Contacts of the strand formed by residues 525 - 530 (chain A) in PDB entry 3AR2
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 CYS 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A VAL* 3.2 26.7 - - - -
522A ILE* 3.5 14.5 - - - +
523A ASP 3.2 5.9 - - - +
524A ARG* 1.3 78.5 - - - +
526A ASN* 1.3 64.4 + - - +
527A TYR 3.5 4.7 - - - +
537A MET* 3.6 30.8 - - + +
542A LYS* 5.8 0.2 + - - -
565A ALA* 3.9 11.4 - - - -
591A LEU* 3.2 26.2 - - - +
593A PHE* 3.8 22.4 - - - -
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Residues in contact with ASN 526 (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 ASP 5.4 1.7 - - - +
524A ARG 5.0 1.0 + - - -
525A CYS* 1.3 78.1 - - - +
527A TYR* 1.3 75.6 + - + +
536A PRO* 3.3 3.8 - - - +
537A MET* 2.8 28.2 + - - +
589A THR* 5.0 4.6 - - - +
590A ASP* 2.6 45.8 + - - +
591A LEU 3.0 4.8 + - - +
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Residues in contact with TYR 527 (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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525A CYS* 3.5 2.7 - - - +
526A ASN* 1.3 97.5 - - + +
528A VAL* 1.3 57.2 + - - +
534A ARG* 3.0 51.5 + - + -
535A VAL 3.1 9.4 - - - +
536A PRO* 4.1 15.9 - - + -
537A MET* 3.7 2.7 - - - +
590A ASP* 3.8 36.6 + - - -
591A LEU 3.4 9.2 + - - +
592A THR* 3.0 27.9 - - - +
593A PHE* 2.6 32.2 + - - +
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Residues in contact with VAL 528 (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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369A ILE* 4.1 19.3 - - + -
372A VAL* 4.1 17.0 - - + -
527A TYR* 1.3 75.1 - - - +
529A ARG* 1.3 60.1 + - - +
530A VAL* 3.9 3.9 + - + -
534A ARG* 3.6 1.9 - - - +
535A VAL* 2.8 53.8 + - + -
537A MET* 3.5 33.0 - - + -
541A VAL* 3.4 27.6 - - + -
545A ILE* 5.6 0.2 - - + -
592A THR* 3.9 2.2 - - - -
593A PHE* 3.6 11.4 - - + +
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Residues in contact with ARG 529 (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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368A ILE* 5.9 0.3 - - - +
369A ILE* 3.5 23.7 + - - +
409A GLY* 5.5 4.3 - - - -
412A GLU* 2.4 57.0 + - - +
511A LYS* 5.7 1.4 - - - +
528A VAL* 1.3 73.5 - - - +
530A VAL* 1.3 60.5 + - - +
531A GLY 3.1 26.2 + - - +
532A THR* 4.5 7.3 + - - +
533A THR 3.3 17.2 + - - +
534A ARG* 4.4 9.5 - - - +
566A THR* 3.5 4.0 + - - -
568A ASP* 2.5 45.2 + - - -
592A THR* 3.3 23.4 - - + +
593A PHE 2.8 20.2 + - - +
594A VAL* 4.5 9.4 - - + +
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Residues in contact with VAL 530 (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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369A ILE* 4.0 19.1 - - + +
370A ASP 3.3 30.5 - - - +
371A LYS* 4.6 3.6 - - - +
372A VAL* 4.1 16.6 - - + +
528A VAL* 4.2 7.4 - - + +
529A ARG* 1.3 77.3 - - - +
531A GLY* 1.3 59.9 + - - +
532A THR 3.1 0.2 + - - -
533A THR* 2.8 49.4 + - + -
535A VAL* 4.3 8.1 - - + -
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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