Contacts of the helix formed by residues 602 - 626 (chain B) in PDB entry 2XWU
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 GLN 602 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B LEU* 1.3 74.6 - - - +
603B VAL* 1.3 57.6 + - - +
604B GLU* 4.4 7.6 - - + +
605B GLU* 2.7 37.3 + - + +
606B ILE 3.0 9.5 + - - -
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Residues in contact with VAL 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B LEU 3.5 1.6 + - - -
602B GLN* 1.3 71.1 - - - +
604B GLU* 1.3 62.7 + - - +
606B ILE* 3.3 13.7 + - - +
607B LEU* 3.2 30.9 + - + +
653B ILE* 6.0 5.6 - - + -
674B PRO* 4.6 23.3 - - + -
676B PRO* 5.0 9.3 - - + +
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Residues in contact with GLU 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B GLN* 3.0 6.6 + - + +
603B VAL* 1.3 79.4 - - - +
605B GLU* 1.3 69.2 + - + +
607B LEU* 3.5 11.7 + - - +
608B LYS* 3.3 19.8 + - - +
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Residues in contact with GLU 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B LEU* 3.9 22.4 - - + -
602B GLN* 2.7 27.2 + - + +
604B GLU* 1.3 76.7 - - + +
606B ILE* 1.3 64.6 + - - +
608B LYS* 3.3 10.1 + - - +
609B ASN* 2.8 36.9 + - - +
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Residues in contact with ILE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B LEU* 3.2 37.6 - - + +
599B SER* 4.6 2.2 - - - +
601B LEU* 3.6 20.9 - - + +
602B GLN 3.0 7.2 + - - +
603B VAL* 3.3 13.9 + - - +
605B GLU* 1.3 76.8 - - - +
607B LEU* 1.3 54.4 + - - +
609B ASN* 3.7 5.4 - - - +
610B LEU* 2.7 58.3 + - + +
651B LEU* 4.4 10.1 - - + -
653B ILE* 3.7 33.9 - - + -
676B PRO* 3.7 11.7 - - + -
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Residues in contact with LEU 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B VAL* 3.2 19.2 + - + +
604B GLU* 3.5 11.7 - - - +
606B ILE* 1.3 78.4 - - - +
608B LYS* 1.3 64.3 + - - +
610B LEU* 3.9 6.0 - - + +
611B HIS* 3.2 48.0 + - + +
674B PRO* 5.7 8.7 - - + +
676B PRO* 3.6 34.5 - - + +
679B VAL* 4.8 12.6 - - + -
680B VAL* 5.4 2.2 - - + -
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Residues in contact with LYS 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B GLU 3.3 9.4 + - - +
605B GLU* 3.3 19.1 + - - +
607B LEU* 1.3 77.9 - - - +
609B ASN* 1.3 62.6 + - - +
611B HIS* 3.9 5.7 + - - +
612B SER* 3.0 25.6 + - - -
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Residues in contact with ASN 609 (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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566B ALA* 5.6 1.4 + - - +
567B ALA* 5.4 4.8 - - - +
570B VAL* 4.2 26.4 - - + +
598B LEU* 4.0 20.0 - - + +
601B LEU* 3.8 21.0 - - - +
605B GLU* 2.8 32.5 + - - +
606B ILE 3.9 2.2 - - - +
608B LYS* 1.3 78.4 - - - +
610B LEU* 1.3 65.1 + - - +
611B HIS 3.2 1.6 - - - -
612B SER* 3.1 9.8 + - - -
613B LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B LEU* 4.5 8.9 - - + +
606B ILE* 2.7 46.9 + - + +
607B LEU* 3.5 6.0 + - + +
609B ASN* 1.3 72.0 - - - +
611B HIS* 1.3 60.6 + - + +
613B LEU* 3.3 4.2 + - + +
614B ILE* 2.9 42.7 + - + +
647B LEU* 3.6 30.7 - - + -
648B PHE* 4.7 3.8 - - + -
651B LEU* 4.1 17.0 - - + -
676B PRO* 3.6 23.1 - - + -
677B VAL* 4.4 2.7 - - + +
680B VAL* 3.9 22.7 - - + -
