Contacts of the strand formed by residues 224 - 231 (chain B) in PDB entry 2C10
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 ALA 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PRO 4.6 0.5 - - - +
216B ARG* 3.0 24.9 + - - +
217B GLY* 3.2 10.7 + - - -
222B ASP* 5.4 2.5 - - + -
223B ARG* 1.3 76.0 - - - +
225B THR* 1.3 60.8 + - - +
226B TRP* 4.1 1.6 + - - -
248B LEU* 3.6 15.9 - - + +
249B VAL 3.0 10.8 - - - +
250B ASN* 4.0 9.9 - - + +
262B GLN* 3.7 27.1 - - - +
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Residues in contact with THR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR* 3.4 25.1 - - - +
213B THR* 3.6 11.2 - - - +
215B PRO 5.3 0.7 - - - -
216B ARG* 2.8 29.0 + - + +
224B ALA* 1.3 72.3 - - - +
226B TRP* 1.3 69.6 + - - +
227B PHE* 3.5 22.6 + - + -
247B LEU 3.3 2.8 - - - +
248B LEU* 3.8 2.7 - - - -
249B VAL 2.8 36.7 + - - +
251B HIS* 2.7 27.7 + - - -
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Residues in contact with TRP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A TRP* 3.4 33.0 - + - +
213B THR* 2.7 45.6 + - - +
215B PRO 5.7 0.6 + - - -
224B ALA 4.1 1.5 + - - -
225B THR* 1.3 71.8 - - - +
227B PHE* 1.3 60.9 + - - +
228B GLY 4.1 0.3 + - - -
246B GLU* 3.6 27.4 - - + -
247B LEU 3.4 13.9 - - - -
248B LEU* 3.3 61.2 - - + +
263B LYS* 3.8 23.8 - - + -
264B VAL 4.5 0.9 - - - -
265B PHE* 4.3 7.0 - - + -
270B TYR* 4.9 0.9 - + - -
377B PRO* 3.5 33.2 - - + -
378B ALA* 4.1 14.1 - - + +
381B THR* 4.2 17.0 - - - -
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B TYR* 4.2 14.6 - + + -
179B ILE* 3.7 42.6 - - + -
180B ASP* 5.5 0.4 - - - -
183B ILE* 4.5 8.1 - - + -
210B THR* 3.8 31.2 - - + -
211B MET 3.6 4.7 - - - -
212B THR* 3.6 36.3 - - - -
216B ARG* 4.9 0.9 - - - -
225B THR* 3.5 37.7 - - + -
226B TRP* 1.3 71.4 - - - +
228B GLY* 1.3 59.3 + - - +
229B LEU* 4.4 2.9 - - + +
246B GLU* 3.2 4.5 - - - -
247B LEU* 2.7 43.5 + - + +
249B VAL* 3.9 15.9 - - + -
251B HIS* 4.7 0.2 - - - -
378B ALA* 5.6 0.2 - - - -
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Residues in contact with GLY 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B THR* 3.2 7.3 - - - -
211B MET 3.1 31.2 + - - -
213B THR* 5.7 0.4 - - - +
226B TRP 4.1 1.4 + - - -
227B PHE* 1.3 74.4 - - - +
229B LEU* 1.3 62.0 + - - +
230B TYR* 3.4 15.9 + - - -
242B HIS* 4.1 4.9 - - - -
245B LEU 3.7 7.6 - - - -
246B GLU* 4.1 12.5 - - - +
378B ALA* 5.2 5.3 - - - +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ILE* 4.6 1.8 - - + -
184B PHE* 3.8 19.5 - - + -
188B LEU* 3.9 14.8 - - + -
208B LEU* 3.7 28.7 - - + -
209B VAL 3.2 6.3 - - - +
210B THR* 4.2 12.3 - - + -
227B PHE* 4.4 3.1 - - + +
228B GLY* 1.3 77.1 - - - +
230B TYR* 1.3 62.3 - - - +
242B HIS* 3.8 5.6 + - - -
243B VAL* 3.1 38.9 + - + +
245B LEU* 3.1 29.3 + - + +
247B LEU* 3.7 35.0 - - + -
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Residues in contact with TYR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.2 8.5 - - - +
209B VAL* 2.7 42.4 + - + +
211B MET* 3.7 34.7 + - + +
228B GLY* 3.4 27.3 - - - -
229B LEU* 1.3 76.4 - - - +
231B TYR* 1.3 62.6 + - - +
238B PHE* 3.5 46.2 - + + +
239B PHE* 3.8 19.3 - - + -
241B HIS 3.3 7.6 - - - +
242B HIS* 3.4 46.9 + + + -
243B VAL* 4.3 1.3 - - - -
496B SER* 5.8 1.7 - - - -
497B SER 4.0 6.6 + - - -
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Residues in contact with TYR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B CYS 3.2 17.2 + - - -
199B CYS* 3.4 27.7 - - - +
200B PHE* 3.7 2.6 - + - -
207B ASN* 3.7 10.5 - - - -
208B LEU* 3.9 11.0 - - + -
209B VAL* 4.5 0.2 - - - -
230B TYR* 1.3 73.1 - - - +
232B ASN* 1.3 60.1 + - - +
233B ILE* 2.8 29.0 + - + +
238B PHE* 3.4 16.8 - - - +
241B HIS* 3.2 22.9 + + + -
243B VAL* 3.7 19.2 - - + +
291B ILE* 2.6 37.5 + - + +
292B PRO 3.3 27.1 - - - -
293B ASP* 3.7 24.2 - - + -
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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