Contacts of the helix formed by residues 633 - 654 (chain A) in PDB entry 3ZNS
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 HIS 633 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A VAL 5.3 0.3 - - - +
530A LYS* 3.4 64.1 - - + +
531A HIS* 5.0 0.2 - - - -
630A ASN* 3.1 25.2 + - - +
632A LEU* 1.3 104.5 + - + +
634A SER* 1.3 67.6 + - - +
635A SER 3.3 2.5 - - - -
636A ASN* 3.2 12.7 + - + +
637A ALA* 2.9 23.5 + - - +
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Residues in contact with SER 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A HIS* 2.7 37.7 + - - -
629A TRP* 3.4 28.9 - - - -
630A ASN* 2.7 35.3 + - - +
633A HIS* 1.3 75.7 - - - +
635A SER* 1.3 57.6 + - - +
637A ALA* 3.3 1.2 + - - +
638A ALA* 2.8 32.6 + - - +
666A PRO* 5.1 1.0 - - - +
681A PHE* 5.0 0.6 - - - -
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Residues in contact with SER 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A TYR 2.7 28.5 + - - -
590A GLY* 3.5 20.1 + - - -
591A THR* 4.0 5.8 + - - -
629A TRP* 3.4 17.6 - - - -
630A ASN 4.6 0.4 + - - -
632A LEU 6.0 1.6 - - - -
633A HIS 3.3 1.0 - - - +
634A SER* 1.3 77.8 - - - +
636A ASN* 1.3 62.9 + - - +
638A ALA* 3.7 3.2 - - - +
639A ARG* 2.9 35.7 + - - +
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Residues in contact with ASN 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A VAL* 4.5 15.1 - - + +
571A LYS* 4.7 17.8 - - + +
632A LEU 3.6 17.2 - - - +
633A HIS* 3.2 13.4 + - + +
635A SER* 1.3 85.3 + - - +
637A ALA* 1.3 57.4 + - - +
639A ARG* 3.4 9.5 + - - +
640A TRP* 2.9 31.2 + - - +
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Residues in contact with ALA 637 (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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527A VAL* 3.9 10.0 - - - +
528A MET* 3.8 21.7 - - - +
531A HIS* 3.8 26.7 - - + +
633A HIS 2.9 16.5 + - - +
634A SER 3.8 1.8 - - - +
636A ASN* 1.3 76.7 - - - +
638A ALA* 1.3 63.3 + - - +
640A TRP* 3.4 7.7 + - - +
641A ALA 3.0 17.7 + - - -
665A ARG 3.6 10.4 - - - +
666A PRO* 3.9 7.4 - - + -
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Residues in contact with ALA 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A TRP* 5.6 0.9 - - + -
634A SER 2.8 19.2 + - - +
635A SER* 3.7 4.3 - - - +
637A ALA* 1.3 75.8 - - - +
639A ARG* 1.3 62.8 + - - +
641A ALA* 3.3 5.1 + - - +
642A ALA* 3.1 22.0 + - - +
666A PRO* 3.9 18.3 - - + +
681A PHE* 4.1 18.8 - - + -
682A PHE* 3.7 28.5 - - + +
684A SER* 4.6 1.0 + - - -
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Residues in contact with ARG 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LYS* 3.8 41.0 - - + +
572A ALA* 2.7 49.3 + - - +
573A SER* 3.8 8.3 - - - +
574A LEU* 3.3 22.9 - - - +
577A LEU* 3.9 19.4 - - + +
590A GLY* 3.0 33.6 + - - -
591A THR* 5.3 0.4 - - - +
635A SER* 2.9 25.1 + - - +
636A ASN* 3.8 8.3 - - - +
638A ALA* 1.3 74.5 - - - +
640A TRP* 1.3 61.6 + - - +
642A ALA* 3.5 2.0 + - - -
643A GLY 2.8 23.9 + - - -
682A PHE* 3.9 7.9 - - + -
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Residues in contact with TRP 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ASP* 3.4 26.8 - - + +
527A VAL* 4.5 22.0 - - + -
528A MET* 3.8 28.7 - - + -
568A ARG* 2.8 43.3 + - - -
569A GLY 3.4 17.3 - - - -
570A ARG* 3.3 17.8 - - + +
571A LYS* 3.5 35.8 - - + +
636A ASN 2.9 17.4 + - - +
637A ALA* 3.6 7.2 - - - +
