Contacts of the helix formed by residues 596 - 617 (chain A) in PDB entry 3GQL
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 596 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A GLN 4.3 0.4 - - - -
595A LEU* 1.3 79.1 - - - +
597A SER* 1.3 65.5 + - - +
598A LYS* 3.3 9.0 + - - +
599A ASP* 2.9 46.4 + - - +
600A LEU* 3.5 7.3 + - - +
763A ASN* 3.4 34.9 - - - +
764A GLN 4.4 0.4 - - - -
765A GLU 3.9 7.6 - - - -
766A TYR* 4.6 12.0 - - - -
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Residues in contact with SER 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A SER* 1.3 74.7 - - - +
598A LYS* 1.3 60.3 + - - +
600A LEU* 3.5 17.6 + - - +
601A VAL* 3.4 19.4 + - - +
694A PHE* 5.0 1.7 - - - -
726A THR* 5.6 5.5 - - - +
761A THR* 3.6 14.8 - - - +
762A SER 4.0 0.4 + - - -
765A GLU* 2.7 37.4 + - - -
767A LEU* 5.6 8.1 - - - +
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Residues in contact with LYS 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A SER* 3.0 6.8 + - - +
597A SER* 1.3 76.8 - - - +
599A ASP* 1.3 68.6 + - - +
600A LEU 3.1 2.2 - - - -
601A VAL* 3.0 3.6 + - - +
602A SER* 2.9 25.5 + - - -
758A VAL* 2.8 48.5 + - + +
759A ALA* 4.3 7.7 + - - +
761A THR* 3.4 25.2 + - + +
762A SER 3.4 14.9 + - - +
763A ASN* 3.2 30.9 + - + +
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Residues in contact with ASP 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A GLN 4.1 2.9 - - - +
595A LEU* 3.5 28.4 - - + +
596A SER* 2.9 41.4 + - - +
598A LYS* 1.3 77.8 - - - +
600A LEU* 1.3 58.5 + - - +
602A SER* 3.5 8.6 + - - -
603A CYS* 2.9 28.4 + - - +
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Residues in contact with LEU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A LEU* 4.1 10.1 - - + -
595A LEU* 3.8 35.7 - - + +
596A SER 3.8 11.0 - - - +
597A SER* 3.7 9.2 - - - +
598A LYS 3.1 0.8 - - - -
599A ASP* 1.3 76.5 - - - +
601A VAL* 1.3 61.1 + - - +
603A CYS* 3.0 8.4 - - + +
604A ALA* 3.0 22.5 + - - +
693A ILE* 3.6 32.2 - - + +
694A PHE* 3.6 26.5 - - + -
696A LEU* 3.8 20.2 - - + -
767A LEU* 4.5 17.0 - - + -
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Residues in contact with VAL 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A SER* 3.4 17.7 - - - +
598A LYS* 3.0 5.7 + - - +
600A LEU* 1.3 72.3 - - - +
602A SER* 1.3 61.8 + - - +
603A CYS 3.0 1.6 - - - -
604A ALA* 3.0 6.6 + - - +
605A TYR* 2.9 24.8 + - - +
694A PHE* 4.1 9.4 - - + -
729A LEU* 4.0 24.7 - - + -
754A LEU* 4.3 14.5 - - + +
757A ILE* 3.6 24.0 - - + -
758A VAL* 3.4 22.2 - - + +
761A THR* 4.1 16.8 - - + +
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Residues in contact with SER 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A LYS* 2.9 15.2 + - - -
599A ASP* 3.5 12.0 + - - -
601A VAL* 1.3 77.8 - - - +
603A CYS* 1.3 63.0 + - - +
605A TYR* 3.0 21.5 - - - +
606A GLN* 3.0 24.6 + - - +
758A VAL* 3.6 27.7 - - - +
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Residues in contact with CYS 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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569A LEU* 3.6 20.2 - - - -
572A TYR* 5.9 2.5 - - - -
573A LEU* 5.5 4.0 - - - -
599A ASP 2.9 19.0 + - - +
600A LEU* 3.0 13.0 - - + +
602A SER* 1.3 83.3 + - - +
604A ALA* 1.3 58.1 + - - +
