Contacts of the strand formed by residues 264 - 275 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D ILE* 3.3 4.2 - - - +
200D TRP* 3.0 58.9 + + + -
201D SER* 4.3 1.6 - - - -
207D ASN* 3.9 17.9 - - - -
210D LEU* 3.9 26.7 - - + -
225D LEU* 3.8 7.2 - - + -
241D MSE 3.5 31.6 - - + -
243D SER* 3.5 13.0 - - - +
244D ASN 3.3 20.9 - - - +
245D LEU* 3.6 16.4 - - + -
249D LEU* 4.0 6.3 - - - -
263D ALA* 1.3 73.2 - - - +
265D LYS* 1.3 63.0 + - - +
266D VAL* 3.6 23.6 - - + -
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Residues in contact with LYS 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLY 3.6 10.8 - - - +
199D ILE* 4.3 3.4 - - + +
241D MSE 3.7 0.2 - - - -
242D SER* 2.8 37.9 + - - +
243D SER* 2.9 28.2 + - - +
246D ARG* 3.9 23.5 - - - +
249D LEU* 4.1 19.1 - - + -
264D PHE* 1.3 77.7 - - - +
266D VAL* 1.3 63.8 + - - +
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Residues in contact with VAL 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D SER* 3.8 10.5 - - - +
198D GLY* 3.0 35.5 + - - +
199D ILE 3.6 13.2 - - - +
200D TRP* 3.9 9.6 - - + +
225D LEU* 4.0 10.8 - - + -
227D PHE* 5.6 0.9 - - + -
239D ALA* 4.2 8.1 - - + -
240D GLU 3.2 14.4 - - - +
241D MSE 4.5 0.4 - - - -
242D SER* 3.3 6.1 + - - -
264D PHE* 3.6 27.6 - - + -
265D LYS* 1.3 79.8 - - - +
267D ARG* 1.3 60.3 + - - +
268D TRP* 4.0 13.2 + - - +
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Residues in contact with ARG 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D LYS* 5.1 10.3 - - - +
239D ALA* 3.2 2.1 - - - -
240D GLU* 2.8 70.1 + - + +
242D SER* 3.9 18.8 + - - +
266D VAL* 1.3 73.9 - - - +
268D TRP* 1.3 65.8 + - - +
269D ILE* 3.5 7.7 + - + +
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Residues in contact with TRP 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ILE* 5.9 1.0 - - - +
191D VAL* 3.6 25.6 - - + -
194D SER* 3.2 30.9 + - - -
195D PHE* 3.5 44.2 - + + +
198D GLY* 5.0 1.6 - - - -
227D PHE* 3.5 44.9 - + + -
236D CYS 4.6 2.7 - - - -
237D GLY* 3.9 24.0 - - - -
238D VAL 3.6 19.3 - - - -
239D ALA* 3.8 7.0 - - + -
266D VAL* 4.0 15.8 + - + +
267D ARG* 1.3 73.9 - - - +
269D ILE* 1.3 61.3 + - - +
270D VAL 3.7 9.0 - - - -
271D VAL* 3.9 14.6 - - + -
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Residues in contact with ILE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ILE* 3.6 15.9 - - - +
169D PRO* 3.5 29.9 - - + +
172D ILE* 4.3 17.0 - - + -
224D TYR* 4.0 15.9 - - + -
238D VAL* 2.8 18.1 + - + +
240D GLU* 3.2 39.5 - - + +
267D ARG* 4.0 12.1 - - + +
268D TRP* 1.3 77.0 - - - +
270D VAL* 1.3 73.8 + - + +
271D VAL* 5.5 0.2 - - - -
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ILE 3.6 9.4 - - - +
168D ILE* 5.2 0.4 - - - -
169D PRO* 3.9 12.6 - - + -
172D ILE* 4.0 15.0 - - + -
237D GLY* 3.1 3.5 - - - -
238D VAL* 2.8 46.3 + - + +
268D TRP* 3.7 1.2 - - - -
269D ILE* 1.3 96.3 - - + +
271D VAL* 1.3 69.5 + - - +
272D ARG* 4.3 9.2 - - + -
313D PHE* 3.5 43.5 - - + +
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Residues in contact with VAL 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLY 5.4 2.7 - - - +
166D ALA* 3.5 7.9 - - - -
167D ILE* 3.0 55.9 + - + +
195D PHE* 4.2 17.0 - - + -
236D CYS 3.8 9.4 - - - +
268D TRP* 3.9 21.5 - - + -
269D ILE 5.5 0.2 - - - -
270D VAL* 1.3 78.8 - - - +
272D ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ALA* 4.6 7.6 - - + -
168D ILE* 3.7 29.8 - - + +
236D CYS* 3.3 24.5 + - - -
270D VAL* 4.0 11.5 - - + +
271D VAL* 1.3 78.6 - - - +
273D ASP* 1.3 83.3 + - - +
274D VAL* 3.6 8.3 + - + +
312D LEU 4.6 5.1 + - - -
313D PHE* 3.5 28.8 + - + +
315D TYR 2.7 45.2 + - - +
316D GLU* 4.0 5.5 - - - +
317D GLN 5.5 0.2 - - - +
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Residues in contact with ASP 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 3.1 41.7 + - - -
235D PHE 3.4 3.1 - - - -
236D CYS* 4.0 13.0 - - - +
272D ARG* 1.3 92.8 + - - +
274D VAL* 1.3 66.1 + - - +
275D HIS* 5.1 11.9 + - + -
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 3.1 3.1 - - - +
235D PHE* 2.8 36.5 + - - +
272D ARG* 4.5 8.3 - - - +
273D ASP* 1.3 80.6 - - - +
275D HIS* 1.3 64.8 + - - +
278D SER* 4.6 9.6 - - - -
279D LEU* 3.9 32.2 - - + +
312D LEU* 4.6 11.7 - - + +
313D PHE* 3.6 48.0 - - + -
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Residues in contact with HIS 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D SER 5.6 0.2 - - - -
233D GLY 3.7 12.6 - - - +
234D ARG* 3.8 27.6 + - + -
273D ASP* 5.1 12.5 + - + -
274D VAL* 1.3 79.2 - - - +
276D ASN* 1.3 66.7 + - - +
277D ARG* 3.7 42.9 + - + +
278D SER* 2.9 21.7 + - - +
279D LEU* 3.7 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