Contacts of the strand formed by residues 293 - 297 (chain A) in PDB entry 1KYZ
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 VAL 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A VAL* 3.5 8.3 - - + +
264A MET* 3.4 28.9 - - + -
280A LEU* 4.7 1.3 - - + -
283A CYS* 4.1 15.9 - - + -
287A LEU* 3.9 7.6 - - + -
292A LYS* 1.3 82.6 - - - +
294A ILE* 1.3 65.9 + - - +
295A VAL* 3.6 20.0 + - + -
344A PHE* 3.5 31.2 - - + -
360A GLU* 3.0 7.4 - - - +
361A PHE* 2.7 44.2 + - + -
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Residues in contact with ILE 294 (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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195A TYR* 3.7 35.0 - - + +
197A GLY 4.8 5.6 - - - +
198A PHE* 3.5 28.3 - - + -
201A LEU* 5.1 2.2 - - + -
204A LEU* 4.6 10.1 - - + -
261A ALA* 5.0 3.6 - - + -
262A VAL 2.7 18.1 + - - +
263A PHE* 3.4 26.6 - - + -
264A MET* 3.1 24.4 + - - +
292A LYS* 4.3 16.4 - - + +
293A VAL* 1.3 74.2 - - - +
295A VAL* 1.3 61.8 + - - +
296A ALA 3.9 0.5 + - - -
358A ILE* 3.9 15.9 - - + -
359A MET 3.7 2.9 - - - +
360A GLU* 4.6 1.6 - - + +
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A MET* 4.8 11.7 - - + -
265A LYS 4.8 2.0 - - - +
267A ILE 6.2 0.2 - - - -
268A CYS* 4.3 17.3 - - - -
293A VAL* 3.6 23.1 - - + -
294A ILE* 1.3 71.2 - - - +
296A ALA* 1.3 62.4 + - - +
297A GLU* 3.7 24.0 - - + -
335A PHE* 4.4 4.7 - - + -
357A TYR 3.3 4.2 - - - +
358A ILE* 3.4 3.4 - - - -
359A MET* 2.7 58.5 + - + +
361A PHE* 3.5 31.0 - - + -
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Residues in contact with ALA 296 (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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191A ILE* 4.2 6.3 - - + -
263A PHE* 4.2 5.2 - - + -
265A LYS* 3.6 33.1 - - + +
266A TRP* 2.9 32.7 + - - -
294A ILE 3.9 0.8 + - - -
295A VAL* 1.3 72.8 - - - +
297A GLU* 1.3 63.9 + - - +
356A THR* 3.9 11.9 - - + -
357A TYR 3.4 6.1 - - - -
358A ILE* 3.7 20.9 - - + -
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Residues in contact with GLU 297 (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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266A TRP* 3.2 21.9 - - - +
267A ILE 3.1 23.4 + - - -
268A CYS* 3.2 5.4 + - + +
269A HIS* 3.2 37.7 + - - +
295A VAL* 3.7 20.1 + - + -
296A ALA* 1.3 84.1 - - - +
298A CYS* 1.3 66.3 + - - +
299A ILE* 4.2 1.6 - - - +
329A GLU* 4.6 1.0 - - - +
335A PHE* 3.6 27.8 - - + -
356A THR* 3.7 6.8 - - - +
357A TYR* 2.8 34.2 + - - +
359A MET* 4.2 3.9 - - + +
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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