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Residues in contact with HIS 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B LEU* 3.2 37.3 + - + +
608B LYS* 4.1 5.6 - - - +
609B ASN 3.2 0.6 - - - -
610B LEU* 1.3 78.0 - - + +
612B SER* 1.3 61.5 + - - +
614B ILE* 4.5 2.0 - - - +
615B SER* 2.8 42.3 + - - +
679B VAL* 6.0 0.9 - - + +
680B VAL* 5.3 12.2 - - + +
683B GLN* 3.5 35.4 + - - -
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Residues in contact with SER 612 (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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570B VAL* 5.3 0.2 - - - -
574B GLN* 3.0 34.2 + - - +
608B LYS 3.0 17.8 + - - -
609B ASN* 3.1 13.4 + - - -
611B HIS* 1.3 78.8 - - - +
613B LEU* 1.3 57.7 + - - +
615B SER* 5.1 1.1 - - - -
616B PRO* 3.2 23.0 - - - +
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Residues in contact with LEU 613 (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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570B VAL* 4.3 8.1 - - + -
574B GLN* 3.7 28.3 - - + +
577B LEU* 4.8 12.6 - - + -
591B MET* 4.5 10.5 - - + -
594B LEU* 3.4 36.1 - - + -
598B LEU* 4.3 20.4 - - + -
609B ASN 2.9 17.2 + - - +
610B LEU* 3.6 5.2 - - - +
612B SER* 1.3 79.0 - - - +
614B ILE* 1.3 64.9 + - + +
616B PRO* 3.4 15.3 - - - +
617B TYR* 3.6 17.8 - - - -
647B LEU* 4.4 18.8 - - + -
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Residues in contact with ILE 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B MET* 6.3 0.7 - - + -
610B LEU* 2.9 26.1 + - + +
611B HIS* 5.0 1.6 - - - +
613B LEU* 1.3 77.5 - - + +
615B SER* 1.3 65.3 + - - +
616B PRO 3.3 2.5 - - - -
617B TYR* 2.9 9.5 + - + +
618B ILE* 2.8 34.6 + - + +
644B LEU* 3.4 36.3 - - + -
647B LEU* 4.4 16.8 - - + -
648B PHE* 4.4 2.9 - - + -
680B VAL* 3.5 28.9 - - + -
684B VAL* 4.6 13.5 - - + -
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Residues in contact with SER 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B HIS* 2.8 29.9 + - - +
612B SER* 5.1 0.7 - - - -
614B ILE* 1.3 74.2 - - - +
616B PRO* 1.3 63.8 - - - +
617B TYR 3.1 4.9 + - - -
618B ILE* 3.4 7.3 + - - +
619B GLN* 3.3 20.4 + - - +
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Residues in contact with PRO 616 (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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574B GLN* 6.1 0.9 - - + -
578B MET* 4.2 23.3 - - + +
612B SER 3.2 23.8 - - - +
613B LEU* 3.4 12.8 - - - +
614B ILE 3.5 0.2 - - - -
615B SER* 1.3 96.4 - - - +
617B TYR* 1.3 62.4 + - + -
619B GLN* 4.3 7.1 - - + +
620B GLN* 3.5 28.1 + - - +
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Residues in contact with TYR 617 (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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577B LEU* 3.6 45.7 + - + +
578B MET* 4.7 5.0 + - + -
591B MET* 6.1 1.3 - - - -
613B LEU* 3.6 21.5 - - + -
614B ILE* 2.9 10.4 + - + +
616B PRO* 1.3 81.9 - - + +
618B ILE* 1.3 59.0 + - - +
619B GLN 2.9 2.2 - - - -
620B GLN* 3.0 36.7 + - - +
621B LEU* 2.7 36.4 + - - +
639B HIS* 5.2 7.0 + + - -
640B ILE* 4.1 26.1 - - + +
643B LEU* 3.8 31.9 - - + +
644B LEU* 6.5 0.4 - - + -
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Residues in contact with ILE 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B ILE* 2.8 26.6 + - + +
615B SER* 3.8 6.7 - - - +
617B TYR* 1.3 76.6 - - - +
619B GLN* 1.3 59.2 + - - +
621B LEU* 3.7 11.2 - - + +
