Contacts of the helix formed by residues 592 - 605 (chain A) in PDB entry 5ZRV
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 GLY 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A VAL 4.1 8.7 + - - -
589A ASP 4.6 3.1 + - - -
590A GLU 3.4 4.2 + - - +
591A VAL* 1.3 82.4 - - - +
593A VAL* 1.3 64.4 + - - -
594A ASP 3.2 4.2 + - - -
595A VAL 3.6 3.7 + - - -
596A ALA* 3.6 14.6 + - - -
629A GLY* 6.0 0.4 - - - -
630A ARG 5.9 4.5 - - - -
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Residues in contact with VAL 593 (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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588A VAL 4.8 5.4 + - - -
592A GLY* 1.3 72.8 - - - -
594A ASP* 1.3 61.7 + - - +
596A ALA* 3.5 12.4 + - - +
597A LYS 4.2 2.9 + - - -
628A LEU 5.2 4.7 + - - -
629A GLY* 5.1 14.1 - - - +
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Residues in contact with ASP 594 (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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592A GLY 3.2 1.4 - - - -
593A VAL* 1.3 79.1 - - - +
595A VAL* 1.3 60.4 + - - +
596A ALA 3.4 0.5 + - - -
597A LYS* 3.9 6.9 + - - -
598A HIS 4.3 3.6 + - - -
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Residues in contact with VAL 595 (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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591A VAL 5.5 2.2 - - - -
592A GLY 3.6 7.2 + - - -
593A VAL 3.5 0.4 - - - -
594A ASP* 1.3 74.4 - - - +
596A ALA* 1.3 58.4 + - - +
597A LYS 3.3 0.4 - - - -
598A HIS* 3.3 4.4 + - - +
599A VAL* 2.9 26.7 + - - -
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Residues in contact with ALA 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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592A GLY 3.6 9.0 + - - -
593A VAL* 3.5 9.9 + - - +
594A ASP 3.2 2.0 - - - -
595A VAL* 1.3 75.1 - - - +
597A LYS* 1.3 59.9 + - - +
599A VAL* 3.6 2.1 - - - +
600A ALA* 2.9 24.9 + - - -
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Residues in contact with LYS 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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593A VAL 4.2 4.4 + - - -
594A ASP 3.9 6.2 + - - -
595A VAL 3.3 0.4 - - - -
596A ALA* 1.3 75.0 - - - +
598A HIS* 1.3 57.8 + - - +
600A ALA* 3.2 2.8 + - - +
601A GLU* 2.9 24.3 + - - -
619A LEU* 6.4 1.8 - - - +
620A THR 6.3 1.1 - - - +
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Residues in contact with HIS 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 ASP 4.3 3.8 + - - -
595A VAL* 3.3 9.4 + - - +
597A LYS* 1.3 76.3 - - - +
599A VAL* 1.3 58.3 + - - +
600A ALA 3.1 0.2 - - - -
601A GLU* 3.1 1.6 + - - +
602A ASP* 2.9 28.9 + - - -
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Residues in contact with VAL 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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478A ALA* 6.4 2.7 - - - +
552A ALA* 5.2 9.7 - - - -
595A VAL 2.9 15.5 + - - -
596A ALA* 3.6 3.1 - - - +
598A HIS* 1.3 74.8 - - - +
600A ALA* 1.3 60.5 + - - +
602A ASP* 4.4 3.2 + - - +
603A LEU 5.1 3.5 + - - -
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Residues in contact with ALA 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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596A ALA 2.9 15.1 + - - -
597A LYS* 3.6 4.7 - - - +
598A HIS 3.1 0.2 - - - -
599A VAL* 1.3 80.4 - - - +
601A GLU* 1.3 60.3 + - - +
602A ASP 3.4 0.4 - - - -
603A LEU 4.5 0.2 + - - -
604A GLY* 3.6 17.3 + - - -
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Residues in contact with GLU 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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597A LYS 2.9 14.6 + - - -
598A HIS* 3.1 3.5 + - - +
600A ALA* 1.3 76.3 - - - +
602A ASP* 1.3 60.8 + - - +
604A GLY* 3.7 1.7 - - - +
605A LYS* 2.8 26.2 + - - +
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Residues in contact with ASP 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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478A ALA* 6.5 1.1 - - - +
598A HIS 2.9 15.0 + - - -
599A VAL* 4.4 2.4 - - - +
600A ALA 3.4 1.2 - - - -
601A GLU* 1.3 80.7 - - - +
603A LEU* 1.3 59.4 + - - +
605A LYS* 3.4 8.8 + - - -
606A VAL 4.0 2.4 + - - -
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Residues in contact with LEU 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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543A PRO 6.1 1.1 - - - -
599A VAL 5.1 3.8 + - - -
600A ALA 4.5 1.6 + - - -
602A ASP* 1.3 71.9 - - - +
604A GLY* 1.3 55.9 + - - +
605A LYS 3.1 1.3 - - - -
606A VAL* 2.8 5.1 + - - +
607A PHE 2.6 16.8 + - - -
608A GLY* 2.5 30.3 + - - -
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Residues in contact with GLY 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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600A ALA 3.6 19.8 + - - -
601A GLU* 3.7 2.2 - - - -
602A ASP 3.4 0.8 - - - -
603A LEU* 1.3 74.5 - - - +
605A LYS* 1.3 63.1 + - - +
606A VAL 3.2 1.6 - - - -
608A GLY* 3.5 22.1 + - - +
609A GLU* 4.1 5.6 + - - -
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Residues in contact with LYS 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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601A GLU 2.8 17.3 + - - -
602A ASP 3.4 4.7 + - - -
603A LEU 3.1 0.6 - - - -
604A GLY* 1.3 79.4 - - - +
606A VAL* 1.3 57.9 + - - +
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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