Contacts of the strand formed by residues 525 - 529 (chain A) in PDB entry 4KSP
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 ALA 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A ILE* 5.1 7.0 - - + -
481A VAL* 4.4 8.5 - - + -
482A LYS 3.1 10.8 - - - +
483A MET* 3.8 24.0 - - + -
497A PHE* 3.6 3.2 - - - -
518A TYR* 3.2 7.8 - - - +
519A SER* 2.8 46.6 + - - +
523A GLN 4.3 2.5 - - - +
524A LEU* 1.3 76.2 - - - +
526A ILE* 1.3 65.1 + - - +
527A VAL* 5.1 0.7 - - + -
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Residues in contact with ILE 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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481A VAL* 3.5 2.3 - - - -
482A LYS* 2.8 43.7 + - + +
497A PHE* 3.5 22.7 - - + -
500A GLU* 3.8 34.1 - - + +
501A VAL* 3.4 26.5 - - + +
504A LEU* 4.0 14.6 - - + -
515A PHE* 4.1 8.7 - - + -
517A GLY 3.7 8.7 - - - +
518A TYR* 4.8 0.2 - - + -
525A ALA* 1.3 77.2 - - - +
527A VAL* 1.3 66.1 + - - +
528A THR* 4.4 0.7 - - + -
901A 1SU 3.0 27.7 - - - -
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Residues in contact with VAL 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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451A ILE* 3.6 26.2 - - + -
456A ILE* 3.8 19.5 - - + -
475A TRP* 4.6 9.4 - - + -
479A VAL* 3.6 37.9 - - + -
480A ALA 3.3 4.9 - - - +
481A VAL* 4.5 8.3 - - + -
515A PHE* 3.9 2.6 - - - -
516A MET* 3.0 29.9 + - + -
517A GLY 2.8 19.7 + - - +
518A TYR* 4.9 2.2 - - - +
525A ALA 5.1 1.6 - - - -
526A ILE* 1.3 76.8 - - - +
528A THR* 1.3 67.8 + - - +
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Residues in contact with THR 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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479A VAL* 3.4 8.5 - - - +
480A ALA* 2.9 36.6 + - - +
504A LEU* 5.0 5.6 - - + -
513A LEU* 3.7 18.5 - - + +
514A LEU 3.4 14.6 - - - +
515A PHE* 4.5 7.2 - - - -
516A MET* 3.8 7.6 - - - +
526A ILE* 4.4 3.1 - - + -
527A VAL* 1.3 79.5 - - - +
529A GLN* 1.3 75.1 + - - +
901A 1SU 3.6 40.1 - - + -
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Residues in contact with GLN 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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478A ASP 4.7 1.3 - - - -
480A ALA* 4.0 0.2 - - - +
512A ILE 4.1 0.5 - - - +
513A LEU* 3.7 20.0 - - + +
514A LEU* 2.8 46.0 + - + +
516A MET* 3.7 13.2 - - - -
528A THR* 1.3 88.4 + - - +
530A TRP* 1.3 62.2 + - - +
531A CYS* 3.7 5.7 + - - -
584A HIS* 4.4 11.9 + - - -
590A LYS* 3.7 32.9 + - - +
901A 1SU 3.6 11.1 - - - -
510B VAL* 4.1 35.7 - - + +
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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
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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