638A ALA 3.3 0.2 - - - -
639A ARG* 1.3 75.2 - - - +
641A ALA* 1.3 57.8 + - - +
644A SER* 2.4 54.3 + - - -
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Residues in contact with ALA 641 (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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528A MET* 4.1 8.2 - - - -
637A ALA 3.0 16.3 + - - +
638A ALA* 3.6 6.3 - - - +
639A ARG 3.3 0.2 - - - -
640A TRP* 1.3 73.1 - - - +
642A ALA* 1.3 66.4 + - - +
644A SER* 4.1 0.3 - - - -
645A VAL* 3.1 30.8 + - - +
664A VAL* 3.9 17.9 - - + +
665A ARG 3.9 15.3 - - - +
666A PRO 4.0 12.3 - - - +
684A SER* 3.4 11.9 - - - +
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Residues in contact with ALA 642 (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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572A ALA* 3.8 17.5 - - + -
577A LEU* 4.1 4.5 - - + -
638A ALA 3.1 14.4 + - - +
639A ARG 3.8 0.4 - - - +
641A ALA* 1.3 80.2 - - - +
643A GLY* 1.3 61.4 + - - +
645A VAL* 4.1 1.6 - - - +
646A THR* 3.0 28.3 + - - -
682A PHE* 4.5 3.6 - - + -
684A SER* 3.2 20.7 + - - +
687A ILE* 3.9 26.7 - - + -
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Residues in contact with GLY 643 (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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570A ARG* 3.3 31.8 - - - +
571A LYS 4.0 0.9 - - - -
572A ALA* 3.5 16.7 - - - +
576A GLU* 5.0 0.2 - - - -
639A ARG 2.8 17.2 + - - -
642A ALA* 1.3 73.2 - - - +
644A SER* 1.3 56.6 + - - +
646A THR* 3.5 5.8 + - - -
647A ASP* 2.9 28.1 + - - +
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Residues in contact with SER 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 3.5 33.4 - - - +
569A GLY* 3.5 12.2 - - - -
570A ARG 3.4 6.8 + - - -
640A TRP* 2.4 45.0 + - - -
641A ALA 4.1 2.5 - - - -
643A GLY* 1.3 74.5 - - - +
645A VAL* 1.3 60.6 + - - +
646A THR 3.2 0.9 - - - -
647A ASP* 3.8 2.3 - - - +
648A LEU* 3.0 30.3 + - - +
664A VAL* 4.5 3.6 - - - -
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Residues in contact with VAL 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A ALA 3.1 18.8 + - - +
642A ALA 4.1 2.5 - - - +
644A SER* 1.3 74.5 - - - +
646A THR* 1.3 57.8 + - - +
648A LEU* 3.5 3.5 + - - +
649A ALA* 3.0 27.4 + - - +
662A ALA* 4.0 18.6 - - + -
664A VAL* 4.1 9.9 - - + -
684A SER* 3.9 22.9 - - - +
685A VAL* 4.4 4.9 - - + -
688A ALA* 3.8 17.0 - - + -
795A LEU* 5.2 4.3 - - + -
836A VAL* 4.7 11.4 - - + +
838A ALA* 3.9 31.2 - - + -
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Residues in contact with THR 646 (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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570A ARG* 3.7 18.8 - - - +
576A GLU* 3.9 9.8 - - - +
642A ALA 3.0 19.2 + - - -
643A GLY* 3.6 6.5 - - - -
645A VAL* 1.3 78.1 - - - +
647A ASP* 1.3 64.1 + - - +
649A ALA* 3.2 3.1 + - - +
650A PHE* 3.0 46.6 + - + -
687A ILE* 3.9 9.0 - - - +
688A ALA* 3.3 28.9 + - - -
691A GLN* 4.2 9.4 - - + -
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Residues in contact with ASP 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 5.5 2.5 - - + +
569A GLY* 5.0 8.6 - - - -
570A ARG* 2.8 35.2 + - + +
643A GLY 2.9 18.6 + - - +
644A SER* 3.3 7.4 + - - +
646A THR* 1.3 77.7 - - - +
648A LEU* 1.3 60.9 + - - +
650A PHE* 3.5 6.5 + - - +
651A LYS* 3.0 62.6 + - - +
