Contacts of the strand formed by residues 290 - 294 (chain V) 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 PHE 290 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153V HIS* 3.6 27.6 - + + -
158V GLU* 3.4 46.9 - - + -
161V LYS* 3.8 15.3 - - + -
162V LEU* 3.7 23.6 - - + -
199V PHE* 5.4 1.3 - + - -
263V PRO* 2.9 18.4 + - + +
264V ILE* 3.6 27.6 - - + -
265V ILE* 3.0 30.0 + - - +
288V GLY 4.2 0.6 + - - -
289V LEU* 1.3 76.0 - - - +
291V LEU* 1.3 58.5 + - - +
324V ASP* 3.3 9.6 - - + +
66W LEU* 3.6 37.9 - - + +
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Residues in contact with LEU 291 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152V PRO* 4.1 12.3 - - + -
264V ILE* 4.9 0.9 - - - -
265V ILE* 3.5 16.8 - - + +
267V HIS* 4.0 13.7 - - + +
277V ASN* 4.4 5.6 - - - +
280V LEU* 3.7 27.8 - - + -
281V ALA* 3.8 33.4 - - + +
284V CYS* 4.0 8.1 - - - -
290V PHE* 1.3 74.4 - - - +
292V HIS* 1.3 64.1 + - - +
293V ILE* 3.7 21.9 + - + -
322V GLY 3.8 11.0 - - - +
323V GLY* 3.8 0.7 - - - -
324V ASP* 2.8 37.7 + - - +
325V HIS* 3.3 3.9 + - - -
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Residues in contact with HIS 292 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201V KCX 3.7 8.0 - - - -
239V TYR* 3.1 42.3 - + + -
264V ILE* 4.2 4.3 - - + +
265V ILE 2.8 17.2 + - - +
266V MET* 3.0 16.4 - - + +
267V HIS 2.9 26.3 + - - -
290V PHE 4.1 0.6 - - - -
291V LEU* 1.3 72.2 - - - +
293V ILE* 1.3 67.0 + - - +
294V HIS* 4.1 1.7 + - - -
325V HIS* 3.1 35.3 + - + +
327V HIS* 2.9 41.6 + + - -
377V VAL* 3.7 17.7 - - + -
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Residues in contact with ILE 293 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267V HIS* 3.4 9.2 - - + +
269V TYR* 3.1 39.3 - - + -
277V ASN* 3.1 29.6 - - - +
291V LEU* 3.7 24.0 - - + -
292V HIS* 1.3 79.6 + - - +
294V HIS* 1.3 60.0 + - - +
318V LEU* 3.7 15.7 - - + -
322V GLY 3.9 2.5 - - - +
323V GLY* 3.7 19.3 - - - -
325V HIS 2.9 24.0 + - - +
326V LEU* 3.5 6.6 - - + +
327V HIS* 3.4 28.4 + - - -
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Residues in contact with HIS 294 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O ASN* 3.2 23.8 - - - -
201V KCX 3.3 28.7 - - - -
204V GLU* 3.1 23.1 + - + +
266V MET* 4.0 10.5 - - + -
267V HIS 3.0 6.5 + - - -
268V ASP* 3.4 19.2 - - - +
269V TYR* 3.3 26.5 + - - -
292V HIS* 3.9 2.0 + - - +
293V ILE* 1.3 73.9 - - - +
295V ARG* 1.3 60.3 + - - +
296V ALA* 2.8 35.9 + - + +
327V HIS* 3.8 16.2 - + - +
1476V CAP 2.8 30.3 + - - -
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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