Contacts of the helix formed by residues 624 - 644 (chain B) in PDB entry 4D2Y
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 LEU 624 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A VAL* 4.3 4.0 - - + +
634A ASN* 3.7 44.6 - - + +
635A ILE* 3.8 10.8 - - + +
638A LEU* 3.9 22.4 - - + -
650A ASP* 4.5 1.6 - - + -
651A HIS* 3.6 24.7 - - + +
652A HIS* 3.8 5.8 - - + -
683A MET* 4.4 5.2 - - + -
621B THR 2.8 23.8 + - - +
622B SER* 4.0 1.8 - - - +
623B SER* 1.3 82.6 - - - +
625B TRP* 1.3 59.4 + - - +
626B LYS 3.2 2.0 - - - -
627B ASP* 3.1 23.8 + - + +
628B GLN* 2.9 29.0 + - - +
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Residues in contact with TRP 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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607B LEU* 4.1 12.3 - - + -
608B GLU* 4.0 17.9 - - + -
611B ALA* 3.4 29.6 - - + -
616B LEU* 3.4 32.4 - - + +
617B ASP 3.3 15.7 - - - +
618B MET* 3.6 43.1 + - + -
620B LYS 3.7 10.3 + - - -
621B THR* 4.2 18.6 - - + +
623B SER* 3.2 25.6 - - - +
624B LEU* 1.3 77.6 - - - +
626B LYS* 1.3 108.6 + - + +
628B GLN* 3.3 5.1 + - - -
629B ALA* 2.8 28.9 + - - +
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Residues in contact with LYS 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A HIS* 4.3 15.4 + - + +
687A ILE* 3.7 30.2 + - + +
601B ASN* 5.1 13.3 + - - +
607B LEU* 3.7 25.4 - - + +
608B GLU* 5.9 1.3 - - - -
621B THR* 6.0 7.4 - - + +
624B LEU* 3.2 0.8 - - - +
625B TRP* 1.3 127.2 - - + +
627B ASP* 1.3 61.5 + - - +
629B ALA* 4.7 2.0 - - - -
630B LEU* 2.8 31.2 + - - +
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Residues in contact with ASP 627 (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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631A VAL* 3.9 11.4 - - + -
651A HIS* 2.8 23.1 + - - -
652A HIS* 2.7 24.5 + - - -
683A MET* 3.2 18.1 - - + +
684A SER* 2.7 31.1 + - - +
687A ILE* 4.2 2.2 - - - -
624B LEU* 3.1 24.6 + - - +
626B LYS* 1.3 78.0 + - - +
628B GLN* 1.3 60.8 + - - +
630B LEU* 3.4 3.9 + - - +
631B VAL* 3.1 29.5 + - - +
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Residues in contact with GLN 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A VAL* 3.5 21.5 - - + -
632A GLU* 3.0 25.4 + - - +
635A ILE* 3.5 20.4 - - - +
614B MET* 4.5 6.8 - - + +
616B LEU* 3.8 29.0 - - + +
623B SER 3.9 8.5 - - - +
624B LEU 2.9 9.7 + - - +
625B TRP* 3.6 10.2 - - - +
627B ASP* 1.3 74.8 - - - +
629B ALA* 1.3 66.3 + - - +
631B VAL* 3.4 6.3 + - - +
632B GLU* 3.2 26.6 + - + +
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Residues in contact with ALA 629 (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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607B LEU* 3.8 33.2 - - + +
610B VAL* 3.9 14.0 - - + +
611B ALA* 4.0 11.4 - - + +
614B MET* 3.8 11.9 - - - -
616B LEU* 4.1 1.0 - - - +
625B TRP 2.8 19.9 + - - +
626B LYS* 4.7 0.4 - - - -
628B GLN* 1.3 73.3 - - - +
630B LEU* 1.3 64.1 + - - +
632B GLU* 3.4 3.1 + - - +
633B ILE* 3.1 26.5 + - - +
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Residues in contact with LEU 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A SER* 4.4 10.1 - - - +
687A ILE* 3.9 28.9 - - + -
594B GLY 3.8 2.7 - - - +
595B VAL* 3.9 15.5 - - + -
599B CYS* 3.6 28.3 - - + -
607B LEU* 3.7 7.6 - - + +
626B LYS 2.8 19.5 + - - +
627B ASP 3.6 5.2 - - - +
628B GLN 3.2 0.4 - - - -
629B ALA* 1.3 78.4 - - - +
631B VAL* 1.3 62.2 + - + +
633B ILE* 3.4 3.1 + - - +
