Contacts of the strand formed by residues 523 - 529 (chain A) in PDB entry 2CKH
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 ILE 523 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A PRO* 3.8 31.9 - - + -
489A SER 3.0 4.2 + - - -
490A VAL* 3.3 19.2 - - + +
491A HIS 3.1 23.9 + - - -
521A VAL* 3.3 5.5 - - - +
522A ASP* 1.3 82.9 - - - +
524A LEU* 1.3 81.0 + - - +
525A LEU* 4.0 12.1 - - + -
538A VAL* 3.5 21.5 - - + -
539A VAL 3.2 3.6 - - - +
540A ASP* 4.1 15.9 - - - +
542A ARG* 3.9 9.0 - - - +
613A ILE* 4.1 23.6 - - + +
614A THR* 4.5 2.2 - - - -
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Residues in contact with LEU 524 (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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491A HIS* 3.4 14.6 - - + +
493A PHE* 4.1 19.3 - - + -
518A VAL* 3.6 35.2 - - + +
521A VAL* 3.5 26.5 - - + -
523A ILE* 1.3 84.0 - - - +
525A LEU* 1.3 61.1 + - - +
526A VAL* 3.9 2.0 + - + -
538A VAL* 3.5 5.7 - - - -
539A VAL* 2.7 61.8 + - + -
541A PHE* 3.9 13.0 - - + -
566A TYR* 5.7 1.1 - - + -
567A LEU* 4.4 11.9 - - + -
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Residues in contact with LEU 525 (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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475A MET* 3.8 28.3 - - - -
478A LEU* 4.3 9.9 - - + -
490A VAL* 3.7 15.5 - - + -
491A HIS 3.0 8.3 + - - -
492A ALA* 3.7 18.1 - - + -
493A PHE* 3.2 27.0 + - - -
523A ILE* 4.0 13.5 - - + -
524A LEU* 1.3 78.7 - - - +
526A VAL* 1.3 63.0 + - - +
527A PRO* 3.4 4.9 - - - +
536A LEU* 4.7 3.6 - - + -
537A ALA 4.1 0.2 - - - -
538A VAL* 4.1 18.4 - - + -
610A ALA* 3.9 22.7 - - + -
613A ILE* 5.2 2.0 - - + -
614A THR* 4.0 20.0 - - + -
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Residues in contact with VAL 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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493A PHE* 4.3 14.6 - - + -
497A PHE* 3.9 27.1 - - + -
498A PHE* 4.1 19.1 - - + -
524A LEU* 4.7 7.9 - - + +
525A LEU* 1.3 77.2 - - - +
527A PRO* 1.3 61.1 - - + +
528A ILE* 3.3 10.0 - - + +
536A LEU* 2.9 6.4 - - - +
537A ALA* 2.7 51.4 + - + +
539A VAL* 5.0 4.9 - - + -
563A LEU* 4.1 28.5 - - + -
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Residues in contact with PRO 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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471A ILE* 4.1 20.2 - - + -
472A ASN* 5.3 0.2 - - - +
475A MET* 4.2 19.1 - - + -
493A PHE* 3.4 28.0 - - + +
494A ASN 3.8 15.4 - - - +
495A THR* 3.4 29.5 - - + +
498A PHE* 4.1 5.5 - - - +
525A LEU* 3.4 6.1 - - + +
526A VAL* 1.3 86.5 - - + +
528A ILE* 1.3 60.9 + - - +
534A TRP* 5.4 3.1 - - + -
535A CYS 3.8 4.9 - - - +
536A LEU* 3.7 8.0 - - + -
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Residues in contact with ILE 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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495A THR 5.4 0.2 - - - -
498A PHE* 3.5 51.4 - - + -
526A VAL* 3.3 28.0 - - + +
527A PRO* 1.3 74.2 - - - +
529A HIS* 1.3 71.1 + - - +
530A LEU* 4.0 18.6 - - + +
533A HIS 3.9 0.2 - - - +
534A TRP* 3.4 14.1 - - - -
535A CYS* 2.8 41.9 + - + +
536A LEU* 3.7 6.1 - - - -
537A ALA* 3.4 28.9 - - + +
548A TYR* 4.4 11.7 - - + -
556A ASN* 5.5 0.9 - - - +
559A ALA* 5.4 0.7 - - + -
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Residues in contact with HIS 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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495A THR 4.9 4.6 + - - +
498A PHE* 5.1 0.4 - - - -
499A THR* 3.2 34.7 + - - +
527A PRO 4.3 0.8 + - - -
528A ILE* 1.3 75.0 - - - +
530A LEU* 1.3 58.2 + - - +
531A GLY* 3.0 33.7 + - - -
533A HIS 3.7 8.1 - - - -
534A TRP* 4.0 15.3 - + + -
89B GLN* 3.3 58.7 + - + +
90B THR 3.2 21.7 + - - -
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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