605A TYR 3.3 0.3 + - - -
606A GLN* 3.6 2.8 + - - +
607A VAL* 3.5 19.2 + - - +
637A MET* 3.5 43.1 - - + +
693A ILE* 4.1 14.6 - - - -
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Residues in contact with ALA 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A LEU 3.0 12.5 + - - +
601A VAL* 3.0 11.4 + - - +
603A CYS* 1.3 74.5 - - - +
605A TYR* 1.3 64.2 + - - +
607A VAL* 3.7 4.4 + - - -
608A ALA* 3.2 16.8 + - - +
686A PHE* 3.6 6.5 - - + -
690A LEU* 3.6 30.7 - - + -
693A ILE* 4.0 15.0 - - + -
694A PHE* 5.2 2.0 - - + -
754A LEU* 3.5 19.5 - - + +
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Residues in contact with TYR 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A VAL 2.9 12.1 + - - +
602A SER* 3.0 20.9 - - - +
604A ALA* 1.3 76.3 - - - +
606A GLN* 1.3 66.6 + - + +
608A ALA* 3.1 6.4 + - - +
609A ARG* 3.0 64.5 + - + +
751A VAL* 3.4 40.4 - - + +
754A LEU* 4.0 11.2 - - + -
755A ASP* 3.8 38.4 + - + -
758A VAL* 4.2 9.6 - - + -
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Residues in contact with GLN 606 (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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542A LYS* 5.5 0.9 + - - -
543A ASN* 3.3 29.2 + - - +
602A SER* 3.0 24.8 + - - +
603A CYS* 4.3 2.8 - - - +
605A TYR* 1.3 82.6 - - + +
607A VAL* 1.3 66.6 + - - +
609A ARG* 2.9 13.4 + - - +
610A GLY 2.9 11.4 + - - -
635A ASN 3.8 12.9 + - - -
636A VAL* 3.3 18.0 - - - +
637A MET* 2.9 46.5 + - + +
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Residues in contact with VAL 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ASN* 5.4 0.2 - - - -
569A LEU* 4.7 3.1 - - + -
603A CYS 3.5 13.2 + - - +
604A ALA* 4.0 7.9 - - - +
605A TYR 3.3 0.8 - - - -
606A GLN* 1.3 78.3 - - - +
608A ALA* 1.3 62.4 + - - +
611A MET* 3.0 25.9 + - + +
624A LEU* 4.7 2.9 - - + -
629A VAL* 3.7 32.3 - - + -
637A MET* 4.0 9.6 - - + -
639A ILE* 3.4 18.9 - - + +
686A PHE* 3.7 23.1 - - + -
689A LEU* 4.0 27.4 - - + -
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Residues in contact with ALA 608 (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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604A ALA 3.2 13.8 + - - +
605A TYR 3.1 8.7 + - - +
606A GLN 3.1 0.8 - - - -
607A VAL* 1.3 76.4 - - - +
609A ARG* 1.3 64.0 + - - +
611A MET* 3.3 6.1 + - - +
612A GLU* 2.9 18.5 + - - +
686A PHE* 3.8 20.2 - - + -
747A PHE* 4.3 5.8 - - + +
750A LEU* 4.6 4.9 - - + -
751A VAL* 3.4 26.7 - - + +
754A LEU* 4.0 10.5 - - + -
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Residues in contact with ARG 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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541A HIS* 4.1 21.3 + - + +
542A LYS* 5.1 12.9 - - - +
543A ASN* 3.0 24.9 + - - +
605A TYR* 3.0 57.5 + - + +
606A GLN* 2.9 4.8 + - - +
608A ALA* 1.3 75.7 - - - +
610A GLY* 1.3 66.6 + - - +
612A GLU* 2.8 26.8 + - - +
613A TYR* 2.9 13.7 + - - +
751A VAL* 4.0 12.1 - - + +
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Residues in contact with GLY 610 (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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541A HIS* 4.4 4.7 - - - -
543A ASN* 3.5 31.4 - - - +
544A ILE* 3.9 6.6 - - - +
606A GLN 2.9 7.7 + - - -
609A ARG* 1.3 77.0 - - - +
