Contacts of the helix formed by residues 580 - 589 (chain A) in PDB entry 1VA2
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 ARG 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567A PHE* 4.0 5.4 - - - -
578A PHE* 3.6 2.4 - - - +
579A THR* 1.3 89.2 + - + +
581A SER* 1.3 66.5 + - - +
582A ASP* 4.3 14.8 + - + +
583A GLU* 3.2 30.5 + - + +
584A LEU* 3.8 8.1 + - - +
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Residues in contact with SER 581 (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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567A PHE* 3.5 27.6 - - - -
580A ARG* 1.3 72.2 - - - +
582A ASP* 1.3 70.6 + - - +
583A GLU 3.2 0.9 + - - -
584A LEU* 3.2 12.9 + - - +
585A GLN* 2.6 34.6 + - - +
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Residues in contact with ASP 582 (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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580A ARG* 3.2 12.7 + - + -
581A SER* 1.3 88.2 + - - +
583A GLU* 1.3 62.5 + - - +
585A GLN* 3.1 14.5 + - - +
586A ARG* 3.1 25.1 + - - +
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Residues in contact with GLU 583 (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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576A LYS* 5.9 0.9 - - - +
578A PHE* 3.3 30.7 - - + -
580A ARG* 3.2 24.4 + - + +
581A SER 3.1 0.6 - - - -
582A ASP* 1.3 79.4 - - - +
584A LEU* 1.3 54.8 + - - +
586A ARG* 3.1 41.7 + - - +
587A HIS* 2.5 42.2 + - + +
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Residues in contact with LEU 584 (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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567A PHE* 3.8 33.4 - - + -
568A MET* 3.3 5.6 - - - +
569A CYS* 2.9 43.5 - - + +
578A PHE* 3.2 27.8 - - + -
580A ARG 3.9 7.6 - - - +
581A SER* 3.2 11.4 + - - +
583A GLU* 1.3 75.1 - - - +
585A GLN* 1.3 60.0 + - - +
587A HIS* 3.9 7.9 - - - -
588A LYS* 2.7 57.8 + - - +
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Residues in contact with GLN 585 (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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581A SER* 2.6 34.2 + - - +
582A ASP* 3.1 19.7 + - - +
584A LEU* 1.3 89.2 - - - +
586A ARG* 1.3 57.4 + - - +
588A LYS* 4.0 10.5 + - - +
589A ARG* 2.9 38.5 + - - +
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Residues in contact with ARG 586 (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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582A ASP* 3.1 9.8 + - - +
583A GLU* 3.1 32.0 + - - +
585A GLN* 1.3 76.8 - - - +
587A HIS* 1.3 69.4 + - - +
589A ARG* 2.8 40.1 + - - +
590A THR* 3.7 7.1 + - - +
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Residues in contact with HIS 587 (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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100A ZN 2.1 37.9 - - - -
569A CYS* 3.5 1.4 - - + +
574A CYS* 3.5 7.0 - - - -
576A LYS* 4.8 5.5 + - + +
578A PHE* 3.3 34.3 - + + -
583A GLU* 2.5 25.6 + - + +
584A LEU* 3.9 5.4 - - - -
586A ARG* 1.3 77.4 - - + +
588A LYS* 1.3 85.9 + - + +
590A THR* 3.1 21.3 + - - +
591A HIS* 3.0 27.2 + + - -
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Residues in contact with LYS 588 (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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568A MET 4.7 1.3 - - - -
569A CYS* 3.7 20.4 - - + +
570A THR* 3.8 14.1 - - - +
571A TRP* 3.2 40.5 - - + -
584A LEU* 2.7 57.3 + - - +
585A GLN* 4.0 11.5 + - - +
587A HIS* 1.3 88.9 - - + +
589A ARG* 1.3 57.1 + - - +
590A THR 2.9 5.6 - - - -
591A HIS* 2.8 29.6 + - + +
592A THR* 4.4 1.4 + - - +
595A LYS* 4.7 5.2 + - - -
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Residues in contact with ARG 589 (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 GLN* 2.9 25.1 + - - +
586A ARG* 2.8 37.2 - - - +
587A HIS 3.0 0.2 - - - -
588A LYS* 1.3 76.2 - - - +
590A THR* 1.3 55.9 + - - +
592A THR 4.7 2.3 - - - +
594A GLU 4.0 12.6 - - - +
595A LYS* 3.7 33.3 + - + +
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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
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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