VAL* 3.4 36.6 - - + -
484B ILE* 3.8 21.8 - - + -
487B PHE* 3.4 39.7 - + + -
549B VAL* 5.6 2.2 - - + -
623B LEU* 4.4 9.9 - - + -
624B GLY* 4.0 20.0 - - - -
626B TYR* 3.8 27.1 - + - -
639B ALA 3.0 13.5 + - - +
640B MET 3.1 10.1 - - - +
642B LYS* 1.3 77.7 - - - +
644B LYS* 1.3 61.8 + - - +
646B ASN* 3.1 9.6 + - - +
647B LEU* 3.0 43.6 + - + +
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA* 4.3 10.5 - - + +
637A HIS* 6.2 0.4 + - - -
624B GLY* 3.5 36.0 + - - +
625B ASP* 4.9 11.0 + - - +
626B TYR 5.6 0.8 - - - +
640B MET* 3.0 22.3 + - + +
641B ALA* 3.7 11.7 - - - +
643B PHE* 1.3 76.1 - - - +
645B SER* 1.3 56.3 + - - +
647B LEU* 3.4 10.8 + - - +
648B ALA* 3.0 27.2 + - - +
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Residues in contact with SER 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA* 3.9 22.4 - - - -
635A ALA* 3.5 22.5 + - - +
638A ALA* 4.0 10.1 - - - +
641B ALA 3.0 13.7 + - - -
642B LYS* 3.5 9.2 - - - -
643B PHE 3.1 0.2 - - - -
644B LYS* 1.3 74.0 - - - +
646B ASN* 1.3 67.0 + - - +
648B ALA* 3.4 2.9 + - - +
649B ASN* 3.2 32.4 + - - +
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Residues in contact with ASN 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B VAL* 3.7 30.7 + - + +
486B GLN* 4.8 9.9 - - - +
642B LYS* 2.9 42.9 + - - +
643B PHE* 3.1 9.3 + - - +
645B SER* 1.3 75.4 + - - +
647B LEU* 1.3 64.5 + - - +
649B ASN* 3.3 15.2 + - - +
650B ILE* 3.2 26.2 + - - +
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Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 4.0 15.0 - - + -
483B VAL* 3.7 23.8 - - + -
484B ILE* 5.7 0.2 - - + -
623B LEU* 3.4 57.0 - - + +
624B GLY* 3.9 9.9 - - - -
643B PHE* 3.0 28.3 + - + +
644B LYS* 3.7 10.8 - - - +
646B ASN* 1.3 75.1 - - - +
648B ALA* 1.3 59.2 + - - +
649B ASN 3.1 0.2 - - - -
650B ILE* 3.0 8.5 + - + +
651B THR* 2.9 32.8 + - - -
670B PRO* 3.6 12.9 - - + +
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Residues in contact with ALA 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA* 4.0 20.0 - - + -
644B LYS 3.0 18.3 + - - +
645B SER 3.6 7.0 - - - +
646B ASN 3.3 0.4 - - - -
647B LEU* 1.3 76.0 - - - +
649B ASN* 1.3 64.5 + - - +
651B THR* 3.5 9.7 - - - +
652B LYS* 3.2 20.8 + - - +
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Residues in contact with ASN 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B SER* 3.2 24.7 + - - +
646B ASN* 3.6 16.5 + - - +
647B LEU 3.1 0.6 - - - -
648B ALA* 1.3 79.6 - - - +
650B ILE* 1.3 63.2 + - + +
652B LYS* 3.3 12.3 + - - +
653B GLN* 3.1 32.6 + - - +
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Residues in contact with ILE 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ASP 5.3 0.7 - - - +
479B LEU* 3.6 45.5 - - + +
480B LEU* 3.9 18.2 - - + +
483B VAL* 3.5 33.7 - - + -
646B ASN 3.2 11.0 + - - +
647B LEU* 3.0 10.6 + - + +
649B ASN* 1.3 75.0 - - + +
651B THR* 1.3 66.8 + - - +
653B GLN* 3.1 13.4 + - - +
654B ILE* 3.0 41.9 + - + +
670B PRO* 4.2 9.4 - - + -
