Contacts of the strand formed by residues 587 - 591 (chain A) in PDB entry 1BAK
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 ARG 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A PHE* 3.0 52.7 + - + +
585A PRO* 5.2 0.4 - - + -
586A ASN* 1.3 86.2 - - + +
588A LEU* 1.3 70.7 + - - +
589A GLU* 4.3 9.2 - - - +
600A LEU* 3.4 35.3 - - - +
601A LEU 3.2 11.7 - - - +
602A THR* 3.8 9.5 - - + +
603A MET* 4.5 3.1 - - - +
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Residues in contact with LEU 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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565A MET* 6.1 0.7 - - + -
581A PHE* 3.9 17.0 - - + -
582A TYR 2.9 26.5 - - - +
583A LEU* 4.5 2.7 - - - -
584A PHE* 4.0 2.7 - - - +
587A ARG* 1.3 83.4 - - - +
589A GLU* 1.3 83.0 + - - +
590A TRP* 4.0 4.7 + - + +
601A LEU* 2.8 46.7 + - + +
602A THR 3.9 17.3 - - - +
603A MET* 6.0 1.1 - - + -
606A ILE* 5.6 4.5 - - + -
643A TRP* 5.1 2.2 - - + -
647A LEU* 5.3 12.8 - - + -
651A TYR* 5.3 4.5 - - + +
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Residues in contact with GLU 589 (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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581A PHE* 3.1 5.2 - - - -
582A TYR* 2.8 52.2 + - + +
584A PHE* 5.4 12.7 - - - -
587A ARG* 4.3 5.7 - - - +
588A LEU* 1.3 82.6 + - - +
590A TRP* 1.3 62.7 + - - +
591A ARG* 4.1 8.1 - - + +
599A SER* 3.9 8.7 - - - +
600A LEU* 2.6 36.0 - - + +
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Residues in contact with TRP 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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567A LYS* 5.1 9.4 - - - -
568A MET* 5.8 7.6 - - + -
579A ARG* 5.5 14.8 - - - -
580A TYR 3.7 0.2 - - - -
581A PHE* 2.9 43.7 - + + -
588A LEU* 4.1 9.6 - - + -
589A GLU* 1.3 74.7 - - - +
591A ARG* 1.3 58.7 + - - +
596A ALA* 5.3 8.1 - - + -
598A GLN 3.8 10.1 - - - -
599A SER* 2.7 82.9 + - - -
600A LEU* 3.3 7.0 + - - +
601A LEU* 4.4 16.5 - - + +
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Residues in contact with ARG 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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579A ARG* 3.6 12.9 - - - +
580A TYR* 2.7 36.9 + - + +
582A TYR* 5.5 7.4 - - + -
589A GLU* 4.1 8.5 - - + -
590A TRP* 1.3 74.1 - - - +
592A GLY* 1.3 61.3 + - - +
599A SER* 3.3 24.3 + - - +
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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