Contacts of the strand formed by residues 225 - 231 (chain C) in PDB entry 2C11
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 THR 225 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C THR* 3.5 9.0 - - - +
213C THR* 3.5 19.3 - - - +
215C PRO 5.5 1.1 - - - +
216C ARG* 2.6 44.3 + - + +
224C ALA* 1.3 73.1 - - - +
226C TRP* 1.3 71.7 + - - +
227C PHE* 3.1 29.4 - - + -
247C LEU 3.5 0.5 - - - +
248C LEU* 3.2 3.8 - - - +
249C VAL 2.9 32.6 + - - +
251C HIS* 2.7 20.0 + - - -
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Residues in contact with TRP 226 (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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211C MET 3.7 1.4 - - - +
213C THR* 3.1 33.3 + - - +
224C ALA 4.6 2.7 - - - -
225C THR* 1.3 80.1 - - - +
227C PHE* 1.3 60.2 - - - +
228C GLY 4.1 0.2 + - - -
246C GLU* 3.5 36.8 - - + -
247C LEU* 3.0 27.1 - - - -
248C LEU* 3.3 42.2 - - + +
263C LYS* 4.2 18.2 - - + -
264C VAL 4.4 0.7 - - - -
265C PHE* 3.8 15.5 - - + -
270C TYR* 4.9 1.8 - + - -
377C PRO* 3.6 28.9 - - + -
378C ALA* 3.9 16.7 - - - +
381C THR* 4.9 4.3 - - - -
553D TRP* 3.3 41.9 - + - +
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Residues in contact with PHE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C TYR* 4.7 11.2 - + - -
179C ILE* 3.9 35.0 - - + -
180C ASP* 5.7 0.4 - - - -
183C ILE* 4.9 6.7 - - + -
210C THR* 3.9 27.1 - - + -
211C MET 3.5 8.7 - - - +
212C THR* 3.3 37.7 - - - -
216C ARG* 4.7 1.3 - - - -
225C THR* 3.1 39.7 - - + -
226C TRP* 1.3 77.7 - - - +
228C GLY* 1.3 62.1 + - - +
229C LEU* 4.0 2.6 - - - +
245C LEU 3.9 0.5 - - - +
246C GLU* 3.1 3.4 - - - -
247C LEU* 2.6 44.4 + - + +
249C VAL* 4.3 16.4 - - + -
251C HIS* 5.2 0.4 - + - -
378C ALA* 5.4 0.2 - - - -
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Residues in contact with GLY 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C THR* 3.1 5.2 - - - -
211C MET 3.1 21.2 + - - -
213C THR* 5.6 0.4 - - - +
226C TRP 4.1 0.8 + - - -
227C PHE* 1.3 75.3 - - - +
229C LEU* 1.3 59.7 + - - +
230C TYR* 3.1 31.4 + - - -
242C HIS* 3.9 11.7 - - - -
245C LEU 3.6 6.5 - - - -
246C GLU* 3.9 8.2 - - - +
378C ALA* 5.1 3.8 - - - +
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Residues in contact with LEU 229 (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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183C ILE* 4.6 2.2 - - + -
184C PHE* 4.6 5.2 - - + -
188C LEU* 4.3 25.4 - - + -
208C LEU* 4.6 16.8 - - + -
209C VAL 3.5 2.7 - - - +
210C THR* 3.4 26.2 - - + -
227C PHE 4.0 4.7 - - - +
228C GLY* 1.3 75.7 - - - +
230C TYR* 1.3 62.1 + - - +
242C HIS* 3.6 3.8 + - - -
243C VAL* 2.9 43.1 + - + +
245C LEU* 2.9 40.4 + - + +
247C LEU* 3.4 31.4 - - + -
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Residues in contact with TYR 230 (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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208C LEU* 3.3 3.8 - - - -
209C VAL* 2.7 52.0 + - - +
211C MET* 3.3 39.2 + - + +
213C THR* 5.9 2.3 - - - +
228C GLY* 3.1 34.0 + - - -
229C LEU* 1.3 73.4 - - - +
231C TYR* 1.3 61.8 + - - +
238C PHE* 3.2 39.9 - + + +
239C PHE* 4.3 10.1 - - + -
241C HIS 2.8 22.2 - - - +
242C HIS* 3.5 33.8 + + - -
243C VAL* 4.2 2.5 - - - -
246C GLU* 5.4 0.3 + - - -
497C SER 4.0 12.2 + - - -
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Residues in contact with TYR 231 (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 CYS 3.8 6.8 + - - -
199C CYS* 3.8 14.4 - - + -
200C PHE* 3.5 11.3 - + - -
207C ASN* 3.7 9.2 - - - +
208C LEU* 3.6 16.6 - - + -
230C TYR* 1.3 76.4 - - - +
232C ASN* 1.3 59.9 + - - +
233C ILE* 3.0 25.3 + - + +
238C PHE* 3.2 19.2 - - - +
241C HIS* 3.3 19.0 + - + -
243C VAL* 3.4 23.6 - - + -
291C ILE* 2.4 42.7 + - + +
292C PRO 3.2 12.1 - - - -
293C ASP* 3.2 43.1 - - + -
300C TRP* 4.9 0.7 - + - -
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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
------------------------------------------------------------
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