Contacts of the helix formed by residues 607 - 628 (chain B) in PDB entry 6WCZ
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 VAL 607 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B GLU* 2.5 43.2 + - + +
490B LEU* 3.7 33.7 - - + +
491B GLY* 3.9 8.7 - - - -
493B LEU* 6.0 1.6 - - + -
494B ASN* 3.3 18.4 - - - +
574B TYR* 3.5 30.5 - - + +
606B VAL* 1.3 68.8 - - + +
608B THR* 1.3 63.9 + - + +
609B TYR 3.2 2.9 - - - -
610B ALA* 3.1 24.8 + - + +
611B LEU* 3.6 4.0 + - - +
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Residues in contact with THR 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B TYR* 4.2 5.6 - - + +
601B ARG* 2.6 56.1 + - + +
602B GLY 4.7 5.4 - - - +
603B SER* 4.7 7.3 + - - -
605B GLN* 2.6 53.9 + - + +
606B VAL 4.3 0.3 - - - -
607B VAL* 1.3 74.2 - - - +
609B TYR* 1.3 64.2 + - - +
610B ALA 3.2 0.2 - - - -
611B LEU* 3.8 2.7 - - - +
612B ASN* 3.0 16.7 + - - -
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Residues in contact with TYR 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ASN* 4.6 7.0 - - - +
499B MET* 4.4 1.4 - - - +
509B GLU* 3.9 26.7 - - + -
606B VAL 3.9 10.6 + - - +
607B VAL 3.2 0.6 - - - -
608B THR* 1.3 82.6 + - - +
610B ALA* 1.3 61.4 + - - +
612B ASN* 2.8 23.5 - - - +
613B THR* 3.0 23.4 + - - -
663B SER* 3.2 27.6 - - - -
664B GLY* 4.2 15.5 - - - -
799B ILE* 3.5 39.9 - - + -
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Residues in contact with ALA 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 6.2 0.7 - - + -
493B LEU* 3.7 38.4 - - + -
494B ASN* 5.6 0.6 - - - +
499B MET* 3.8 11.8 - - + +
551B GLU* 4.8 6.5 - - - +
607B VAL* 3.1 17.9 + - + +
609B TYR* 1.3 79.4 - - - +
611B LEU* 1.3 50.3 + - - +
614B PHE* 2.5 42.9 + - - +
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Residues in contact with LEU 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ILE* 4.0 26.9 - - + -
547B ASP 4.5 8.1 - - - +
548B LEU* 5.0 9.2 - - + -
551B GLU* 3.3 44.4 + - + +
601B ARG* 3.3 43.7 - - + +
607B VAL 3.6 3.3 + - - +
608B THR* 3.3 4.9 + - - +
610B ALA* 1.3 80.0 - - - +
612B ASN* 1.3 58.3 + - - +
614B PHE* 3.6 2.1 - - - +
615B THR* 2.2 52.8 + - + +
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Residues in contact with ASN 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B TRP* 3.7 17.3 - - - +
601B ARG* 3.0 26.8 - - - +
608B THR* 3.0 21.2 + - - +
609B TYR* 2.8 22.1 - - - +
611B LEU* 1.3 76.2 - - - +
613B THR* 1.3 83.6 + - - +
615B THR* 2.8 19.4 + - - -
616B ASN* 2.8 18.2 + - - +
664B GLY* 3.1 33.7 - - - +
665B ASP* 4.0 1.2 - - - +
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Residues in contact with THR 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B MET* 3.6 21.8 - - + -
507B GLY* 5.0 2.2 - - - -
509B GLU* 4.8 8.0 + - - +
609B TYR* 3.0 18.2 + - - -
612B ASN* 1.3 80.9 + - - +
614B PHE* 1.3 63.7 + - - +
616B ASN* 2.9 18.0 - - - +
617B LEU* 3.1 21.8 + - + +
662B VAL* 3.6 30.5 - - + +
663B SER* 3.7 0.9 - - - -
664B GLY 2.8 29.6 + - - -
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Residues in contact with PHE 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B SER* 4.5 15.5 - - - -
382B LEU* 3.6 31.0 - - + +
383B TRP* 3.3 51.1 - + - -
499B MET* 3.3 21.5 - - + -
547B ASP 5.8 1.6 - - - -
550B ASN* 5.5 2.9 - - - -
551B GLU* 3.1 26.9 - - - -
610B ALA 2.5 25.3 + - - +
611B LEU 3.6 1.6 - - - +
613B THR* 1.3 77.7 - - - +
615B THR* 1.3 66.3 + - - +
