Contacts of the helix formed by residues 587 - 592 (chain A) in PDB entry 5Y7K
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 587 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A GLY 3.1 15.0 - - - -
381A TYR* 4.2 11.9 - - - -
403A GLU* 3.3 17.0 + - - +
583A SER 4.9 0.3 - - - +
585A TYR 4.7 0.4 + - - +
586A GLN* 1.3 80.8 + - - +
588A ASP* 1.3 63.3 + - - -
589A LYS* 3.2 4.6 + - - -
590A ILE* 3.4 2.9 + - - +
591A MET* 3.1 26.9 + - - +
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Residues in contact with ASP 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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349A SER* 5.2 0.7 + - - -
351A THR* 4.3 7.3 + - + +
376A SER* 2.6 32.2 + - - -
380A GLY* 2.6 21.3 + - - +
382A ARG* 3.3 25.3 + - - -
587A GLY* 1.3 71.1 - - - -
589A LYS* 1.3 61.2 + - - +
590A ILE 3.2 0.2 - - - -
591A MET* 3.6 10.8 - - - +
592A HIS* 2.9 61.0 + - - +
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Residues in contact with LYS 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU 5.3 6.6 + - - +
380A GLY* 5.3 1.8 - - - -
381A TYR* 6.1 4.7 - - + +
581A ARG* 5.8 0.2 - - - +
586A GLN 5.7 1.1 - - - +
587A GLY* 3.2 2.8 - - - -
588A ASP* 1.3 79.6 - - - +
590A ILE* 1.3 64.5 + - + +
593A ALA* 3.7 17.2 + - - +
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Residues in contact with ILE 590 (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 THR* 4.3 16.2 - - + -
523A LYS 4.5 2.0 - - - +
524A PHE* 3.7 29.8 - - + -
580A GLY 3.8 18.6 - - - +
581A ARG* 3.6 3.3 - - + +
582A GLY 2.6 28.6 + - - +
583A SER* 3.5 20.9 - - - +
586A GLN* 3.7 37.2 - - + +
587A GLY 3.4 7.3 + - - +
589A LYS* 1.3 84.7 - - + +
591A MET* 1.3 57.9 + - - +
593A ALA* 3.5 11.0 - - - +
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Residues in contact with MET 591 (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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353A TRP* 3.7 22.1 - - + +
355A GLY 4.1 0.9 - - - +
356A ARG* 4.6 2.7 - - - -
382A ARG* 3.2 36.1 - - - +
403A GLU* 6.1 0.2 - - - +
551A CYS* 3.5 37.5 - - - +
582A GLY* 3.6 25.6 - - - +
583A SER 3.6 12.6 - - - +
584A GLY* 4.4 5.4 - - - -
585A TYR 5.3 1.6 - - - +
587A GLY 3.1 17.1 + - - +
588A ASP* 3.6 6.3 - - - +
590A ILE* 1.3 80.4 - - - +
592A HIS* 1.3 80.7 + - + +
593A ALA 3.1 4.6 + - - -
594A ILE* 3.6 12.3 - - - +
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Residues in contact with HIS 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 3.6 9.4 - - - -
351A THR* 2.7 44.5 + - - +
352A GLY* 3.6 5.6 + - - -
353A TRP* 3.2 50.2 + + - -
382A ARG* 4.0 1.5 + - - -
588A ASP* 2.9 39.5 + - - +
591A MET* 1.3 99.1 - - + +
593A ALA* 1.3 62.6 + - - +
594A ILE 3.1 2.9 - - - -
595A ASN* 3.1 18.4 + - - +
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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