Contacts of the strand formed by residues 264 - 275 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C ILE* 3.3 2.3 - - - -
200C TRP* 2.8 57.1 + + + +
201C SER* 4.3 0.7 - - - -
202C SER 4.6 0.2 - - - -
207C ASN* 3.7 21.3 - - - -
210C LEU* 3.7 31.6 - - + -
211C SER 6.3 0.4 - - - -
225C LEU* 4.4 1.1 - - + -
241C MSE 3.5 29.4 - - + -
243C SER* 3.5 13.2 - - - +
244C ASN 3.3 21.1 - - - +
245C LEU* 3.4 17.5 - - + -
249C LEU* 4.0 6.7 - - - -
263C ALA* 1.3 72.5 - - - +
265C LYS* 1.3 72.5 + - - +
266C VAL* 4.0 15.5 - - + -
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLY 3.4 10.5 - - - +
199C ILE* 4.3 4.5 - - + +
241C MSE 3.5 3.5 - - - +
242C SER* 2.7 43.4 + - - +
243C SER* 3.0 29.8 + - - +
246C ARG* 3.4 28.5 - - - +
249C LEU* 4.4 20.9 - - + -
264C PHE* 1.3 74.0 - - - +
266C VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C SER* 3.6 18.6 - - - +
198C GLY* 2.8 39.7 + - - +
199C ILE 3.6 5.2 - - - +
200C TRP* 3.8 21.5 - - + -
225C LEU* 4.1 12.1 - - + -
227C PHE* 5.5 0.4 - - + -
239C ALA* 4.2 8.1 - - + -
240C GLU 3.2 11.4 - - - +
241C MSE 4.2 0.9 - - - -
242C SER* 3.7 5.5 + - - -
264C PHE* 4.0 13.7 - - + -
265C LYS* 1.3 80.6 - - - +
267C ARG* 1.3 61.8 + - - +
268C TRP* 3.8 14.0 + - - +
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Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C LYS* 5.4 2.6 - - - +
239C ALA* 3.3 1.8 - - - -
240C GLU* 2.9 55.2 + - + +
242C SER* 3.7 26.1 + - - -
266C VAL* 1.3 72.3 + - - +
268C TRP* 1.3 71.6 + - - +
269C ILE* 3.4 9.4 + - - +
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Residues in contact with TRP 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ILE* 6.0 0.7 - - - +
191C VAL* 3.6 24.2 - - + -
194C SER* 3.0 32.1 + - - -
195C PHE* 3.7 42.9 - + + +
198C GLY* 5.2 1.3 - - - -
227C PHE* 3.5 44.6 - + + -
237C GLY* 3.9 25.6 - - - -
238C VAL 3.7 9.0 - - - -
239C ALA* 3.9 7.8 - - + +
266C VAL* 3.8 15.8 + - + +
267C ARG* 1.3 78.7 - - - +
269C ILE* 1.3 60.3 + - - +
270C VAL 3.6 16.4 - - - -
271C VAL* 3.9 9.9 - - + -
323C PHE* 4.1 12.8 - + - -
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ILE* 3.8 13.8 - - - +
169C PRO* 3.5 30.2 - - + +
172C ILE* 4.6 17.0 - - + -
224C TYR* 4.4 11.2 - - + -
238C VAL* 2.8 13.9 + - + +
239C ALA 5.5 0.2 - - - -
240C GLU* 2.8 41.1 - - + +
267C ARG* 3.9 14.1 - - - +
268C TRP* 1.3 78.6 - - - +
270C VAL* 1.3 76.5 + - + +
271C VAL* 5.6 0.2 - - - -
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ILE 3.5 9.9 - - - +
168C ILE* 5.1 0.7 - - - -
169C PRO* 4.0 11.4 - - + -
172C ILE* 4.1 16.2 - - + -
237C GLY* 3.2 2.6 - - - -
238C VAL* 2.9 47.5 + - + +
268C TRP* 3.6 1.6 - - - -
269C ILE* 1.3 95.8 - - + +
271C VAL* 1.3 71.4 + - - +
272C ARG* 4.2 8.7 - - + -
313C PHE* 3.8 43.3 - - + +
314C LYS* 6.5 0.2 - - + -
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ALA* 3.4 5.9 - - - +
167C ILE* 3.0 35.7 + - + +
195C PHE* 3.8 35.2 - - + -
236C CYS 3.8 2.5 - - - -
268C TRP* 3.9 13.0 - - + -
269C ILE 5.6 0.4 - - - -
270C VAL* 1.3 79.5 - - - +
272C ARG* 1.3 63.9 + - - +
322C SER* 3.9 8.2 - - - -
323C PHE* 3.5 36.1 - - + +
324C LEU* 3.8 20.6 - - + -
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ALA* 4.6 1.6 - - + -
168C ILE* 4.0 24.2 - - + +
235C PHE 3.5 1.4 - - - +
236C CYS* 3.3 22.0 + - - -
270C VAL* 4.0 12.8 - - + +
271C VAL* 1.3 76.9 - - - +
273C ASP* 1.3 84.8 + - - +
274C VAL* 4.3 6.9 - - + +
312C LEU 3.7 8.5 + - - -
313C PHE* 3.3 27.5 + - + -
314C LYS 3.9 0.2 - - - -
315C TYR* 2.8 68.2 - - - +
320C VAL* 4.5 23.3 - - + +
321C GLN 3.7 13.0 - - - +
322C SER* 4.3 1.6 - - - -
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Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ARG* 3.3 35.3 + - - -
235C PHE 3.2 3.8 - - - -
236C CYS* 3.7 16.6 - - - +
272C ARG* 1.3 97.3 + - - +
274C VAL* 1.3 61.6 + - - +
275C HIS* 5.5 4.5 + - + -
321C GLN* 3.1 39.6 + - - +
322C SER* 3.7 20.9 + - - -
323C PHE* 4.2 1.6 + - - +
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ARG* 3.2 2.5 - - - +
235C PHE* 2.8 35.1 + - - +
272C ARG* 4.3 5.8 - - - +
273C ASP* 1.3 79.3 - - - +
275C HIS* 1.3 74.1 + - - +
278C SER* 4.5 4.5 - - - -
279C LEU* 4.0 22.3 - - + +
312C LEU* 3.9 35.9 - - + +
313C PHE* 3.8 36.8 - - + -
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Residues in contact with HIS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C GLY 3.8 10.5 - - - +
234C ARG* 3.9 24.9 + - + -
273C ASP* 5.5 3.5 + - + +
274C VAL* 1.3 79.6 - - - +
276C ASN* 1.3 66.7 + - - +
277C ARG* 3.1 56.0 + - + +
278C SER* 2.9 20.6 + - - +
279C LEU* 3.6 4.8 + - - +
321C GLN* 3.9 32.6 + - - -
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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