634B ASN* 2.9 50.2 + - - +
682B PRO 5.1 0.4 - - - +
683B MET* 4.0 29.4 - - + -
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Residues in contact with VAL 631 (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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624A LEU* 4.3 3.7 - - + +
627A ASP* 4.2 12.8 - - + +
628A GLN* 4.0 35.4 - - + +
631A VAL* 3.6 24.5 - - + -
627B ASP 3.1 17.7 + - - +
628B GLN* 3.8 5.4 - - - +
630B LEU* 1.3 76.4 - - + +
632B GLU* 1.3 66.0 + - - +
634B ASN* 3.1 4.0 + - - +
635B ILE* 2.9 31.8 + - + +
683B MET* 3.8 23.3 - - + -
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Residues in contact with GLU 632 (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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628A GLN* 2.9 33.4 + - - +
548B HIS* 2.7 50.1 + - + +
551B PHE* 3.7 19.5 - - + -
554B PHE* 4.7 1.8 - - + -
610B VAL* 5.4 2.0 - - + -
614B MET* 3.6 27.0 - - + +
628B GLN 3.2 15.9 + - - +
629B ALA 3.9 4.0 - - - +
631B VAL* 1.3 78.0 - - - +
633B ILE* 1.3 57.9 + - + +
635B ILE* 3.4 11.2 + - - +
636B ALA* 2.9 22.7 + - - +
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Residues in contact with ILE 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PHE* 3.9 25.6 - - + -
594B GLY* 3.6 21.3 - - - +
598B TYR* 4.0 22.4 - - + -
599B CYS* 3.6 23.6 - - - -
606B ILE* 3.9 11.7 - - + -
607B LEU* 4.1 9.4 - - + -
610B VAL* 3.7 26.9 - - + -
629B ALA 3.1 17.0 + - - +
630B LEU 3.6 6.1 - - - +
632B GLU* 1.3 76.2 - - - +
634B ASN* 1.3 58.7 + - - +
636B ALA* 3.1 4.0 + - - +
637B VAL* 2.9 26.8 + - + +
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Residues in contact with ASN 634 (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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624A LEU* 3.7 18.8 - - + -
590B GLY* 3.7 3.9 - - - +
591B THR* 3.5 15.5 + - + +
594B GLY* 3.3 28.9 + - - -
595B VAL* 3.2 32.2 - - - +
630B LEU* 2.9 28.1 + - - +
631B VAL 3.1 3.1 + - - +
633B ILE* 1.3 76.8 - - - +
635B ILE* 1.3 64.8 + - - +
637B VAL* 3.5 5.0 + - - +
638B LEU* 3.2 30.5 + - + +
683B MET* 3.7 11.5 - - - -
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Residues in contact with ILE 635 (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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622A SER 5.1 3.0 - - - +
623A SER* 3.7 22.0 - - - +
624A LEU* 4.0 13.9 - - + -
628A GLN* 3.7 30.3 - - - +
548B HIS* 3.8 13.2 - - + +
549B PRO* 3.9 20.6 - - + -
631B VAL* 2.9 22.8 + - + +
632B GLU* 3.5 26.2 - - - +
634B ASN* 1.3 76.3 - - - +
636B ALA* 1.3 58.0 + - - +
638B LEU* 3.4 3.5 + - - +
639B TYR* 2.9 29.4 + - + +
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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
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546B ILE* 3.9 2.5 - - + -
547B ARG 3.2 19.5 - - - +
548B HIS* 4.0 13.0 - - + +
554B PHE* 3.8 27.1 - - + -
632B GLU 2.9 14.4 + - - +
633B ILE 3.1 9.8 + - - +
635B ILE* 1.3 77.7 - - - +
637B VAL* 1.3 57.0 + - - +
639B TYR* 3.4 2.7 + - - +
640B SER* 2.8 35.7 + - - -
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Residues in contact with VAL 637 (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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546B ILE* 4.3 15.0 - - + -
590B GLY* 4.0 9.4 - - - +
593B ILE* 4.0 32.8 - - + -
594B GLY* 3.9 20.9 - - - -
598B TYR* 3.9 23.3 - - + -
633B ILE* 2.9 20.5 + - + +
634B ASN* 3.9 6.7 - - - +
636B ALA* 1.3 74.6 - - - +
