Contacts of the strand formed by residues 587 - 594 (chain A) in PDB entry 2P0C
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 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583A ASP 4.6 0.4 - - - +
584A ARG* 2.9 41.8 + - - +
585A ASN* 4.5 1.9 - - - -
586A LEU* 1.3 80.1 - - - +
588A ILE* 1.3 74.7 + - - +
589A LEU* 4.1 20.4 - - + -
605A ASN 3.6 13.7 - - - +
606A LEU* 4.5 10.8 - - + -
616A VAL* 3.9 23.6 - - + -
618A VAL* 4.1 11.7 - - + -
656A CYS* 3.6 32.5 - - + -
668A MET* 4.6 4.0 - - + -
670A ILE* 3.7 19.1 - - + -
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Residues in contact with ILE 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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584A ARG* 5.6 0.4 - - - +
585A ASN 5.4 5.4 - - - +
586A LEU 5.5 2.5 - - - +
587A LEU* 1.3 83.9 - - - +
589A LEU* 1.3 72.0 + - - +
604A GLY* 3.1 7.3 - - - -
605A ASN* 3.0 52.2 + - + +
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Residues in contact with LEU 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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584A ARG* 3.4 30.8 - - - +
587A LEU* 4.1 12.8 + - + -
588A ILE* 1.3 83.0 - - - +
590A GLY* 1.3 58.8 + - - +
602A MET* 3.9 31.6 - - + -
603A GLU 3.9 4.3 - - - +
604A GLY* 4.9 0.2 - - - -
618A VAL* 3.7 38.8 - - + -
668A MET* 4.0 15.0 - - - -
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Residues in contact with GLY 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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588A ILE 4.1 0.2 + - - -
589A LEU* 1.3 75.8 - - - +
591A LYS* 1.3 67.5 + - - +
592A ILE* 3.9 1.6 + - - +
602A MET* 4.1 12.6 - - - +
603A GLU* 2.9 23.5 + - - -
604A GLY* 4.5 0.8 - - - -
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Residues in contact with LYS 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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590A GLY* 1.3 73.5 - - - -
592A ILE* 1.3 66.8 + - - +
593A LEU* 6.1 0.2 - - + -
602A MET* 3.3 4.1 - - - -
603A GLU* 2.8 55.1 + - + +
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Residues in contact with ILE 592 (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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590A GLY 5.2 1.8 - - - +
591A LYS* 1.3 78.7 - - - +
593A LEU* 1.3 65.6 + - - +
594A GLY* 3.4 21.3 - - - +
595A GLU* 3.4 27.4 - - - +
600A SER* 4.7 9.9 - - - +
601A VAL 3.7 6.7 - - - +
602A MET* 4.0 20.6 - - + -
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Residues in contact with LEU 593 (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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1A ANP 3.6 36.5 + - - +
591A LYS* 3.6 0.6 + - + -
592A ILE* 1.3 76.1 - - - +
594A GLY* 1.3 55.3 + - - +
601A VAL* 2.7 33.5 + - + +
602A MET 3.8 13.2 - - - +
603A GLU* 3.7 24.7 - - + +
617A ALA* 4.0 7.9 - - + -
673A PHE* 3.8 35.0 - - + -
805B GLN* 4.5 5.0 - - - +
808B GLU* 5.5 2.4 - - - +
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Residues in contact with GLY 594 (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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1A ANP 3.6 16.6 - - - -
592A ILE* 3.4 15.3 - - - +
593A LEU* 1.3 79.6 - - - +
595A GLU* 1.3 60.8 + - - +
600A SER* 4.1 0.5 - - - -
601A VAL* 3.2 31.4 + - - +
805B GLN* 4.0 12.8 - - - -
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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