Contacts of the helix formed by residues 595 - 613 (chain A) in PDB entry 2VZ9
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 THR 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A TYR* 5.3 0.2 - - - -
593A CYS 4.3 0.2 - - - -
594A LEU* 1.3 75.3 - - - +
596A GLN* 1.3 60.6 + - - +
597A GLU* 3.3 31.2 - - + +
598A GLU* 3.1 37.6 + - - +
599A ALA* 2.7 31.0 + - - +
706A LYS* 3.8 6.7 + - - +
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Residues in contact with GLN 596 (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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519A SER* 2.8 26.7 + - - -
522A ARG* 3.2 35.6 + - + +
523A SER* 2.7 34.4 + - - +
526A ALA* 6.2 0.2 - - + -
561A ILE* 4.1 19.5 - - + +
565A ASP* 4.5 0.5 - - - +
589A TYR* 4.2 27.6 + - + +
594A LEU 3.8 1.6 + - - -
595A THR* 1.3 74.5 - - - +
597A GLU* 1.3 66.4 + - - +
599A ALA* 3.4 5.3 - - - +
600A VAL* 2.8 40.0 + - + +
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Residues in contact with GLU 597 (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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522A ARG* 4.4 15.6 - - - +
525A GLN* 5.8 1.0 - - - +
526A ALA* 3.7 29.1 + - + +
595A THR* 3.3 29.1 - - + +
596A GLN* 1.3 79.1 + - - +
598A GLU* 1.3 65.4 + - + +
600A VAL* 2.9 2.3 + - - +
601A LEU* 2.8 36.4 + - + +
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Residues in contact with GLU 598 (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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594A LEU* 3.5 24.7 - - + +
595A THR* 3.1 18.9 + - - +
597A GLU* 1.3 81.4 - - + +
599A ALA* 1.3 56.2 + - - +
601A LEU* 5.4 0.4 - - - -
602A SER* 2.5 35.4 + - - -
701A VAL* 3.8 28.0 - - + +
702A ILE* 4.6 8.5 - - + +
703A LEU 3.5 19.8 - - - +
704A ASP 4.2 3.4 - - - +
706A LYS* 2.4 35.8 + - - +
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Residues in contact with ALA 599 (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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557A THR* 4.5 1.6 - - - -
561A ILE* 3.7 20.6 - - + -
585A VAL* 3.5 17.6 - - + +
589A TYR* 4.8 3.4 - - + -
594A LEU* 3.6 27.5 - - + +
595A THR 2.7 19.6 + - - +
596A GLN 3.4 3.6 - - - +
598A GLU* 1.3 74.9 - - - +
600A VAL* 1.3 66.3 + - - +
602A SER* 3.2 4.9 + - - -
603A SER* 3.1 18.7 + - - -
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Residues in contact with VAL 600 (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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523A SER* 3.9 30.1 - - - +
526A ALA* 4.6 6.1 - - + -
527A LEU* 3.7 33.4 - - + -
554A VAL* 4.6 5.3 - - + +
557A THR* 4.3 8.5 - - + -
558A SER* 3.9 17.3 - - - +
561A ILE* 4.3 9.9 - - + -
596A GLN* 2.8 31.8 + - + +
597A GLU* 3.7 3.4 - - - +
599A ALA* 1.3 71.5 - - - +
601A LEU* 1.3 65.4 + - - +
603A SER* 3.1 6.6 + - - -
604A TYR* 3.0 19.1 + - - +
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Residues in contact with LEU 601 (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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526A ALA* 3.4 38.4 - - + +
527A LEU* 3.7 12.3 - - + -
529A PRO* 6.3 0.2 - - + -
530A LEU* 3.5 32.5 - - + -
597A GLU* 2.8 27.3 + - + +
598A GLU* 5.4 0.2 - - - -
600A VAL* 1.3 73.4 - - - +
602A SER* 1.3 62.0 + - - +
604A TYR* 3.3 3.8 - - + +
605A TRP* 3.0 35.7 + - + +
701A VAL* 3.7 22.2 - - + -
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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
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585A VAL* 4.5 6.7 - - - -
594A LEU* 4.6 3.0 - - - +
598A GLU 2.5 25.2 + - - -
599A ALA* 3.3 8.4 - - - -
600A VAL 3.1 0.2 - - - -
601A LEU* 1.3 74.8 - - - +
603A SER* 1.3 65.9 + - - +
605A TRP* 3.8 0.7 - - - +
606A ARG* 2.7 40.0 + - - +
698A LEU* 3.9 18.5 - - - +
701A VAL* 4.4 1.7 - - - +
702A ILE* 3.8 23.6 - - - +
730A PHE* 6.2 0.9 - - - -
735A SER* 4.8 3.6 - - - -
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Residues in contact with SER 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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553A PHE* 3.3 35.7 + - - +
554A VAL* 4.4 1.3 - - - -
557A THR* 2.6 35.6 + - - +
582A LEU* 3.6 9.2 - - - +
585A VAL* 3.7 7.8 - - - +
599A ALA 3.1 1.4 + - - -
600A VAL 3.1 9.4 + - - -
602A SER* 1.3 78.8 - - - +
604A TYR* 1.3 64.7 + - - +
606A ARG* 3.3 10.2 + - - +
607A GLY 2.9 19.9 + - - -
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Residues in contact with TYR 604 (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 LEU* 4.0 8.5 - - + -
530A LEU* 3.4 41.9 + - + +