617B LEU* 3.2 4.6 + - - +
618B VAL* 3.0 46.2 + - + +
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Residues in contact with THR 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B TRP* 4.4 13.7 - - + -
543B ILE* 5.1 6.5 - - + -
547B ASP* 4.9 21.8 + - + +
611B LEU* 2.2 47.2 + - + +
612B ASN* 2.8 11.6 + - - -
614B PHE* 1.3 79.7 - - - +
616B ASN* 1.3 58.9 + - - +
618B VAL* 3.2 9.7 - - + +
619B VAL* 3.0 24.7 + - + +
688B LYS* 5.3 7.0 - - - -
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Residues in contact with ASN 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B TRP* 3.5 20.4 - - + -
612B ASN 2.8 16.0 + - - +
613B THR* 2.9 18.2 - - - +
615B THR* 1.3 74.2 - - - +
617B LEU* 1.3 62.9 + - - +
618B VAL 3.1 0.9 - - - -
619B VAL* 3.6 10.8 - - + -
620B GLN* 2.9 39.9 + - + +
662B VAL* 3.2 11.5 - - - +
664B GLY 3.3 14.1 + - - -
665B ASP* 3.2 15.0 + - - +
666B ASP 3.0 26.9 + - - -
667B CYS* 4.9 0.4 - - - +
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Residues in contact with LEU 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 5.9 11.4 - - + -
499B MET* 5.0 10.1 - - + -
504B SER* 5.2 4.5 - - - +
506B GLY* 4.1 25.4 - - - +
507B GLY 5.0 0.7 - - - +
613B THR* 3.1 27.0 + - + +
614B PHE* 3.2 4.2 + - - +
616B ASN* 1.3 85.0 + - - +
618B VAL* 1.3 62.0 + - + +
620B GLN* 5.0 0.2 - - - -
621B LEU* 3.0 36.6 + - + +
657B LEU* 5.1 15.3 - - + -
660B MET* 3.7 33.2 - - + -
662B VAL* 4.0 18.4 - - + -
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Residues in contact with VAL 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B MET* 4.4 14.4 - - - -
378B VAL* 3.7 21.9 - - + +
379B SER* 4.5 12.8 - - - +
382B LEU* 5.0 7.0 - - + -
550B ASN* 5.7 0.4 - - - +
614B PHE* 3.0 44.7 + - + +
615B THR* 3.2 11.7 - - + +
617B LEU* 1.3 77.4 - - - +
619B VAL* 1.3 64.5 + - + +
620B GLN 3.2 0.2 + - - -
621B LEU* 3.3 5.6 + - - +
622B ILE* 3.0 43.9 + - + +
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Residues in contact with VAL 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B TRP* 4.8 9.0 - - + -
615B THR* 3.0 13.2 + - + +
616B ASN* 3.6 23.1 - - + +
618B VAL* 1.3 78.5 - - + +
620B GLN* 1.3 72.1 + - + +
622B ILE* 3.4 8.3 + - - +
623B ARG* 2.9 24.3 + - - +
682B PHE* 4.9 0.9 - - + -
683B LEU* 5.1 14.8 - - + +
686B MET* 3.7 37.7 - - + -
688B LYS* 5.2 16.2 - - + -
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Residues in contact with GLN 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASP* 5.1 6.3 + - - +
536B THR* 5.8 1.6 + - - -
616B ASN* 2.9 21.9 + - - +
617B LEU 4.6 0.4 - - - +
619B VAL* 1.3 90.9 - - + +
621B LEU* 1.3 60.8 + - - +
622B ILE 3.2 0.2 - - - -
623B ARG* 3.7 13.1 - - + +
624B ASN* 3.0 27.2 + - - +
660B MET* 4.5 17.4 - - - +
662B VAL* 4.7 1.1 - - - +
667B CYS* 2.7 46.9 - - - +
669B VAL* 3.3 23.3 - - + +
676B PHE* 4.8 11.9 - - + -
683B LEU* 6.3 1.3 - - + -
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B VAL* 5.7 10.1 - - + +
381B TRP* 4.8 15.9 - - + -
382B LEU* 4.9 9.4 - - + -
617B LEU* 3.0 26.0 + - + +
618B VAL* 3.8 5.4 - - - +
620B GLN* 1.3 77.8 - - - +
622B ILE* 1.3 57.6 + - + +
624B ASN* 3.3 3.6 + - + +
625B MET* 2.9 30.9 + - - +
648B TRP* 4.0 10.3 - - + -
649B LEU* 4.8 10.3 - - + -
653B GLY* 3.9 15.5 - - - +
656B ARG* 4.5 9.6 - - + -
657B LEU* 3.7 45.8 - - + +
660B MET* 4.7 7.6 - - + +
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Residues in contact with ILE 622 (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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374B VAL* 3.8 23.6 - - + -
