Contacts of the strand formed by residues 534 - 537 (chain A) in PDB entry 4RS6
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 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A TYR* 2.6 33.5 + - - -
527A VAL 3.2 26.7 + - - -
528A LEU* 3.7 21.8 - - + -
529A PHE* 4.5 0.4 - - - -
532A GLY 4.8 0.9 - - - +
533A ALA* 1.3 76.7 - - - +
535A MET* 1.3 70.2 + - - +
536A SER* 3.5 21.5 + - - -
545A HIS 3.8 0.7 + - - +
546A TYR* 3.3 6.0 - - - -
547A TYR* 2.9 47.5 + - + +
601A TYR* 3.4 30.5 - + + +
602A LEU* 3.7 11.6 + - + +
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Residues in contact with MET 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLY* 3.3 2.3 - - - -
527A VAL* 2.8 38.9 + - + +
529A PHE* 3.9 13.0 - - + -
534A HIS* 1.3 75.2 - - - +
536A SER* 1.3 60.7 + - - +
544A VAL* 3.9 12.8 - - + -
545A HIS 3.3 3.8 - - - -
546A TYR* 3.6 30.5 - - + -
556A PHE* 5.1 3.1 - - - -
565A PHE* 4.8 2.5 - - - +
568A GLN* 3.8 28.7 - - - +
569A VAL* 3.7 25.6 - - + -
572A LEU* 2.9 43.9 - - + +
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Residues in contact with SER 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 4.6 0.7 + - - -
520A LEU* 6.1 0.7 - - - +
524A THR* 4.3 15.7 - - - +
525A VAL 3.1 9.4 + - - -
526A GLY* 3.9 3.1 - - - -
534A HIS* 3.5 21.4 - - - -
535A MET* 1.3 71.8 + - - +
537A LEU* 1.3 59.1 + - - +
538A LEU* 4.5 5.1 - - - +
543A THR 3.6 0.9 - - - +
544A VAL* 3.2 9.2 - - - +
545A HIS* 2.9 44.3 + - - -
572A LEU* 4.3 4.5 - - - -
599A ARG* 5.9 2.0 - - - -
600A LEU 4.3 9.6 + - - -
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Residues in contact with LEU 537 (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 HIS 4.4 0.2 - - - +
524A THR* 3.2 3.6 - - - +
525A VAL* 2.7 40.4 + - + +
536A SER* 1.3 69.9 - - - +
538A LEU* 1.3 71.0 + - - +
541A LYS* 3.8 50.0 - - + +
542A LYS 4.3 1.3 - - - -
543A THR 3.4 17.5 - - - +
544A VAL* 3.9 16.2 - - + -
558A ALA* 4.7 3.8 - - + -
572A LEU* 3.7 24.6 - - + +
573A LYS* 4.7 18.2 - - + -
576A SER* 4.7 9.6 - - - +
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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