Contacts of the strand formed by residues 257 - 263 (chain B) in PDB entry 5X61
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 TYR 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLY* 3.3 27.6 - - - -
194B ILE 3.4 4.5 - - - +
195B PRO* 3.5 31.5 - - + +
196B TYR* 3.4 7.6 - - - -
225B PRO* 3.6 32.5 - - + -
226B ASN* 4.8 6.4 + - + -
254B ASP* 3.0 44.8 + - - -
255B CYS* 2.9 26.2 + - - +
256B LEU* 1.3 74.1 - - - +
258B ILE* 1.3 62.6 + - - +
259B ASN* 5.1 0.7 + - - -
307B LEU* 3.8 0.2 - - - -
308B GLN* 3.0 29.5 + - + +
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Residues in contact with ILE 258 (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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193B GLY 3.1 7.6 + - - -
194B ILE* 2.8 41.9 + - + +
196B TYR* 3.5 36.8 - - + -
257B TYR* 1.3 74.3 - - - +
259B ASN* 1.3 76.9 + - - +
260B VAL* 4.0 11.2 - - + -
305B VAL* 3.9 13.0 - - + -
306B SER 3.5 11.0 - - - +
307B LEU* 4.3 4.0 - - + -
336B ALA* 3.8 26.5 - - + +
339B TRP* 3.7 29.4 - - + -
340B VAL* 4.7 3.4 - - + -
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Residues in contact with ASN 259 (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 TRP 3.4 5.4 - - - +
192B LEU* 3.2 21.2 - - + +
193B GLY 3.0 24.9 + - - -
225B PRO* 3.4 26.5 - - - +
257B TYR 5.1 1.8 + - - -
258B ILE* 1.3 75.4 - - - +
260B VAL* 1.3 63.2 + - - +
261B VAL* 4.3 0.7 - - - -
286B ALA* 3.9 16.0 + - - +
287B THR* 4.9 3.6 - - - +
293B HIS* 4.4 9.5 + - + +
304B VAL 4.6 0.4 - - - -
305B VAL* 3.3 10.6 - - - +
306B SER* 2.8 54.9 + - - +
308B GLN* 5.2 0.2 - - - +
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Residues in contact with VAL 260 (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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190B VAL* 3.5 1.0 - - - -
191B TRP* 2.8 50.7 + - + -
194B ILE* 3.8 22.2 - - + -
258B ILE* 4.0 10.3 - - + -
259B ASN* 1.3 77.7 - - - +
261B VAL* 1.3 67.8 + - - +
262B ALA* 5.0 0.4 - - + +
303B ILE* 4.4 6.7 - - + -
304B VAL 3.7 2.2 - - - -
305B VAL* 4.4 7.2 - - + -
339B TRP* 4.3 13.9 - - + -
344B ILE* 4.2 18.2 - - + -
347B PHE* 3.9 33.4 - - + -
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Residues in contact with VAL 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 VAL* 3.9 15.3 - - + -
189B ASP 3.5 2.5 - - - -
190B VAL* 3.7 30.1 - - + -
192B LEU* 4.7 7.2 - - + -
260B VAL* 1.3 80.2 - - - +
262B ALA* 1.3 61.5 + - - +
293B HIS* 3.7 34.1 - - + -
294B ARG* 4.3 11.0 - - + +
297B ALA* 3.8 21.8 - - + +
303B ILE* 3.3 5.2 - - - +
304B VAL* 2.9 41.4 + - + +
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Residues in contact with ALA 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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188B VAL* 3.2 7.2 - - - +
189B ASP* 2.8 36.7 + - + +
191B TRP* 3.8 23.5 - - + -
260B VAL* 5.4 0.4 - - + -
261B VAL* 1.3 74.3 - - - +
263B PRO* 1.4 74.5 - - + +
266B ARG* 4.7 6.1 - - - +
267B PRO* 5.1 1.6 - - + -
297B ALA* 4.8 0.7 - - - -
303B ILE* 3.8 13.7 - - + -
347B PHE* 4.0 14.1 - - + +
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Residues in contact with PRO 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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188B VAL* 3.9 10.1 - - + -
189B ASP* 5.3 1.2 - - - +
262B ALA* 1.4 89.4 - - + +
264B ARG* 1.3 63.8 + - - +
265B PRO 3.4 15.6 - - - +
266B ARG* 3.4 10.9 + - - +
267B PRO* 3.8 10.2 - - + +
297B ALA* 3.4 25.8 - - - +
298B SER* 4.7 4.7 - - - +
301B ASN* 3.5 21.5 - - - +
302B VAL 3.6 22.2 - - - +
303B ILE* 3.5 19.5 - - + -
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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