375B MET* 3.6 28.7 - - + -
378B VAL* 3.8 16.4 - - + -
618B VAL* 3.0 31.3 + - + +
619B VAL* 3.4 10.3 - - - +
620B GLN 3.2 0.2 - - - -
621B LEU* 1.3 77.5 - - + +
623B ARG* 1.3 60.8 + - - +
625B MET* 3.2 18.5 - - + +
626B GLU* 3.0 21.1 + - - +
631B LEU* 5.1 4.0 - - + -
682B PHE* 3.8 23.5 - - + -
686B MET* 4.5 7.4 - - + -
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Residues in contact with ARG 623 (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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534B ASP* 3.5 28.5 + - - +
619B VAL 2.9 16.8 + - - +
620B GLN* 3.5 12.1 + - + +
621B LEU 3.3 0.2 - - - -
622B ILE* 1.3 79.3 - - - +
624B ASN* 1.3 56.8 + - - +
626B GLU* 3.3 3.1 + - - +
627B ALA* 2.9 24.9 + - - +
676B PHE* 2.4 65.6 + - + -
677B ALA* 3.8 7.1 - - - +
679B ALA* 3.1 25.4 + - + +
680B LEU* 3.4 25.4 - - - +
682B PHE* 3.6 14.1 - - + -
683B LEU* 3.7 19.4 - - + +
690B ARG* 5.0 1.0 - - - +
699B SER* 3.8 10.9 + - - -
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Residues in contact with ASN 624 (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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620B GLN 3.0 18.9 + - - +
621B LEU* 4.0 5.2 - - + +
623B ARG* 1.3 79.0 - - - +
625B MET* 1.3 56.7 + - - +
627B ALA* 3.0 13.9 + - - +
628B GLU* 2.9 32.3 + - - +
648B TRP* 4.3 4.9 - - + -
656B ARG* 3.5 34.3 + - + +
660B MET* 5.0 10.8 - - + +
671B PRO* 3.9 25.8 - - - +
676B PHE* 4.3 8.4 - - + -
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Residues in contact with MET 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 6.0 3.6 - - + -
621B LEU 2.9 16.2 + - - +
622B ILE* 3.2 23.8 - - + +
624B ASN* 1.3 73.3 - - - +
626B GLU* 1.3 65.8 + - - +
628B GLU* 3.7 1.6 + - - +
629B GLU 3.6 1.6 + - - -
630B VAL* 3.1 38.4 + - + +
631B LEU* 3.6 44.1 + - + +
645B VAL* 3.7 30.7 - - + -
648B TRP* 3.5 42.5 - - + -
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Residues in contact with GLU 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B ILE 3.0 10.0 + - - +
623B ARG 3.6 7.4 - - - +
625B MET* 1.3 81.6 - - - +
627B ALA* 1.3 54.5 + - - +
629B GLU* 2.7 31.4 + - - +
631B LEU* 2.9 49.0 - - + +
632B GLU* 3.7 9.5 + - - -
679B ALA* 3.7 13.1 - - + +
681B ARG* 4.8 13.3 + - - +
682B PHE* 3.5 37.9 - - + -
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Residues in contact with ALA 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B ARG 2.9 15.4 + - - +
624B ASN* 3.0 23.5 + - - +
626B GLU* 1.3 75.7 - - - +
628B GLU* 1.3 57.8 + - - +
629B GLU 3.3 1.1 - - - -
671B PRO* 5.5 2.0 - - + -
673B ASP* 3.8 8.7 - - + +
675B ARG* 3.3 30.4 - - - +
676B PHE* 3.8 32.5 - - + +
679B ALA* 4.3 6.9 - - + +
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Residues in contact with GLU 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B ASN* 2.9 17.4 + - - +
625B MET 3.7 0.8 + - - +
626B GLU 3.1 0.8 - - - -
627B ALA* 1.3 76.8 - - - +
629B GLU* 1.3 67.7 + - - +
630B VAL* 3.1 16.7 + - + +
648B TRP* 2.4 39.7 + - - +
656B ARG* 2.6 44.1 + - - +
672B ILE* 5.3 10.6 - - + +
673B ASP* 4.8 6.7 - - - +
675B ARG* 3.5 12.0 + - - +
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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) + - + + + + + -
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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