Contacts of the strand formed by residues 293 - 297 (chain A) in PDB entry 1KY5
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A GLY 4.7 2.0 - - - +
269A ASN* 3.4 15.0 - - - +
271A PHE* 4.4 7.9 - - + -
289A MET* 4.0 30.7 - - + -
290A LYS* 3.3 18.3 + - - +
291A ASP 3.1 3.7 + - - -
292A ASP* 1.3 76.7 - - - +
294A ILE* 1.3 60.6 + - - +
295A VAL 3.8 0.9 + - - -
334A ARG 3.3 3.0 + - - -
335A ILE* 3.8 7.2 - - + +
336A ILE* 2.9 25.8 + - - +
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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
----------------------------------------------------------
202A ILE* 4.9 4.7 - - + -
206A THR* 3.8 19.1 - - + +
208A VAL* 3.6 43.1 - - + -
213A LYS* 6.2 0.2 - - + -
269A ASN 2.7 13.3 + - - +
270A ILE* 3.2 19.3 - - + +
271A PHE* 2.8 31.9 + - - +
292A ASP 4.1 8.7 - - - +
293A ALA* 1.3 75.2 - - - +
295A VAL* 1.3 58.6 + - - +
296A CYS* 5.0 2.5 - - - +
336A ILE* 3.5 17.7 - - + +
338A LEU* 3.7 31.9 - - + -
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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
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271A PHE* 3.6 9.9 - - + +
281A ILE* 4.2 14.1 - - + -
286A PHE* 4.0 12.1 - - + -
289A MET* 3.8 34.5 - - + -
293A ALA 4.6 1.6 - - - +
294A ILE* 1.3 77.9 - - - +
296A CYS* 1.3 64.0 + - - +
305A ILE* 3.3 37.9 - - + -
335A ILE* 4.1 8.3 - - + -
336A ILE 2.9 8.9 + - - +
337A LEU* 3.3 14.0 - - + +
338A LEU* 3.1 25.3 + - - +
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Residues in contact with CYS 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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202A ILE* 4.0 23.8 - - - -
270A ILE* 5.0 0.7 - - - -
271A PHE 2.9 19.6 + - - +
272A VAL* 3.2 28.7 - - - -
273A THR* 3.2 14.9 + - - +
294A ILE* 5.0 4.0 - - - -
295A VAL* 1.3 77.4 - - - +
297A ASN* 1.3 61.1 + - - +
305A ILE* 3.6 9.7 - - - +
338A LEU* 3.9 17.7 - - + +
344A VAL* 3.8 30.3 - - + -
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Residues in contact with ASN 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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272A VAL* 5.2 0.2 - - - -
273A THR* 2.9 24.2 + - - +
296A CYS* 1.3 78.2 - - - +
298A ILE* 1.3 58.3 + - - +
299A GLY 2.8 29.5 + - - -
301A PHE 3.1 22.2 + - - -
302A ASP* 4.2 0.6 - - - +
304A GLU* 3.1 16.3 - - - +
305A ILE* 3.7 13.4 - - + +
341A GLY 2.6 29.8 + - - +
342A ARG 3.1 14.3 + - - +
343A LEU* 3.4 1.2 - - - +
344A VAL* 3.1 24.2 + - - -
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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