Contacts of the strand formed by residues 260 - 265 (chain B) in PDB entry 5H2U
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 VAL 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B LYS 3.5 0.9 - - - +
220B VAL* 3.4 5.5 - - - -
221B ILE* 2.8 42.8 + - + +
223B ARG* 3.3 33.2 - - - +
226B LEU* 3.7 26.5 - - + -
232B LEU* 4.6 5.8 - - + -
236B ILE* 5.7 1.6 - - + -
254B VAL 3.3 13.7 - - - +
255B SER* 3.8 14.8 - - - -
258B ASP* 4.5 0.2 + - - -
259B PRO* 1.3 73.8 - - - +
261B TYR* 1.3 73.7 + - - +
262B ILE* 4.1 17.0 - - + -
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ARG* 4.1 37.3 + - + +
191B PHE* 4.4 15.3 - + + -
193B LEU* 3.8 31.9 - - + +
218B ILE* 3.7 13.9 - - + -
219B LYS 3.2 3.4 - - - -
220B VAL* 3.9 32.1 - - + -
253B VAL* 3.4 5.0 - - - +
254B VAL* 2.9 54.1 + - + +
259B PRO* 4.0 6.5 + - + -
260B VAL* 1.3 82.8 - - - +
262B ILE* 1.3 65.8 + - - +
263B ILE* 3.7 16.6 - - + -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE* 3.5 0.9 - - - -
219B LYS* 2.7 42.1 + - + +
221B ILE* 3.8 20.2 - - + -
226B LEU* 5.7 0.9 - - + -
232B LEU* 5.8 0.4 - - + -
236B ILE* 5.2 6.5 - - + -
239B MET* 5.2 1.6 - - - -
250B LEU* 3.9 25.8 - - + -
252B ALA 4.1 2.0 - - - -
253B VAL* 4.3 13.0 - - + -
260B VAL* 4.1 13.0 - - + -
261B TYR* 1.3 79.0 - - - +
263B ILE* 1.3 63.0 + - - +
333B LEU* 4.1 5.4 - - + -
336B LEU* 3.3 33.9 - - + -
501B 1N1 3.3 30.8 - - + +
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PHE* 3.7 37.0 - - + -
216B VAL* 3.5 33.7 - - + -
217B ALA 3.3 10.5 - - - +
218B ILE* 3.8 19.3 - - + -
250B LEU* 3.7 3.3 - - - +
251B TYR* 2.8 38.3 + - + -
252B ALA 3.0 29.1 + - - +
254B VAL* 4.1 3.8 - - + -
261B TYR* 3.7 22.4 - - + +
262B ILE* 1.3 80.0 - - - +
264B THR* 1.3 63.4 + - - +
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Residues in contact with THR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B VAL* 3.2 7.2 - - - +
217B ALA* 2.8 26.2 + - - +
248B LEU* 3.6 15.4 - - + +
249B ALA 3.4 23.6 - - - +
250B LEU* 4.2 6.5 - - + -
251B TYR* 3.7 12.6 - - - +
263B ILE* 1.3 79.3 - - - +
265B GLU* 1.3 70.7 + - - +
501B 1N1 3.0 52.9 + - + +
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B VAL* 4.8 8.0 - - + +
215B GLN 4.0 14.5 - - - +
216B VAL* 4.2 3.4 - - + +
248B LEU* 3.9 14.9 - - + +
249B ALA 4.7 1.6 + - - -
251B TYR* 4.0 31.6 - - + +
264B THR* 1.3 88.7 + - - +
266B LEU* 1.3 65.3 + - - +
267B MET* 3.5 3.9 + - - -
501B 1N1 3.8 4.9 - - - -
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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