Contacts of the strand formed by residues 264 - 275 (chain B) in PDB entry 4U8T
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 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B ILE* 3.3 3.6 - - - +
200B TRP* 2.9 53.9 + + + -
201B SER* 4.5 0.2 - - - -
207B ASN* 3.6 22.4 - - - -
210B LEU* 3.8 29.4 - - + -
211B SER 6.3 0.2 - - - -
225B LEU* 4.2 2.9 - - + -
241B MSE 4.0 26.5 - - + -
243B SER* 3.5 14.1 - - - +
244B ASN 3.3 21.1 - - - +
245B LEU* 3.5 19.5 - - + -
249B LEU* 3.9 7.2 - - - -
263B ALA* 1.3 74.0 - - - +
265B LYS* 1.3 71.4 + - - +
266B VAL* 3.7 19.1 - - + -
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Residues in contact with LYS 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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198B GLY 3.4 11.7 - - - +
199B ILE* 4.3 2.0 - - + +
241B MSE 3.5 3.3 - - - -
242B SER* 2.9 33.9 + - - +
243B SER* 2.9 29.8 + - - +
246B ARG* 3.1 34.8 - - - +
249B LEU* 4.3 23.3 - - + -
264B PHE* 1.3 77.3 - - - +
266B VAL* 1.3 65.8 + - - +
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Residues in contact with VAL 266 (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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194B SER* 3.8 2.7 - - - +
198B GLY* 2.9 38.6 + - - +
199B ILE 3.6 9.9 - - - +
200B TRP* 3.8 13.0 - - + +
225B LEU* 4.2 13.2 - - + -
227B PHE* 5.5 0.7 - - + -
239B ALA* 4.2 7.9 - - + -
240B GLU 3.0 12.3 - - - +
242B SER* 3.3 6.4 + - - -
264B PHE* 3.7 23.3 - - + -
265B LYS* 1.3 79.8 - - - +
267B ARG* 1.3 58.3 + - - +
268B TRP* 3.7 26.6 + - + +
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Residues in contact with ARG 267 (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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222B LYS* 5.0 12.9 - - - +
239B ALA* 3.3 1.1 - - - -
240B GLU* 2.7 61.0 + - - +
241B MSE 3.5 17.6 + - - -
242B SER* 3.1 22.4 + - - +
266B VAL* 1.3 72.9 - - - +
268B TRP* 1.3 68.1 + - - +
269B ILE* 3.4 6.7 + - + +
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Residues in contact with TRP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 5.7 1.8 - - + +
191B VAL* 3.8 26.2 - - + -
194B SER* 3.1 34.9 + - - -
195B PHE* 3.7 41.3 - + + -
198B GLY* 5.2 1.8 - - - -
227B PHE* 3.5 37.7 - + + -
237B GLY* 3.9 10.5 - - - -
238B VAL 3.6 29.6 - - - -
239B ALA* 3.8 8.7 - - + -
266B VAL* 3.7 17.8 + - + +
267B ARG* 1.3 75.1 - - - +
269B ILE* 1.3 59.8 + - - +
270B VAL 3.6 10.8 - - - -
271B VAL* 4.0 9.9 - - + -
323B PHE* 4.1 10.8 - + - -
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Residues in contact with ILE 269 (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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167B ILE* 3.7 14.6 - - - +
169B PRO* 3.4 30.0 - - + +
171B TRP 5.6 0.4 - - - +
172B ILE* 4.2 16.2 - - + -
224B TYR* 3.9 18.4 - - + -
238B VAL* 2.8 17.2 + - + +
240B GLU* 3.1 39.9 - - + +
267B ARG* 3.9 11.4 - - + +
268B TRP* 1.3 77.9 - - - +
270B VAL* 1.3 75.8 + - + +
271B VAL* 4.3 0.4 - - - -
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Residues in contact with VAL 270 (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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167B ILE 3.3 10.1 - - - +
168B ILE* 4.2 12.3 - - + -
169B PRO* 3.5 13.5 - - + -
172B ILE* 3.8 16.2 - - + -
237B GLY* 3.2 3.2 - - - -
238B VAL* 2.9 45.2 + - + +
268B TRP* 3.6 1.7 - - - -
269B ILE* 1.3 96.7 - - + +
271B VAL* 1.3 71.1 + - - +
272B ARG* 4.2 6.5 - - + -
313B PHE* 3.8 32.1 - - + -
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Residues in contact with VAL 271 (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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166B ALA* 3.2 6.8 - - - +
167B ILE* 2.7 61.1 + - + +
195B PHE* 4.1 11.0 - - + -
236B CYS 3.8 2.9 - - - -
268B TRP* 4.0 12.6 - - + -
270B VAL* 1.3 78.8 - - - +
272B ARG* 1.3 64.9 + - - +
322B SER* 3.9 13.5 - - - -
323B PHE* 3.6 44.0 - - + -
324B LEU* 3.9 14.4 - - + -
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Residues in contact with ARG 272 (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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166B ALA* 4.2 7.0 - - + -
168B ILE* 4.2 21.9 - - + +
236B CYS 3.2 23.7 + - - +
270B VAL* 4.0 12.3 - - + +
271B VAL* 1.3 77.2 - - - +
273B ASP* 1.3 81.0 + - - +
274B VAL* 4.8 1.6 - - - +
312B LEU 4.5 5.3 + - - -
313B PHE* 3.1 44.1 + - + +
314B LYS 3.9 16.6 + - - -
315B TYR* 4.0 14.8 + - - +
320B VAL* 4.1 31.6 - - + +
321B GLN 3.4 13.0 - - - +
322B SER* 3.9 2.2 - - - -
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Residues in contact with ASP 273 (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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234B ARG* 3.2 37.2 + - - -
235B PHE 3.5 2.9 - - - -
236B CYS* 3.7 17.3 - - - +
272B ARG* 1.3 91.3 + - - +
274B VAL* 1.3 65.9 + - - +
275B HIS* 4.3 8.8 + - + +
321B GLN* 2.8 44.7 + - + +
322B SER* 3.8 13.8 + - - -
323B PHE* 4.3 1.4 + - - +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ARG* 3.2 3.2 - - - +
235B PHE* 2.9 31.6 + - + +
272B ARG* 4.8 2.9 - - - +
273B ASP* 1.3 78.4 - - - +
275B HIS* 1.3 67.9 + - - +
278B SER* 4.3 10.5 - - - -
279B LEU* 3.7 37.1 - - + +
312B LEU* 4.2 21.1 - - + +
313B PHE* 3.6 41.1 - - + -
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Residues in contact with HIS 275 (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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233B GLY 3.9 9.0 - - - +
234B ARG* 3.9 28.1 + - + -
273B ASP* 5.5 7.7 + - + +
274B VAL* 1.3 77.6 - - - +
276B ASN* 1.3 67.2 + - - +
277B ARG* 3.0 46.0 + - + +
278B SER* 2.9 21.5 + - - +
279B LEU* 3.6 9.4 + - - +
321B GLN* 5.0 15.9 + - - -
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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