Contacts of the strand formed by residues 509 - 513 (chain A) in PDB entry 1KEK
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 THR 509 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A ASP 2.8 14.6 + - - +
486A TYR* 3.4 25.0 - - + +
487A VAL 2.8 26.7 + - - +
504A ILE* 3.8 4.1 - - - +
507A GLY 4.9 0.7 - - - +
508A GLY* 1.3 76.2 - - - -
510A PHE* 1.3 61.7 + - - +
511A VAL* 4.5 1.4 - - - +
540A LYS* 3.4 36.2 + - + +
542A TYR* 4.3 12.1 - - + -
570A LEU* 4.2 18.5 + - + +
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Residues in contact with PHE 510 (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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487A VAL* 3.1 17.9 - - + +
489A CYS* 4.0 20.6 - - + -
495A VAL* 4.9 9.2 - - + -
500A ILE* 4.2 10.1 - - + -
501A LEU* 3.5 38.8 - - + -
504A ILE* 4.3 6.3 - - + -
508A GLY 4.2 0.6 + - - -
509A THR* 1.3 73.9 - - - +
511A VAL* 1.3 72.9 + - - +
512A LEU* 4.2 17.7 - - + -
530A ILE* 4.4 6.7 - - + -
534A ILE* 3.9 18.4 - - + -
539A LEU* 4.6 7.2 - - + -
540A LYS 3.0 10.0 + - - +
541A PHE* 3.4 37.4 - + + -
542A TYR* 2.8 26.3 + - - +
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A TYR* 3.2 40.2 - - + +
487A VAL 2.9 5.3 + - - +
488A ALA* 3.3 3.6 - - + -
489A CYS 2.8 27.4 + - - +
509A THR* 4.5 2.5 - - - +
510A PHE* 1.3 79.2 - - - +
512A LEU* 1.3 64.6 + - - +
542A TYR* 3.2 14.8 - - + +
544A ILE* 4.5 5.8 - - + -
563A MET* 3.4 29.8 - - + -
566A ALA* 4.1 13.7 - - + -
570A LEU* 4.4 15.3 - - + -
613A LEU* 5.2 0.7 - - + -
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Residues in contact with LEU 512 (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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489A CYS* 3.6 27.4 - - + +
492A PRO* 4.3 6.5 - - + -
495A VAL* 4.2 11.9 - - + -
510A PHE* 4.1 6.5 - - + -
511A VAL* 1.3 79.4 - - - +
513A ASN* 1.3 74.9 + - - +
514A SER* 3.8 10.3 - - - +
516A TRP* 4.0 9.9 - - + -
522A MET* 4.5 0.4 - - - -
526A LEU* 3.9 27.8 - - + -
541A PHE* 4.0 17.9 - - + -
542A TYR 2.7 12.5 + - - +
543A ASN* 3.4 22.9 - - - +
544A ILE* 2.9 28.9 + - - +
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Residues in contact with ASN 513 (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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489A CYS 3.0 16.5 + - - +
490A HIS* 2.9 23.3 - - - +
492A PRO* 3.1 30.4 - - - +
512A LEU* 1.3 73.7 - - - +
514A SER* 1.3 69.7 + - - +
544A ILE* 3.3 5.4 - - - -
545A ASP* 4.2 1.2 + - - +
546A ALA* 3.2 36.8 - - - +
547A VAL* 4.0 13.8 - - - +
559A ILE* 3.8 12.3 - - - +
563A MET* 4.0 16.8 - - - -
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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