Contacts of the strand formed by residues 289 - 293 (chain A) in PDB entry 1UWV
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 ARG 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLU 3.5 1.9 + - - +
288A ASP* 1.3 72.1 - - - +
290A VAL* 1.3 60.4 + - - +
309A ALA* 5.4 0.7 - - + -
310A SER* 3.3 39.3 + - - +
312A VAL* 3.7 25.9 - - + +
352A TRP* 2.8 32.5 + - - +
354A LYS* 4.0 8.9 - - - +
355A ASN* 3.5 28.7 - - - +
356A GLY 3.2 27.3 + - - +
357A PHE* 3.7 11.5 - - + -
358A ASP* 2.9 39.6 + - - +
359A LYS 3.5 5.4 + - - -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.4 4.9 - - + -
284A VAL* 4.3 9.9 - - + -
288A ASP* 4.1 11.9 - - + -
289A ARG* 1.3 76.9 - - - +
291A LEU* 1.3 68.2 + - - +
304A LEU* 3.8 33.0 - - + -
308A ALA* 3.7 24.0 - - + -
310A SER 2.9 9.1 + - - +
311A VAL* 3.3 9.6 - - + +
312A VAL 2.9 26.7 + - - +
357A PHE* 3.5 6.6 - - - -
359A LYS* 3.4 24.5 - - + +
361A LEU 5.1 0.2 - - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 1.3 78.3 - - - +
292A ASP* 1.3 60.6 + - - +
293A LEU* 3.8 37.7 - - + -
312A VAL* 3.4 11.0 - - + +
314A VAL* 4.1 8.3 - - + -
347A VAL* 6.4 0.2 - - + -
352A TRP* 3.9 25.8 - - + -
357A PHE* 3.4 28.0 - - + -
359A LYS 2.9 6.9 + - - +
360A VAL* 3.2 15.8 - - + -
361A LEU 2.9 31.0 + - - +
379A LEU* 3.8 28.7 - - + -
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Residues in contact with ASP 292 (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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291A LEU* 1.3 73.1 - - - +
293A LEU* 1.3 70.9 + - - +
294A PHE 4.7 0.2 - - - +
295A CYS* 3.4 14.3 - - - +
300A PHE* 3.6 9.5 + - - +
301A THR* 2.3 48.4 + - + +
304A LEU* 4.2 13.9 - - + -
311A VAL* 4.9 0.7 - - + -
312A VAL 2.7 14.1 + - - +
313A GLY* 3.4 1.0 - - - -
314A VAL* 3.0 26.5 + - - +
361A LEU* 3.3 24.8 - - - +
363A ASP* 5.7 0.5 - - - +
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Residues in contact with LEU 293 (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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291A LEU* 3.8 37.2 - - + -
292A ASP* 1.3 76.5 - - - +
294A PHE* 1.3 83.9 + - + +
314A VAL* 4.0 10.3 - - + -
343A LEU* 4.0 24.0 - - + -
347A VAL* 5.1 3.4 - - + -
352A TRP* 4.9 4.7 - - + -
360A VAL* 4.2 5.8 - - + -
361A LEU 2.8 10.0 + - - +
362A LEU* 3.4 9.9 - - + -
363A ASP 3.3 17.5 + - - -
372A VAL* 3.8 27.4 - - + -
376A ILE* 3.9 21.3 - - + -
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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