Contacts of the strand formed by residues 210 - 216 (chain X) in PDB entry 2Q0Z
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 210 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208X PRO* 3.7 3.0 - - + -
209X ASN* 1.3 84.1 + - - +
211X GLU* 1.3 74.0 + - - +
212X LEU 3.7 0.6 + - - +
234X LEU* 3.9 19.3 - - + -
235X GLU 3.4 19.1 - - - +
236X ARG* 4.2 14.4 - - + +
238X GLU* 4.5 1.8 - - - +
257X TRP* 3.4 34.1 - - + -
277X LEU* 3.6 23.8 - - + -
301X PHE* 3.6 14.4 - - + -
311X GLN* 2.9 32.9 + - - +
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Residues in contact with GLU 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209X ASN* 5.9 0.7 - - - +
210X ILE* 1.3 73.6 - - - +
212X LEU* 1.3 59.7 + - - +
213X SER* 4.0 0.8 + - - -
233X GLN 3.5 1.7 - - - +
234X LEU* 3.5 4.3 - - - -
235X GLU* 2.9 40.1 + - + +
237X GLU* 2.8 40.6 - - + +
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Residues in contact with LEU 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X ILE 3.7 3.0 + - - -
211X GLU* 1.3 73.2 - - - +
213X SER* 1.3 68.2 + - - +
214X TYR* 4.0 18.2 - - + -
232X VAL* 3.7 20.6 - - + -
233X GLN 3.5 2.7 - - - -
234X LEU* 3.6 23.3 - - + -
259X VAL* 5.9 0.9 - - + -
299X LEU* 4.0 13.7 - - + -
300X TYR 5.5 0.4 - - - +
301X PHE* 3.5 33.9 - - + -
311X GLN* 3.8 19.4 + - - +
313X TYR* 4.0 26.8 + - + -
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Residues in contact with SER 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X GLU* 4.0 1.1 + - - -
212X LEU* 1.3 75.8 - - - +
214X TYR* 1.3 63.9 + - - +
232X VAL* 3.5 2.6 - - - +
233X GLN* 2.8 51.7 + - - +
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Residues in contact with TYR 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212X LEU* 4.0 11.2 - - + -
213X SER* 1.3 77.2 - - - +
215X GLU* 1.3 67.0 + - - +
216X VAL* 4.8 9.2 - - + -
230X VAL* 4.4 10.8 - - + -
231X LEU 3.2 9.6 - - - +
232X VAL* 4.1 7.0 - - + -
299X LEU* 3.8 29.4 - - + -
313X TYR* 3.8 32.8 - + + +
314X LYS 4.3 5.2 + - - -
315X PHE* 3.6 37.0 - + + +
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Residues in contact with GLU 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X TYR* 1.3 77.7 - - - +
216X VAL* 1.3 72.8 + - - +
217X VAL* 3.3 15.8 + - + +
218X ASP 5.1 1.7 + - - -
230X VAL* 3.4 2.3 - - - -
231X LEU* 2.8 62.5 + - + +
233X GLN* 5.5 4.5 + - - -
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Residues in contact with VAL 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X TYR* 4.8 12.8 - - + -
215X GLU* 1.3 74.9 - - - +
217X VAL* 1.3 67.6 + - - +
218X ASP 3.3 2.6 + - - -
219X LYS* 3.4 29.7 + - + +
222X ILE* 3.9 28.7 - - + -
228X VAL* 4.5 6.1 - - + -
229X VAL 3.6 9.9 - - - +
230X VAL* 4.6 8.1 - - + +
315X PHE* 4.3 24.0 - - + -
316X SER 4.7 7.9 - - - +
317X VAL* 4.3 9.9 - - + -
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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