532A LEU* 3.4 38.9 - - + +
550A VAL* 3.7 24.0 - - + +
554A VAL* 3.6 23.2 - - + +
600A VAL 3.0 10.7 + - - +
601A LEU* 3.3 13.0 - - - +
603A SER* 1.3 78.5 - - - +
605A TRP* 1.3 90.2 + + - +
607A GLY* 3.3 1.6 + - - -
608A TYR* 2.9 36.6 + + + +
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Residues in contact with TRP 605 (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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530A LEU* 3.8 33.9 - - + +
601A LEU* 3.0 26.7 + - + +
602A SER 4.0 1.3 - - - +
604A TYR* 1.3 91.2 - + - +
606A ARG* 1.3 70.0 + - - +
607A GLY 2.9 1.8 - - - -
608A TYR* 2.7 59.5 + + + -
609A CYS* 3.0 18.8 + - - -
694A LEU* 4.1 4.9 - - + -
697A GLN* 2.9 38.2 + - + +
698A LEU* 4.3 10.3 - - + -
701A VAL* 3.7 20.7 - - + +
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Residues in contact with ARG 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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553A PHE* 3.9 7.9 - - + -
582A LEU* 3.6 32.3 - - - +
585A VAL* 3.7 26.1 - - - +
602A SER* 2.7 33.8 + - - +
603A SER* 3.5 3.6 - - - +
605A TRP* 1.3 73.1 - - - +
607A GLY* 1.3 57.5 + - - +
610A ILE* 3.1 30.1 + - - +
694A LEU* 3.7 14.4 - - + +
698A LEU* 3.9 11.7 - - + -
735A SER* 3.2 42.0 + - - +
738A ASN* 3.3 17.8 + - - -
739A LEU* 3.1 52.0 - - + +
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Residues in contact with GLY 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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549A ILE* 3.5 20.1 - - - +
550A VAL* 3.4 13.1 - - - +
553A PHE* 3.8 19.7 - - - -
603A SER 2.9 13.5 + - - -
604A TYR 3.7 3.6 - - - -
605A TRP 2.8 3.8 + - - -
606A ARG* 1.3 74.9 - - - +
608A TYR* 1.3 57.1 + - - +
610A ILE 3.5 0.7 + - - -
611A LYS* 3.0 22.0 + - - +
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Residues in contact with TYR 608 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550A VAL* 3.3 18.3 - - + +
604A TYR* 2.9 31.2 + + + +
605A TRP* 2.7 49.1 + + + +
607A GLY* 1.3 67.1 - - - +
609A CYS* 1.3 67.4 + - - +
610A ILE 3.0 1.1 - - - -
611A LYS* 2.7 31.0 + - - +
612A GLU* 2.8 52.5 + - + +
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Residues in contact with CYS 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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605A TRP* 3.0 16.7 + - - +
606A ARG 4.8 0.2 - - - +
608A TYR* 1.3 92.1 - - - +
610A ILE* 1.3 60.8 + - - +
612A GLU* 4.0 3.5 - - - +
613A ALA* 3.2 23.4 + - - +
690A ILE* 3.7 18.7 - - + +
693A THR* 4.1 16.6 + - - +
694A LEU* 3.8 29.4 - - + -
697A GLN* 4.4 15.9 - - - -
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Residues in contact with ILE 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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549A ILE* 3.2 25.8 - - + -
553A PHE* 4.6 2.0 - - + -
606A ARG 3.1 18.1 + - - +
607A GLY 3.5 2.8 + - - +
608A TYR 3.0 1.0 - - - -
609A CYS* 1.3 74.6 - - - +
611A LYS* 1.3 67.8 + - - +
613A ALA* 3.3 13.3 + - - +
615A VAL* 3.8 10.2 - - - +
680A ILE* 3.3 22.8 - - + +
682A PHE* 3.6 27.8 - - + -
687A MET* 4.0 11.2 - - - -
690A ILE* 3.4 27.8 - - + -
694A LEU* 5.6 0.2 - - + -
739A LEU* 3.8 22.2 - - + -
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Residues in contact with LYS 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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548A ASP* 3.6 33.3 + - - +
549A ILE* 3.6 24.5 - - + -
550A VAL* 4.3 15.1 - - + +
607A GLY 3.0 8.5 + - - +
608A TYR* 2.7 20.0 + - - +
610A ILE* 1.3 73.7 - - - +
612A GLU* 1.3 72.7 + - - +
613A ALA 3.2 1.4 + - - -
614A ASN* 3.2 18.2 + - - -
615A VAL* 5.7 0.2 - - - +
680A ILE* 5.2 2.5 - - - -
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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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608A TYR* 2.8 55.5 + - + +
609A CYS* 4.0 4.0 - - - +
611A LYS* 1.3 88.2 - - + +
613A ALA* 1.3 56.4 + - - +
614A ASN* 3.1 15.7 + - - +
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Residues in contact with ALA 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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609A CYS 3.2 17.8 + - - +
610A ILE 3.8 1.3 - - - +
611A LYS 3.2 1.8 - - - -
612A GLU* 1.3 74.6 - - - +
614A ASN* 1.3 55.5 + - - +
615A VAL* 2.5 22.5 + - + +
689A SER* 5.6 5.2 - - - +
690A ILE* 3.6 33.2 - - + +
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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
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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