Contacts of the helix formed by residues 602 - 625 (chain A) in PDB entry 3A8P
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 SER 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A HIS* 3.5 19.5 + - - -
600A ALA* 3.4 3.6 - - - +
601A THR* 1.3 82.9 + - - +
603A GLN* 1.3 60.6 + - - +
604A THR* 3.4 8.7 + - - -
605A ASP* 3.0 23.8 + - - +
606A LEU* 2.9 27.5 + - - +
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Residues in contact with GLN 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A HIS* 3.4 20.5 + - + +
602A SER* 1.3 74.5 - - - +
604A THR* 1.3 64.5 + - - +
606A LEU* 3.2 22.6 + - - +
607A GLU* 2.7 59.6 + - - +
712B ALA* 3.4 38.6 - - + +
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Residues in contact with THR 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A SER* 3.2 7.9 + - - -
603A GLN* 1.3 80.1 - - - +
605A ASP* 1.3 61.7 + - - +
607A GLU* 3.2 11.5 + - + +
608A ASN* 2.9 39.7 + - - +
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Residues in contact with ASP 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A LYS* 3.2 24.8 + - - -
509A GLY* 6.0 0.9 - - - -
510A TRP 4.5 1.0 - - - +
511A LEU* 4.3 1.2 - - - +
600A ALA* 3.2 9.1 - - - +
601A THR* 3.0 40.0 + - - +
602A SER* 3.0 23.3 + - - +
604A THR* 1.3 76.4 - - - +
606A LEU* 1.3 63.0 + - - +
608A ASN* 3.2 9.2 + - - +
609A TRP* 3.0 40.0 + - - -
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Residues in contact with LEU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A SER* 4.1 22.9 - - - -
584A HIS* 3.5 22.9 - - - +
585A VAL 3.3 28.7 - - - +
586A PHE* 3.9 15.9 - - + -
600A ALA* 3.5 14.1 - - + +
602A SER 2.9 13.2 + - - +
603A GLN* 3.5 27.8 - - - +
605A ASP* 1.3 77.1 - - - +
607A GLU* 1.3 70.3 + - + +
609A TRP* 3.2 4.0 + - - +
610A VAL* 3.0 37.6 + - + +
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Residues in contact with GLU 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A GLN* 2.7 50.2 + - - +
604A THR* 3.6 11.6 - - + +
606A LEU* 1.3 81.5 - - + +
608A ASN* 1.3 60.1 + - - +
610A VAL* 3.5 5.0 + - - +
611A THR* 2.9 37.1 + - - +
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Residues in contact with ASN 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A LYS* 3.3 23.7 - - - +
604A THR* 2.9 37.0 + - - +
605A ASP* 3.5 8.8 + - - +
607A GLU* 1.3 79.7 - - - +
609A TRP* 1.3 56.9 + - - +
611A THR* 3.7 6.2 - - - -
612A ALA* 2.9 30.3 + - - +
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Residues in contact with TRP 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A LYS* 3.4 26.7 - - + +
508A ALA* 4.0 10.1 - - - -
509A GLY* 3.7 24.0 - - - -
510A TRP 4.8 0.8 + - - -
511A LEU* 3.3 40.3 - - + +
538A VAL* 3.7 30.1 - - + -
540A LEU* 4.4 10.5 - - + -
545A LEU* 3.9 22.9 - - + -
586A PHE* 3.8 22.4 - + + -
605A ASP* 3.0 41.6 + - - -
606A LEU 3.2 6.7 + - - +
608A ASN* 1.3 74.8 - - - +
610A VAL* 1.3 61.3 + - - +
612A ALA* 3.3 2.0 + - + +
613A ILE* 2.9 53.3 + - + +
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Residues in contact with VAL 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A VAL* 3.7 31.4 - - + +
574A GLN* 5.5 0.2 - - - -
575A SER* 5.2 4.5 - - - +
586A PHE* 4.5 9.2 - - + -
606A LEU* 3.0 34.3 + - + +
607A GLU* 3.8 5.6 - - - +
609A TRP* 1.3 74.6 - - - +
611A THR* 1.3 66.6 + - - +
613A ILE* 3.5 1.1 + - - +
614A HIS* 3.0 49.4 + - + +
698A SER* 4.3 3.4 - - - +
704A LEU* 3.9 21.3 - - + -
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Residues in contact with THR 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A GLU* 2.9 23.1 + - - +
608A ASN* 3.7 6.5 - - - -
610A VAL* 1.3 79.0 - - - +
612A ALA* 1.3 56.0 + - - +
614A HIS* 3.5 1.0 + - - +
615A SER* 2.8 42.4 + - - +
698A SER* 3.6 36.1 + - - +
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Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ARG* 3.2 23.3 - - + +
507A LYS* 3.9 22.2 - - + -
540A LEU* 3.7 17.9 - - + -
608A ASN 2.9 19.1 + - - +
609A TRP* 3.3 4.7 + - + +
611A THR* 1.3 77.8 - - - +
613A ILE* 1.3 62.5 + - + +
615A SER* 3.3 2.8 + - - -
616A ALA* 3.0 19.6 + - - +
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Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 4.0 20.2 - - + -
545A LEU* 4.3 16.2 - - + -
568A ALA* 4.6 7.0 - - + -
571A SER* 4.9 1.1 - - - -
573A VAL* 3.5 28.5 - - + -
586A PHE* 4.4 17.5 - - + -
588A LEU* 4.0 26.7 - - + -
598A PHE* 5.8 0.2 - - + -
609A TRP* 2.9 39.2 + - + +
610A VAL 4.1 0.2 - - - +
612A ALA* 1.3 71.4 - - - +
614A HIS* 1.3 63.4 + - + +
616A ALA* 3.3 4.0 + - - +
