Contacts of the strand formed by residues 290 - 294 (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 PHE 290 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K HIS* 3.5 27.6 - + + -
158K GLU* 3.4 48.7 - - + -
161K LYS* 3.7 14.6 - - + -
162K LEU* 3.7 22.7 - - + -
199K PHE* 5.4 1.3 - + - -
263K PRO* 3.0 18.0 + - + +
264K ILE* 3.5 27.5 - - + -
265K ILE* 3.1 30.3 + - - +
289K LEU* 1.3 74.1 - - - +
291K LEU* 1.3 60.0 + - - +
324K ASP* 3.3 10.5 - - + +
66P LEU* 3.5 39.2 - - + +
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Residues in contact with LEU 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K PRO* 4.1 12.3 - - + -
264K ILE* 4.9 1.3 - - - -
265K ILE* 3.5 18.2 - - + +
267K HIS* 4.0 13.2 - - + +
277K ASN* 4.4 4.7 - - - +
280K LEU* 3.7 27.8 - - + -
281K ALA* 3.8 33.7 - - + +
284K CYS* 3.9 8.5 - - - -
290K PHE* 1.3 74.6 - - - +
292K HIS* 1.3 64.1 + - - +
293K ILE* 3.6 20.7 + - + -
322K GLY 3.8 10.5 - - - +
323K GLY* 3.8 1.4 - - - -
324K ASP* 2.9 39.1 + - - +
325K HIS 3.3 3.5 + - - -
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Residues in contact with HIS 292 (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 7.2 - - - -
239K TYR* 3.1 42.7 - + + -
264K ILE* 4.1 5.4 - - + +
265K ILE 2.8 16.3 + - - +
266K MET* 3.0 18.1 - - + +
267K HIS 2.9 26.2 + - - -
290K PHE 4.0 0.6 - - - -
291K LEU* 1.3 72.6 - - - +
293K ILE* 1.3 66.5 + - - +
294K HIS* 4.1 2.2 + - - -
325K HIS* 3.1 34.6 + - + +
327K HIS* 2.9 41.8 + + - -
377K VAL* 3.8 16.4 - - + -
401K GLN* 4.0 2.2 - - - -
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Residues in contact with ILE 293 (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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267K HIS* 3.5 8.1 - - + +
269K TYR* 3.1 41.5 - - + -
277K ASN* 3.2 28.7 - - - +
291K LEU* 3.6 25.6 - - + +
292K HIS* 1.3 78.7 + - - +
294K HIS* 1.3 61.2 - - - +
318K LEU* 3.7 15.5 - - + -
322K GLY 4.0 0.9 - - - +
323K GLY* 3.7 19.5 - - - -
325K HIS 2.9 23.7 + - - +
326K LEU* 3.5 5.4 - - + +
327K HIS* 3.4 27.9 + - - -
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Residues in contact with HIS 294 (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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123E ASN* 3.3 23.1 - - - -
201K KCX 3.3 28.3 - - - -
204K GLU* 3.1 24.2 + - + +
266K MET* 4.0 10.8 - - + -
267K HIS 3.0 6.1 + - - -
268K ASP* 3.4 20.4 - - - +
269K TYR* 3.3 25.6 + - - -
270K LEU 4.7 0.2 + - - -
292K HIS* 4.0 2.2 + - - +
293K ILE* 1.3 74.5 - - - +
295K ARG* 1.3 60.0 + - - +
296K ALA* 2.9 34.4 + - + +
327K HIS* 3.6 16.8 - + - +
1478R CAP 2.9 30.0 + - - -
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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