Contacts of the strand formed by residues 237 - 243 (chain C) in PDB entry 6PUO
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 ILE 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C LEU* 4.4 22.9 - - + -
165C ASP* 4.7 10.3 - - - +
202C GLY 6.4 0.9 - - - -
203C ALA 4.1 7.7 + - - +
204C TRP* 3.4 38.3 - - + +
205C ILE* 3.5 19.8 + - - +
234C GLY 3.7 16.2 - - - +
235C GLU 3.1 11.4 + - - +
236C LEU* 1.3 77.4 - - - +
238C THR* 1.3 61.3 + - - +
239C ILE* 4.2 3.9 + - + +
282C SER* 4.5 6.5 - - - +
283C HIS* 4.4 21.5 - - + +
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Residues in contact with THR 238 (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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205C ILE* 3.4 33.0 - - + -
218C VAL* 5.9 1.3 - - + -
222C VAL* 4.1 27.5 - - + +
236C LEU* 4.9 6.3 - - + +
237C ILE* 1.3 79.5 - - - +
239C ILE* 1.3 64.0 + - - +
280C ASN 4.3 2.4 + - - -
281C HIS* 3.3 25.4 + - + +
282C SER* 2.9 37.7 + - - -
283C HIS* 3.0 7.6 + - - -
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Residues in contact with ILE 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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158C MET* 4.6 27.1 - - + -
164C LEU* 5.4 5.8 - - + -
204C TRP* 5.4 18.4 - - + -
205C ILE 3.1 9.1 + - - +
206C ILE* 3.9 39.3 - - + -
207C THR* 3.5 21.5 + - - +
237C ILE* 5.0 4.3 - - + +
238C THR* 1.3 78.9 - - - +
240C GLY* 1.3 60.1 + - - +
241C VAL* 4.7 5.8 - - + -
281C HIS* 4.3 4.3 + - - -
283C HIS* 3.4 26.5 - - + +
285C ILE* 4.6 15.9 - - + -
305C LEU* 4.9 6.7 - - + -
309C ILE* 6.3 0.9 - - + -
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Residues in contact with GLY 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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207C THR 3.3 6.5 - - - -
209C GLY* 4.0 17.9 - - - -
239C ILE* 1.3 77.8 - - - +
241C VAL* 1.3 63.9 + - - -
242C ALA* 3.9 1.1 + - - +
281C HIS* 5.0 4.3 - - - -
283C HIS 2.9 13.8 + - - -
284C PHE* 3.6 9.5 - - - -
285C ILE* 2.9 29.4 + - - +
286C LEU* 5.2 0.2 - - - +
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Residues in contact with VAL 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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206C ILE* 4.6 20.9 - - + -
207C THR 2.9 12.5 + - - +
208C GLY* 3.3 20.3 - - - -
209C GLY 3.9 0.2 - - - +
239C ILE* 4.7 9.6 - - + -
240C GLY* 1.3 73.0 - - - +
242C ALA* 1.3 62.4 + - - +
285C ILE* 3.3 22.0 - - + +
287C VAL* 4.6 13.9 - - + -
298C GLU* 3.9 32.6 - - + +
301C LEU* 5.3 6.1 - - + -
302C ARG* 4.8 15.9 - - + -
305C LEU* 5.3 5.8 - - + -
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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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209C GLY* 4.4 20.9 - - - +
210C SER* 5.2 2.9 - - - +
240C GLY 3.9 1.1 + - - +
241C VAL* 1.3 75.3 - - - +
243C THR* 1.3 64.3 + - - +
247C VAL* 5.4 1.1 - - + -
277C LEU* 4.9 7.2 - - + -
284C PHE* 6.1 1.1 - - + -
285C ILE 3.0 6.9 + - - -
286C LEU* 3.0 22.6 - - + -
287C VAL* 2.9 29.6 + - - +
298C GLU* 4.6 2.7 - - - -
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Residues in contact with THR 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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242C ALA* 1.3 73.8 - - - +
244C TRP* 1.3 67.3 + - - +
245C GLY* 3.3 11.3 + - - +
246C THR* 3.5 21.0 + - - +
247C VAL* 3.4 17.6 - - - +
286C LEU* 4.8 0.4 - - - -
287C VAL* 3.5 8.3 - - - +
288C ASP* 5.6 2.2 - - - -
289C ASP* 5.8 2.5 - - + +
291C THR 5.8 0.9 - - - +
294C GLN* 4.1 17.2 + - + +
295C TYR* 5.2 2.2 - - - -
296C GLY 4.6 4.9 + - - -
297C VAL* 3.9 26.9 + - + +
298C GLU* 4.0 18.2 + - - +
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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