617A CYS* 3.0 41.3 + - - -
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Residues in contact with HIS 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A SER 4.4 4.0 - - - -
572A ILE* 3.8 3.6 - - - -
573A VAL* 2.9 54.2 + - + +
610A VAL* 3.0 27.6 + - + +
613A ILE* 1.3 77.8 - - + +
615A SER* 1.3 56.8 - - - +
617A CYS* 3.4 3.5 + - - +
618A ALA* 2.9 30.7 + - - +
694A CYS* 3.6 26.0 + - + +
695A TYR* 3.9 31.0 - + + -
698A SER* 3.2 32.2 + - - +
704A LEU* 3.9 6.0 - - + +
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ARG* 3.7 20.7 + - - -
611A THR* 2.8 35.5 + - - +
612A ALA* 3.7 4.0 - - - -
614A HIS* 1.3 74.4 - - - +
616A ALA* 1.3 64.7 + - - +
618A ALA* 3.4 2.5 + - - +
619A SER* 3.0 23.7 + - - -
698A SER* 4.1 5.2 + - - -
699A LEU* 3.6 30.9 - - - +
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Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ARG* 3.6 22.1 - - - +
540A LEU* 4.3 6.3 - - + -
542A GLY 3.3 27.8 - - - +
543A CYS* 3.4 13.1 - - - -
612A ALA 3.0 16.5 + - - +
613A ILE 3.7 4.7 - - - +
615A SER* 1.3 74.9 - - - +
617A CYS* 1.3 58.3 + - - +
619A SER* 3.1 5.8 + - - -
620A LEU* 2.9 25.5 + - - +
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Residues in contact with CYS 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A CYS* 3.5 14.1 - - - -
568A ALA* 3.2 28.9 - - - -
570A ASP* 4.1 6.6 + - - +
571A SER* 3.9 12.6 - - - -
613A ILE* 3.0 35.9 + - - +
614A HIS* 3.6 2.9 - - - +
616A ALA* 1.3 74.2 - - - +
618A ALA* 1.3 60.6 + - - +
620A LEU* 3.3 2.2 + - - +
621A PHE* 2.9 30.7 + - - +
695A TYR* 3.4 26.5 - - + +
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Residues in contact with ALA 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A HIS 2.9 18.2 + - - +
615A SER 3.8 4.7 - - - +
617A CYS* 1.3 75.8 - - - +
619A SER* 1.3 57.9 + - - +
621A PHE* 3.4 4.4 + - - +
622A ALA* 2.9 30.8 + - - +
630A THR* 3.5 20.8 - - + +
634A LEU* 4.4 2.5 - - + -
695A TYR* 3.8 31.1 - - + -
699A LEU* 4.1 14.4 - - + -
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Residues in contact with SER 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ARG* 4.5 9.8 + - - -
615A SER 3.0 14.5 + - - -
616A ALA* 3.1 13.5 - - - -
618A ALA* 1.3 77.7 - - - +
620A LEU* 1.3 62.7 + - - +
622A ALA* 3.2 7.0 + - - +
623A LYS* 2.9 24.8 + - - +
630A THR* 4.6 5.4 - - - +
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A CYS* 3.9 20.9 - - + -
569A GLU* 3.5 50.5 - - + +
616A ALA 2.9 15.1 + - - +
617A CYS* 3.8 3.8 - - - +
619A SER* 1.3 75.6 + - - +
621A PHE* 1.3 58.0 + - - +
623A LYS* 3.0 35.9 + - - +
624A LYS* 2.8 40.0 + - + +
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Residues in contact with PHE 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A GLU* 5.9 0.2 - - - -
570A ASP* 3.9 19.7 - - - +
617A CYS 2.9 18.2 + - - +
618A ALA* 3.4 8.1 - - - +
620A LEU* 1.3 76.9 - - - +
622A ALA* 1.3 61.4 + - + +
624A LYS* 3.2 10.0 + - + +
625A HIS* 2.9 53.0 + + - -
633A LEU* 3.8 30.3 - - + -
634A LEU* 4.0 15.5 - - + -
637A GLN* 3.3 30.1 - - + -
691A ARG* 4.7 9.2 - - - -
692A MET* 3.9 31.0 - - + -
695A TYR* 4.7 3.4 - - + -
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Residues in contact with ALA 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A ALA 2.9 16.7 + - - +
619A SER* 3.6 3.8 - - - +
621A PHE* 1.3 76.8 - - - +
623A LYS* 1.3 61.6 + - - +
625A HIS* 3.2 2.8 + - - +
626A GLY 3.1 4.3 + - - -
627A LYS 3.0 39.2 + - - +
630A THR* 3.7 28.3 - - + +
633A LEU* 3.4 21.5 - - + -
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Residues in contact with LYS 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A SER* 2.9 15.7 + - - +
620A LEU* 3.3 33.1 - - - +
622A ALA* 1.3 76.8 - - - +
624A LYS* 1.3 64.3 + - - +
626A GLY* 3.1 13.0 + - - -
627A LYS 4.3 4.9 + - - +
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Residues in contact with LYS 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A GLU* 3.0 31.8 + - - +
570A ASP* 4.9 7.0 + - - +
620A LEU* 2.8 27.3 + - + +
621A PHE* 3.2 12.8 + - + +
623A LYS* 1.3 79.0 - - + +
625A HIS* 1.3 67.9 + - + +
626A GLY 3.1 1.5 + - - -
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Residues in contact with HIS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A PHE* 2.9 53.4 + + - -
622A ALA 3.2 2.2 + - - +
624A LYS* 1.3 83.6 - - + +
626A GLY* 1.3 64.5 + - - +
627A LYS* 3.3 20.4 - - + +
633A LEU* 3.8 36.6 - - + -
637A GLN* 4.1 10.5 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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