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Residues in contact with THR 651 (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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647B LEU 2.9 13.3 + - - -
648B ALA* 3.5 13.0 - - - +
650B ILE* 1.3 77.1 - - - +
652B LYS* 1.3 58.4 + - - +
654B ILE* 3.5 4.2 + - - +
655B THR* 3.0 42.4 + - - +
669B ILE* 4.3 16.3 - - + +
670B PRO* 3.2 30.0 - - - +
671B GLY 4.6 1.7 + - - -
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Residues in contact with LYS 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 6.4 0.2 - - - +
648B ALA 3.2 11.0 + - - +
649B ASN* 3.5 14.8 - - - +
650B ILE 3.1 0.6 - - - -
651B THR* 1.3 79.5 - - - +
653B GLN* 1.3 65.7 + - + +
655B THR* 3.5 6.1 + - - -
656B GLU* 3.1 56.0 + - + +
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Residues in contact with GLN 653 (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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479B LEU* 3.6 36.6 - - + +
649B ASN* 3.1 23.2 + - - +
650B ILE* 3.1 14.7 + - - +
652B LYS* 1.3 73.9 - - + +
654B ILE* 1.3 66.0 + - - +
656B GLU* 3.1 14.0 + - - +
657B ARG* 3.0 23.1 + - - +
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Residues in contact with ILE 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ASP* 3.4 33.2 - - + +
479B LEU* 5.3 2.0 - - + -
650B ILE* 3.0 35.1 + - + +
651B THR 3.8 3.6 - - - +
653B GLN* 1.3 78.1 - - + +
655B THR* 1.3 57.3 + - - +
657B ARG* 3.4 18.0 + - - +
658B ASN* 2.9 44.2 + - - +
665B TYR 4.0 2.2 - - - +
668B LEU 3.6 28.7 - - - +
669B ILE* 3.6 26.7 - - + -
670B PRO* 4.4 1.3 - - + -
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Residues in contact with THR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B THR* 3.0 28.9 + - - +
652B LYS* 3.7 7.4 - - - -
654B ILE* 1.3 79.3 - - - +
656B GLU* 1.3 65.4 + - + +
658B ASN* 3.3 8.0 + - - +
659B GLN* 3.2 31.7 + - - +
669B ILE* 5.2 8.0 - - - +
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Residues in contact with GLU 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B LYS* 3.1 53.5 + - + +
653B GLN* 3.1 11.3 + - - +
655B THR* 1.3 78.4 - - + +
657B ARG* 1.3 61.5 + - - +
659B GLN* 3.2 21.4 - - - +
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Residues in contact with ARG 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B TYR* 3.6 43.7 + - + +
475B ASP* 4.4 10.3 - - - +
476B ASP* 2.9 42.2 + - - -
653B GLN 3.0 15.2 + - - +
654B ILE* 3.7 12.5 - - - +
656B GLU* 1.3 72.9 - - - +
658B ASN* 1.3 81.2 + - - +
659B GLN 3.0 13.5 + - - +
661B MET* 3.4 21.2 - - + +
665B TYR* 3.1 22.4 + - - +
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Residues in contact with ASN 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B ILE* 2.9 26.4 + - - +
655B THR* 3.3 8.4 + - - +
657B ARG* 1.3 103.0 + - - +
659B GLN* 1.3 63.5 + - - +
660B GLY 3.2 3.3 + - - -
661B MET* 3.2 26.2 + - - +
664B PRO* 3.5 27.9 - - + +
665B TYR 2.9 27.8 + - - +
666B THR* 3.7 8.3 - - - +
669B ILE* 4.7 2.6 - - - +
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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