638B LEU* 1.3 64.7 + - - +
640B SER* 3.9 0.3 - - - -
641B PHE* 3.1 30.7 + - + -
648B ILE* 4.0 11.9 - - + -
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Residues in contact with LEU 638 (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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622A SER* 3.7 17.0 - - - +
624A LEU* 3.7 24.7 - - + -
590B GLY* 4.0 13.7 - - - -
634B ASN* 3.2 18.9 + - + +
635B ILE* 3.9 2.9 - - - +
637B VAL* 1.3 76.2 - - - +
639B TYR* 1.3 63.8 + - - +
641B PHE* 4.0 0.9 - - - +
642B GLN* 3.1 40.8 + - - +
648B ILE* 3.9 31.8 - - + +
649B VAL 4.2 0.2 - - - +
650B ASP* 3.6 42.4 - - + +
651B HIS* 5.4 2.5 - - - +
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Residues in contact with TYR 639 (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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622A SER 5.6 0.4 + - - -
547B ARG* 3.7 33.0 - - + -
548B HIS 4.1 0.9 - - - -
549B PRO* 3.6 51.7 + - + +
635B ILE* 2.9 18.9 + - + +
636B ALA 3.6 2.7 - - - +
638B LEU* 1.3 77.2 - - - +
640B SER* 1.3 60.6 + - - +
642B GLN* 4.1 9.8 + - + +
643B SER* 2.8 50.7 + - - -
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Residues in contact with SER 640 (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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544B VAL* 3.6 9.6 - - - +
545B PRO 3.4 20.4 - - - -
546B ILE* 3.4 7.8 - - - -
547B ARG* 2.8 41.9 + - - -
636B ALA 2.8 22.1 + - - -
637B VAL 3.9 3.1 - - - -
638B LEU 3.2 0.2 - - - -
639B TYR* 1.3 77.6 - - - +
641B PHE* 1.3 63.9 + - - +
643B SER* 3.8 1.4 - - - -
644B ASP* 3.1 27.5 + - - +
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Residues in contact with PHE 641 (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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544B VAL* 3.9 30.3 - - + -
546B ILE* 4.3 13.0 - - + -
561B TRP* 4.6 3.8 - - + -
562B TYR 3.7 15.3 - - - -
563B GLY* 3.9 23.3 - - - -
588B TYR* 4.6 4.3 - + - -
593B ILE* 3.6 29.6 - - + -
637B VAL* 3.1 20.9 + - + +
640B SER* 1.3 74.5 - - - +
642B GLN* 1.3 59.5 + - - +
644B ASP* 3.2 2.5 + - - -
645B LYS 2.9 9.9 + - - -
646B VAL* 2.9 57.5 + - + +
647B THR 4.0 3.1 - - - -
648B ILE* 3.6 32.5 - - + -
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Residues in contact with GLN 642 (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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620A LYS* 4.1 14.2 + - - -
622A SER* 3.2 32.7 + - - +
638B LEU* 3.1 30.9 + - - +
639B TYR* 4.1 8.2 - - + +
641B PHE* 1.3 74.7 - - - +
643B SER* 1.3 59.1 + - - +
645B LYS* 3.0 22.8 + - - +
646B VAL 4.7 3.1 - - - -
648B ILE* 4.2 17.9 + - + +
650B ASP* 5.9 1.0 - - - +
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Residues in contact with SER 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ARG* 3.6 21.3 + - - -
639B TYR* 2.8 48.6 + - - -
640B SER 3.8 0.4 - - - -
642B GLN* 1.3 76.5 - - - +
644B ASP* 1.3 60.2 + - - +
645B LYS* 3.1 18.4 + - - +
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Residues in contact with ASP 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LYS 5.6 0.9 - - - +
543B GLU 4.8 1.9 - - - +
544B VAL* 3.6 7.9 - - + +
545B PRO* 3.4 18.5 - - - +
547B ARG* 2.7 43.3 + - - -
640B SER 3.1 13.1 + - - +
641B PHE 3.2 2.4 + - - +
643B SER* 1.3 75.6 - - - +
645B LYS* 1.3 71.0 + - - +
646B VAL* 3.3 17.7 + - + +
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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