611A MET* 1.3 57.1 + - - +
613A TYR* 3.5 2.7 + - - +
614A LEU* 3.1 33.6 + - - +
639A ILE* 3.5 9.9 - - - -
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Residues in contact with MET 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A VAL* 3.0 16.5 + - + +
608A ALA 3.7 0.4 - - - +
609A ARG 3.0 0.8 - - - -
610A GLY* 1.3 77.4 - - - +
612A GLU* 1.3 60.0 + - - +
614A LEU* 3.2 30.8 - - + +
615A ALA* 3.0 26.7 + - - +
621A HIS* 3.9 20.6 - - + -
624A LEU* 3.5 33.9 - - + -
639A ILE* 3.0 42.8 - - + -
682A ASP* 4.6 5.6 - - - +
747A PHE* 3.6 33.2 - - + -
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Residues in contact with GLU 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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541A HIS* 5.9 0.8 + - - +
608A ALA 2.9 9.6 + - - +
609A ARG* 2.8 28.6 + - - +
611A MET* 1.3 72.5 - - - +
613A TYR* 1.3 58.5 + - + +
615A ALA* 3.3 4.7 + - - +
616A SER* 2.7 35.6 + - - -
747A PHE* 3.5 26.0 - - + +
748A LYS* 3.7 24.2 - - - +
751A VAL* 3.8 24.6 - - - +
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Residues in contact with TYR 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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538A ILE* 2.7 33.5 + - + -
539A GLY* 3.1 22.7 - - - -
540A LYS 2.9 23.5 + - - -
541A HIS* 3.4 41.5 - + + +
544A ILE* 4.2 8.3 - - + -
609A ARG 2.9 8.8 + - - +
610A GLY 3.6 8.3 - - - +
612A GLU* 1.3 80.2 - - + +
614A LEU* 1.3 69.1 - - + +
616A SER* 2.5 29.2 + - - -
617A LYS* 3.0 26.7 + - + +
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Residues in contact with LEU 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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538A ILE* 3.7 25.8 - - + -
544A ILE* 4.2 15.9 - - + -
610A GLY 3.1 15.1 + - - +
611A MET* 3.2 36.3 - - + +
613A TYR* 1.3 79.8 - - + +
615A ALA* 1.3 64.2 + - - +
617A LYS* 2.9 13.9 + - - +
619A CYS* 3.0 38.7 + - + +
621A HIS* 4.7 1.6 - - + -
639A ILE* 4.3 5.2 - - + -
642A PHE* 3.5 43.1 - - + -
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Residues in contact with ALA 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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611A MET 3.0 20.7 + - - +
612A GLU* 3.4 9.6 - - - +
614A LEU* 1.3 78.2 - - - +
616A SER* 1.3 62.1 + - - +
618A LYS* 3.0 11.3 + - - -
619A CYS 3.7 2.4 + - - -
679A HIS* 3.3 42.0 + - + +
747A PHE* 4.4 12.1 - - + -
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Residues in contact with SER 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A GLU 2.7 16.8 + - - -
613A TYR* 2.5 26.6 + - - -
615A ALA* 1.3 73.7 - - - +
617A LYS* 1.3 65.9 + - - +
618A LYS* 3.0 9.9 + - - +
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Residues in contact with LYS 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A MET 4.5 7.2 + - - +
538A ILE* 3.3 49.6 + - + +
613A TYR* 3.0 25.3 + - + +
614A LEU 2.9 9.6 + - - +
616A SER* 1.3 90.8 + - - +
618A LYS* 1.3 66.2 + - - +
619A CYS* 2.9 10.3 + - + +
537B MET* 3.5 19.5 - - + +
617B LYS* 5.5 7.3 - - - +
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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
------------------------------------------------------------
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