Contacts of the strand formed by residues 317 - 323 (chain B) in PDB entry 1U0O
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 LYS 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B GLU 3.1 12.5 - - - +
220B TRP* 4.0 6.5 - - - +
221B MET 3.0 18.7 + - - +
262B ASP* 5.7 3.0 + - - +
263B VAL* 3.3 45.8 - - + +
265B TRP* 3.6 41.3 - - + +
311B ILE* 5.2 7.0 - - - -
315B ARG* 4.1 26.8 - - - +
316B PHE* 1.3 82.1 + - - +
318B ASN* 1.3 67.2 + - - +
319B PHE* 3.7 5.7 - - - -
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Residues in contact with ASN 318 (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 PHE* 3.7 23.7 - - + -
217B PHE 3.6 5.4 - - - +
218B LYS* 3.1 29.7 + - - +
219B GLU 2.6 28.5 + - - -
220B TRP* 3.4 29.9 - - - +
258B MET* 4.8 11.2 - - + +
262B ASP* 5.5 2.4 - - - +
263B VAL 4.1 4.1 + - - +
264B VAL* 3.1 11.8 - - + -
265B TRP 3.1 20.6 + - - -
317B LYS* 1.3 76.2 - - - +
319B PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 319 (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 PHE* 3.4 6.9 - - - -
217B PHE* 2.7 64.9 + + + +
219B GLU* 3.2 44.9 - - + -
221B MET* 3.6 25.1 - - + -
226B ALA* 4.4 9.0 - - + -
229B PHE* 3.6 21.3 - + - -
230B CYS* 4.1 6.7 - - - -
239B LEU* 3.9 18.8 - - + -
264B VAL* 4.2 2.2 - - - -
265B TRP* 3.9 14.4 - - + +
317B LYS 3.7 8.1 - - - -
318B ASN* 1.3 78.9 - - - +
320B VAL* 1.3 62.1 + - - +
321B CYS* 4.0 11.0 - - - -
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Residues in contact with VAL 320 (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 TYR* 4.4 8.1 - - + -
215B ARG 3.2 22.2 - - - +
216B PHE* 4.3 3.1 - - + +
230B CYS* 4.4 0.7 - - - -
239B LEU* 3.4 7.1 - - - +
240B VAL* 2.7 49.1 + - + +
251B VAL* 3.9 31.0 - - + -
254B LEU* 5.0 3.4 - - + -
255B THR* 4.1 18.2 - - + -
264B VAL* 4.2 13.7 - - + -
265B TRP 3.9 2.9 + - - +
319B PHE* 1.3 83.3 - - - +
321B CYS* 1.3 65.3 + - - +
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Residues in contact with CYS 321 (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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206B TRP* 3.8 22.2 - - + -
214B TYR* 3.3 23.7 - - - +
215B ARG 3.0 8.9 + - - -
217B PHE* 3.2 32.8 - - + -
230B CYS* 2.0 53.2 - - + -
233B GLN* 4.6 0.9 - - - -
237B ALA* 5.0 1.8 - - + -
238B HIS 3.1 6.7 - - - +
319B PHE* 4.0 4.0 - - - -
320B VAL* 1.3 76.4 - - - +
322B GLU* 1.3 65.2 + - - +
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Residues in contact with GLU 322 (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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86A ASP* 5.1 3.9 - - - +
206B TRP* 4.2 1.0 - - - -
212B HIS* 3.0 32.5 + - + -
213B CYS 3.1 10.5 - - - +
214B TYR* 3.2 25.2 + - + -
236B GLY 3.9 0.7 - - - +
237B ALA* 2.9 24.9 - - - -
238B HIS* 3.0 13.1 + - + +
239B LEU 4.4 2.1 - - - +
240B VAL* 3.3 11.3 - - - +
241B SER* 2.9 39.1 + - - +
243B GLN* 6.0 0.2 - - - +
247B GLU* 3.1 10.7 - - - +
321B CYS* 1.3 79.8 - - - +
323B PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 323 (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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201B ASP 5.6 0.9 - - - -
203B PRO* 3.5 19.5 - - + -
206B TRP* 3.6 24.7 - + - -
212B HIS* 3.4 6.2 - - - -
213B CYS* 2.8 53.4 + - + +
234B GLN* 3.4 45.5 - - + -
235B THR 4.3 2.0 - - - +
236B GLY 4.0 7.9 - - - +
237B ALA* 3.6 18.8 - - + +
322B GLU* 1.3 82.0 - - - +
324B GLN* 1.3 68.2 + - - +
325B ALA* 3.3 31.4 - - - +
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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