Contacts of the strand formed by residues 264 - 268 (chain K) in PDB entry 1UW9
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 264 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K PHE* 4.3 8.7 - - + -
237K GLY* 4.2 9.4 - - - -
238K HIS 3.0 53.1 + - - +
239K TYR* 3.6 30.7 - - + -
240K LEU* 3.3 8.2 + - - +
262K VAL* 3.6 5.3 - - - +
263K PRO* 1.3 82.2 - - + +
265K ILE* 1.3 78.8 + - - +
289K LEU* 4.1 2.3 - - - +
290K PHE* 3.5 30.3 - - + +
291K LEU 4.9 0.2 - - - -
292K HIS* 4.1 9.2 - - + +
325K HIS* 3.9 19.1 - - + +
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Residues in contact with ILE 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218K PHE* 5.4 1.1 - - + -
239K TYR* 4.3 2.2 - - - -
240K LEU* 3.2 19.5 - - + +
242K ALA* 4.2 8.1 - - + -
253K ARG 5.1 0.9 - - - +
254K ALA* 4.0 16.8 - - + -
257K ALA* 3.4 32.8 - - + -
264K ILE* 1.3 84.3 - - - +
266K MET* 1.3 62.5 + - - +
280K LEU* 3.9 29.8 - - + -
284K CYS* 3.7 22.9 - - - -
289K LEU* 4.3 9.9 - - + -
290K PHE 3.1 13.0 + - - +
291K LEU* 3.5 6.0 - - + -
292K HIS 2.8 24.1 + - - -
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Residues in contact with MET 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K KCX 3.7 26.2 - - - +
202K ASP* 3.3 26.5 - - - +
204K GLU* 4.0 4.9 - - - -
239K TYR* 3.6 28.9 - - + +
240K LEU 2.9 7.3 + - - -
241K ASN* 3.4 33.0 + - - +
242K ALA* 2.9 29.5 + - - +
265K ILE* 1.3 75.0 - - - +
267K HIS* 1.3 63.3 + - - +
268K ASP* 3.9 17.0 - - - +
291K LEU* 4.2 3.1 - - - +
292K HIS* 3.0 17.5 - - + +
294K HIS* 4.0 13.2 - - + -
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Residues in contact with HIS 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E THR* 5.0 2.5 - - - -
243K THR* 3.5 23.1 + - - -
244K ALA 5.3 0.2 - - - -
250K MET* 3.9 19.4 - - - -
266K MET* 1.3 77.1 - - - +
268K ASP* 1.3 78.1 + - - +
269K TYR* 3.3 14.5 + - - -
272K GLY* 4.0 14.6 - - - -
273K GLY 4.0 4.4 + - - -
276K ALA* 4.5 2.5 - - + -
277K ASN* 2.8 54.9 + - + +
280K LEU* 3.6 23.8 - - + +
291K LEU* 4.0 5.6 - - + +
292K HIS 2.9 5.5 + - - -
293K ILE* 3.5 6.7 - - + +
294K HIS* 3.0 21.8 + - - -
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Residues in contact with ASP 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E THR* 3.2 16.7 - - - +
204K GLU* 2.7 33.5 - - - +
241K ASN* 4.2 0.2 - - - +
243K THR* 2.9 29.8 + - + +
266K MET* 3.9 6.8 - - - +
267K HIS* 1.3 72.1 + - - +
269K TYR* 1.3 59.5 + - - +
270K LEU 3.2 2.9 - - - -
271K THR* 3.1 17.9 - - - +
272K GLY* 2.8 27.7 + - - -
294K HIS* 3.4 27.5 - - - +
296K ALA* 4.4 6.5 - - + -
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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