Contacts of the strand formed by residues 238 - 245 (chain C) in PDB entry 4GUP
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 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C SER* 3.6 25.3 + - - -
204C GLY 2.9 25.3 + - - -
205C PHE* 3.0 44.5 + - + -
206C TYR* 4.0 14.3 - + - -
208C PRO* 3.6 42.2 - - + -
230C ILE* 3.9 9.6 - - + -
231C LEU 3.3 24.9 - - - +
232C PRO* 3.7 18.4 - - + -
233C SER* 3.7 4.5 - - - -
236C GLY 4.1 7.4 - - - -
237C THR* 1.3 76.7 - - - +
239C GLN* 1.4 59.0 + - - +
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Residues in contact with GLN 239 (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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202C ALA 3.4 12.1 - - - +
203C HIS* 4.0 13.6 - - + +
205C PHE* 3.7 3.4 - - - -
229C ASP 3.8 0.7 - - - +
230C ILE* 3.6 1.6 - - - +
231C LEU* 2.8 55.2 + - + +
233C SER* 3.2 18.8 + - - +
238C TYR* 1.4 72.8 - - - +
240C ALA* 1.4 61.2 + - - +
10D TYR* 3.5 33.6 - - + +
11D SER 3.6 12.5 + - - +
12D ARG 3.5 16.0 + - - +
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Residues in contact with ALA 240 (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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201C LYS* 3.8 1.7 - - - +
202C ALA* 2.9 32.8 + - - +
205C PHE* 4.0 6.5 - - + -
210C ILE* 4.5 1.8 - - + -
212C MET* 3.8 21.1 - - + -
228C GLY 4.8 2.7 - - - +
229C ASP 3.8 16.8 - - - +
230C ILE* 4.2 18.4 - - + -
231C LEU* 5.6 0.9 - - - -
239C GLN* 1.4 75.5 - - - +
241C TRP* 1.4 67.8 + - - +
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Residues in contact with TRP 241 (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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199C PHE* 3.8 31.4 - + + -
200C CYS 3.1 17.7 - - - +
201C LYS* 4.4 5.6 - - + -
212C MET* 3.7 9.5 - - - +
226C ASP* 3.2 38.4 - - - -
227C TYR* 4.0 2.2 - - - +
228C GLY* 2.9 50.4 + - - +
229C ASP 4.7 3.7 + - - +
231C LEU* 5.5 9.0 - - + +
240C ALA* 1.4 79.7 - - - +
242C ALA* 1.3 68.2 + - - +
243C SER* 3.5 11.4 - - - -
6D LYS* 6.2 1.3 - - - -
8D GLN* 5.0 12.5 - - - +
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Residues in contact with ALA 242 (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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199C PHE* 3.9 0.9 - - - -
200C CYS* 3.0 22.8 + - + +
212C MET* 4.0 24.4 - - + +
213C THR* 4.9 1.1 - - - +
214C TRP* 3.0 26.2 + - + +
225C ILE* 4.3 3.8 - - + -
226C ASP 3.7 3.8 - - - -
227C TYR* 4.1 21.8 - - + +
241C TRP* 1.3 81.7 - - - +
243C SER* 1.3 62.2 - - - +
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Residues in contact with SER 243 (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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197C ALA* 5.1 1.8 - - - -
198C LEU 3.3 11.2 - - - -
199C PHE* 3.6 31.6 - - - -
214C TRP* 3.7 2.9 - - - +
224C GLU 4.2 0.2 - - - +
225C ILE* 3.4 10.0 - - - +
226C ASP* 2.9 47.6 + - - +
241C TRP* 3.5 9.9 - - - -
242C ALA* 1.3 76.5 - - - +
244C ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 244 (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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197C ALA* 3.2 8.0 - - - +
198C LEU* 3.0 58.4 + - + -
214C TRP* 3.7 29.8 - - + +
221C ILE* 4.6 3.4 - - + +
224C GLU* 3.8 28.7 - - + +
225C ILE* 3.4 33.4 - - + -
243C SER* 1.3 74.2 - - - +
245C GLU* 1.3 67.1 + - - +
246C LEU* 4.9 1.1 - - - +
254C TYR* 5.0 17.5 - - + -
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Residues in contact with GLU 245 (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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196C THR 4.3 5.8 - - - +
197C ALA* 4.6 5.2 - - + +
224C GLU* 3.9 33.0 + - + +
244C ILE* 1.3 77.3 - - - +
246C LEU* 1.3 64.3 + - - +
247C ASP* 3.0 18.1 - - - +
254C TYR* 4.9 2.6 + - - -
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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