622B GLU* 2.9 36.7 + - + +
684B VAL* 5.6 7.2 - - + -
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Residues in contact with GLN 619 (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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615B SER 3.3 12.9 + - - +
616B PRO* 4.4 7.6 - - + +
617B TYR 2.9 0.4 - - - -
618B ILE* 1.3 76.7 - - - +
620B GLN* 1.3 66.6 + - + +
622B GLU* 3.0 13.5 + - - +
623B LYS* 3.0 25.8 + - - +
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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
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578B MET* 4.7 17.2 - - - +
616B PRO 3.5 21.1 + - - +
617B TYR* 3.0 34.4 + - - +
619B GLN* 1.3 74.2 - - + +
621B LEU* 1.3 63.6 + - - +
623B LYS* 3.5 8.6 + - - +
624B LEU* 3.0 23.3 + - - +
640B ILE* 4.1 16.3 - - + +
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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
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617B TYR 2.7 18.6 + - - +
618B ILE* 3.7 11.0 - - - +
620B GLN* 1.3 72.6 - - - +
622B GLU* 1.3 52.0 + - - +
624B LEU* 2.9 10.0 + - + +
625B ALA* 2.6 35.1 + - + +
637B ILE* 4.7 13.2 - - + +
640B ILE* 4.3 28.4 - - + +
641B LEU* 4.5 18.8 - - + -
644B LEU* 6.3 3.4 - - + -
684B VAL* 5.6 7.6 - - + -
687B LEU* 3.7 31.0 - - + -
688B ILE* 5.0 1.8 - - - +
691B VAL* 4.3 24.5 - - + -
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Residues in contact with GLU 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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618B ILE* 2.9 23.8 + - + +
619B GLN* 3.0 14.3 + - - +
621B LEU* 1.3 74.0 - - + +
623B LYS* 1.3 68.7 + - - +
624B LEU 3.1 0.3 + - - -
625B ALA* 3.1 16.7 + - + +
626B GLU* 3.1 15.6 + - - +
687B LEU* 4.9 17.6 - - + +
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Residues in contact with LYS 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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619B GLN 3.0 16.1 + - - +
620B GLN* 3.9 9.6 - - - +
622B GLU* 1.3 76.9 - - - +
624B LEU* 1.3 54.1 + - - +
626B GLU* 3.6 4.7 + - - +
627B GLU* 2.5 44.7 + - - +
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Residues in contact with LEU 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 15.0 + - - +
621B LEU* 2.9 16.2 + - + +
623B LYS* 1.3 77.2 - - - +
625B ALA* 1.3 61.5 + - - +
627B GLU* 3.1 29.4 + - - +
633B ASN* 3.7 22.0 + - - +
636B ALA* 5.8 3.4 - - + -
637B ILE* 5.2 15.9 - - + +
640B ILE* 5.7 2.7 - - + -
695B TRP* 5.1 5.0 + - - -
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Residues in contact with ALA 625 (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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621B LEU* 2.6 19.9 + - + +
622B GLU* 3.1 9.4 + - + +
624B LEU* 1.3 73.8 - - - +
626B GLU* 1.3 62.1 + - - +
627B GLU 3.2 7.3 + - - +
687B LEU* 5.0 2.0 - - + +
690B LYS* 4.2 24.0 - - + +
691B VAL* 4.2 27.5 - - + +
694B LYS* 5.2 7.8 - - - +
695B TRP* 5.4 5.8 + - - +
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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
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622B GLU 3.1 14.3 + - - +
623B LYS* 3.9 4.9 - - - +
625B ALA* 1.3 75.3 - - - +
627B GLU* 1.3 62.7 + - - +
628B ILE 4.0 0.2 + - - -
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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