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Residues in contact with LEU 648 (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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521A GLY* 4.2 8.5 - - - +
523A ILE* 4.2 12.7 - - + +
567A LEU* 4.9 7.4 - - + -
644A SER 3.0 18.3 + - - +
645A VAL* 3.8 4.9 - - - +
647A ASP* 1.3 73.1 - - - +
649A ALA* 1.3 60.6 + - - +
651A LYS* 3.2 5.8 + - - +
652A VAL* 2.9 36.4 + - + +
657A LEU* 3.8 26.2 - - + -
660A GLY* 3.8 17.0 - - - -
661A PHE 3.6 39.7 - - - +
662A ALA* 3.9 13.2 - - + +
836A VAL* 4.1 12.3 - - + -
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Residues in contact with ALA 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A VAL 3.0 18.6 + - - +
646A THR 3.6 4.7 - - - +
648A LEU* 1.3 75.9 - - - +
650A PHE* 1.3 53.1 + - - +
652A VAL 3.4 0.7 + - - -
653A ALA* 2.7 35.5 + - - +
688A ALA* 4.4 6.7 - - + -
692A LEU* 3.5 26.9 - - + -
793A LEU* 3.7 4.6 - - + +
795A LEU* 4.2 17.9 - - + -
836A VAL* 3.9 13.0 - - + +
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Residues in contact with PHE 650 (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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570A ARG* 5.7 1.8 - - - -
576A GLU* 5.7 0.2 - - - -
646A THR* 3.0 36.4 + - + +
647A ASP* 3.7 8.3 - - - +
648A LEU 3.2 0.2 - - - -
649A ALA* 1.3 78.1 - - - +
651A LYS* 1.3 57.7 + - + +
653A ALA* 3.3 2.0 + - - +
654A SER* 3.0 30.5 + - - -
688A ALA 4.8 0.4 - - - -
691A GLN* 3.5 45.1 - - + -
692A LEU* 3.3 29.8 - - + -
695A GLN* 3.5 29.4 - - + -
697A LYS* 4.4 17.3 - - + +
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Residues in contact with LYS 651 (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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516A LEU* 3.3 29.5 - - + +
567A LEU* 3.9 29.2 - - + -
647A ASP* 3.0 41.5 + - - +
648A LEU* 3.2 7.4 + - - +
650A PHE* 1.3 76.4 - - + +
652A VAL* 1.3 58.1 + - - +
654A SER* 3.0 19.5 + - - -
656A GLU* 3.0 18.2 + - + +
657A LEU* 3.0 34.6 + - + -
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Residues in contact with VAL 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A LEU* 2.9 26.1 + - + +
649A ALA 3.8 3.4 - - - +
651A LYS* 1.3 75.7 - - - +
653A ALA* 1.3 59.3 + - - +
655A ARG* 2.6 48.8 + - - +
657A LEU* 3.4 13.0 - - + -
658A LYS 3.6 11.4 - - - +
659A ASN* 3.7 26.0 - - - +
660A GLY 4.1 0.2 - - - +
793A LEU* 4.5 2.0 - - + -
834A ALA* 3.8 18.9 - - + +
835A VAL 3.9 7.6 - - - +
836A VAL* 3.7 20.6 - - + -
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Residues in contact with ALA 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ALA 2.7 22.1 + - - +
650A PHE 3.3 2.2 + - - +
652A VAL* 1.3 73.6 - - - +
654A SER* 1.3 60.1 + - - +
655A ARG* 3.2 10.9 + - - +
692A LEU* 4.1 9.9 - - + -
697A LYS* 3.6 41.3 - - + +
698A ALA* 5.1 0.7 - - + -
792A ASP 6.2 0.2 - - - -
793A LEU* 3.8 18.4 - - + +
834A ALA* 5.5 1.8 - - - -
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Residues in contact with SER 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A PHE 3.0 12.2 + - - -
651A LYS* 3.0 17.0 + - - -
653A ALA* 1.3 74.5 - - - +
655A ARG* 1.3 67.6 + - - +
656A GLU* 3.1 21.0 + - - +
697A LYS* 3.6 27.5 - - - +
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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
------------------------------------------------------------
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