Contacts of the strand formed by residues 583 - 591 (chain A) in PDB entry 5BPW
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 LEU 583 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A ASN* 3.4 11.9 + - - +
578A ASN* 2.9 29.2 + - + -
581A SER* 3.7 22.4 - - - +
582A ASN* 1.3 90.9 - - - +
584A HIS* 1.3 68.5 - - - +
585A TYR* 3.5 36.3 - - + +
602A ARG* 3.9 23.3 - - + +
603A ARG 3.5 7.9 - - - +
604A HIS* 3.7 31.2 - - + +
605A THR* 4.1 3.1 - - - +
611A VAL* 3.9 14.6 - - + -
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Residues in contact with HIS 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A CYS* 3.6 33.3 - - - -
211A SER* 3.0 19.1 + - - -
216A SER* 2.9 28.8 + - - -
218A SER* 3.1 30.5 + - - +
233A TYR* 3.9 16.8 - - + +
235A GLN* 4.4 10.8 - - - -
575A LEU* 4.8 1.5 - - + +
576A TRP 3.6 2.2 - - - -
577A ASN* 4.4 4.0 - - - -
583A LEU* 1.3 75.9 + - - +
585A TYR* 1.3 64.2 + - - +
601A LEU* 5.6 1.2 - - + +
602A ARG* 3.0 9.5 - - - +
603A ARG 2.9 34.0 + - - +
605A THR* 3.9 16.4 - - - -
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Residues in contact with TYR 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 6.0 0.2 - - - -
575A LEU* 3.4 11.2 - - - +
576A TRP* 2.8 46.9 + + + +
578A ASN* 3.9 27.9 - - + -
581A SER* 4.7 2.9 + - - -
583A LEU* 3.5 19.4 - - + +
584A HIS* 1.3 75.6 - - - +
586A LEU* 1.3 60.0 + - - +
587A LEU 4.2 0.4 - - - -
600A ILE* 3.8 14.4 - - + -
601A LEU 3.4 2.7 - - - -
602A ARG* 3.0 48.2 + - + -
643A PHE* 3.4 39.0 - + + -
646A ASP 5.2 0.8 + - - -
671A LEU* 4.4 13.0 - - + +
675A TYR* 4.0 16.0 - + - -
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Residues in contact with LEU 586 (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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220A VAL* 3.6 21.1 - - + -
233A TYR* 3.9 21.5 - - + -
556A LEU* 3.6 33.2 - - + -
573A PRO* 3.9 11.0 - - + -
574A PHE 3.3 18.4 - - - +
575A LEU* 4.0 11.0 - - + -
584A HIS 4.2 0.2 - - - -
585A TYR* 1.3 74.0 - - - +
587A LEU* 1.3 71.9 + - - +
588A PHE* 3.9 14.6 - - + -
599A CYS 3.8 0.5 - - - +
600A ILE* 3.6 4.0 - - - +
601A LEU* 2.8 55.5 + - + +
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Residues in contact with LEU 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PHE* 3.6 14.0 - - + -
573A PRO* 3.3 4.3 - - - +
574A PHE* 2.9 47.7 + - + +
585A TYR* 5.6 0.2 - - + -
586A LEU* 1.3 71.1 - - - +
588A PHE* 1.3 64.6 + - - +
598A MET* 4.0 11.2 - - + -
599A CYS 3.5 2.9 - - - +
600A ILE* 3.6 31.9 - - + -
641A ALA* 4.0 20.0 - - + +
642A GLN 4.0 1.1 - - - +
643A PHE* 3.5 42.2 - - + -
649A VAL* 3.8 20.6 - - + -
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Residues in contact with PHE 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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556A LEU* 3.6 36.1 - - + -
557A TYR* 3.9 14.6 - + + -
572A PHE* 3.6 9.8 - - - -
573A PRO* 3.9 20.6 - - + -
586A LEU* 3.9 15.9 - - + -
587A LEU* 1.3 78.3 - - - +
589A THR* 1.3 62.5 + - - +
590A ILE* 3.4 31.6 - - + -
598A MET* 3.7 2.5 - - - +
599A CYS* 2.8 61.8 + - + +
601A LEU* 4.0 20.2 - - + -
615A LEU* 4.4 4.0 - - + -
693A LEU* 4.0 15.9 - - + -
700A ILE* 6.4 0.7 - - + -
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Residues in contact with THR 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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557A TYR* 3.7 6.1 - - - -
561A ARG* 2.6 46.1 + - - +
572A PHE* 3.5 25.1 - - + -
573A PRO* 5.7 0.2 - - - +
588A PHE* 1.3 77.5 - - - +
590A ILE* 1.3 61.9 + - - +
596A TYR* 3.8 19.1 - - + +
597A LYS 3.2 10.3 - - - +
598A MET* 4.1 3.1 - - + -
638A CYS* 3.7 41.0 + - + +
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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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556A LEU 4.5 1.3 - - - +
557A TYR* 4.1 16.8 - - + -
561A ARG* 3.6 4.7 - - - +
588A PHE* 3.4 28.3 - - + -
589A THR* 1.3 78.3 - - - +
591A LEU* 1.3 61.6 + - - +
592A GLU* 3.8 1.0 + - + +
596A TYR* 4.4 1.3 - - - -
597A LYS* 2.9 45.1 + - + +
599A CYS* 3.9 22.0 - - - -
693A LEU* 5.1 0.9 - - + -
694A ASP* 4.4 18.8 - - + -
697A CYS* 4.3 19.5 - - - -
700A ILE* 4.0 23.1 - - + -
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Residues in contact with LEU 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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557A TYR* 6.0 0.4 - - - +
559A ASP* 3.3 34.2 + - + +
561A ARG* 4.0 7.5 - - + +
590A ILE* 1.3 74.9 - - - +
592A GLU* 1.3 61.4 + - - +
594A SER* 3.9 24.9 - - - +
595A LEU 3.3 8.7 - - - +
596A TYR* 3.4 36.3 - - + +
694A ASP* 6.1 0.4 - - - +
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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