Contacts of the strand formed by residues 580 - 583 (chain B) in PDB entry 1RL3
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 MET 580 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B VAL* 3.6 24.9 - - + -
575B ILE* 3.3 16.6 - - + -
579B GLU* 1.3 75.3 - - - +
581B ASP* 1.3 56.8 + - - +
591B SER* 2.4 38.0 + - - -
592B VAL* 2.7 26.5 + - + +
598B PHE* 3.3 43.1 - - + -
613B VAL* 3.8 14.4 - - + -
614B LYS 3.6 16.2 - - - +
615B ALA* 3.9 5.2 - - - -
619B VAL* 3.9 24.2 - - + -
621B LEU* 4.2 7.6 - - + -
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Residues in contact with ASP 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B MET* 1.3 72.9 - - - +
582B VAL* 1.3 61.6 + - - +
583B TYR* 3.7 25.0 + - + -
588B TRP* 2.9 35.2 - - - -
591B SER* 2.8 22.2 + - - +
612B THR 3.7 0.2 - - - +
613B VAL* 3.0 8.8 - - - +
614B LYS* 2.7 42.2 + - + +
615B ALA 4.7 0.4 - - - +
616B LYS* 3.4 24.3 + - - +
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Residues in contact with VAL 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ASP* 1.3 76.9 - - - +
583B TYR* 1.3 62.2 - - - +
584B VAL* 4.8 0.7 - - + -
588B TRP* 3.5 7.3 - - - +
589B ALA* 2.8 39.5 + - + -
590B THR* 3.1 28.5 + - - +
591B SER* 3.6 20.4 - - - +
592B VAL* 4.1 19.3 - - + -
611B ALA* 3.8 22.4 - - + -
612B THR 3.5 3.1 - - - +
613B VAL* 4.6 7.6 - - + +
801B PCG 4.4 20.6 - - + +
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Residues in contact with TYR 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B GLN* 4.1 1.6 + - - -
581B ASP* 3.7 34.4 + - + -
582B VAL* 1.3 75.7 - - - +
584B VAL* 1.3 64.1 + - - +
585B ASN 4.2 0.2 - - - -
586B ASN* 4.6 9.0 - - - -
587B GLU* 3.3 12.8 - - - +
588B TRP* 3.2 45.3 - - + -
611B ALA* 3.1 3.7 - - - +
612B THR* 2.6 53.7 + - + +
614B LYS* 3.8 41.7 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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