Contacts of the strand formed by residues 226 - 234 (chain B) in PDB entry 2GQ3
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 SER 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B PHE 4.2 4.0 - - - -
223B ALA* 3.1 17.0 + - - +
225B GLU* 1.3 81.4 - - - +
227B PRO* 1.4 71.4 - - - +
228B THR* 3.8 4.5 + - - +
243B ILE* 6.6 0.4 - - - -
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Residues in contact with PRO 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE 3.4 24.2 - - - +
194B THR* 4.2 2.2 - - - -
195B VAL* 4.8 5.2 - - + -
220B TYR* 4.3 9.2 - - + -
221B THR 3.3 13.2 - - - +
223B ALA 2.9 16.7 - - - +
224B ALA 3.8 8.7 - - - +
226B SER* 1.4 87.4 - - - +
228B THR* 1.3 61.0 + - - +
229B SER 3.1 17.2 + - - +
230B VAL* 3.8 20.2 - - + -
243B ILE* 3.7 26.0 - - + +
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Residues in contact with THR 228 (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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221B THR* 2.5 34.2 + - - -
222B GLY* 3.2 11.4 + - - -
226B SER 5.0 2.9 - - - +
227B PRO* 1.3 72.0 - - - +
229B SER* 1.3 63.1 + - - +
242B LEU* 4.0 4.3 - - - +
243B ILE 3.2 29.4 + - - +
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 3.2 8.1 - - - +
221B THR* 2.8 44.9 + - - +
227B PRO* 3.1 5.1 - - - +
228B THR* 1.3 84.1 - - - +
230B VAL* 1.3 67.0 + - - +
240B GLU* 2.5 31.1 + - - +
241B ILE 3.1 15.0 - - - -
242B LEU* 3.7 9.2 - - - -
243B ILE* 4.2 2.5 - - - +
320B TYR* 4.6 0.5 - - - -
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 4.5 11.7 - - + -
194B THR 5.7 0.2 - - - +
195B VAL* 5.4 2.0 - - + -
200B LEU* 3.3 35.0 - - + -
217B PHE* 5.2 1.1 - - + -
219B GLY 4.0 6.7 - - - +
220B TYR* 4.4 5.8 - - + -
227B PRO* 3.8 22.0 - - + -
229B SER* 1.3 80.5 - - - +
231B LEU* 1.3 61.2 + - - +
232B LEU* 3.8 15.4 + - + -
239B ILE 3.5 2.1 - - - +
240B GLU* 3.1 5.0 - - - -
241B ILE* 2.7 51.8 + - + +
243B ILE* 4.2 10.5 - - + -
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Residues in contact with LEU 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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135B TRP* 4.5 2.2 - - + -
217B PHE* 3.9 1.0 - - - -
218B ALA* 3.0 30.0 + - + +
219B GLY 3.0 22.4 + - - +
220B TYR* 4.2 0.6 - - - +
230B VAL* 1.3 72.7 - - - +
232B LEU* 1.3 67.1 - - - +
238B HIS* 3.9 33.9 - - + -
239B ILE 3.4 1.8 - - - +
240B GLU* 4.1 12.3 - - + +
320B TYR* 3.6 49.8 - - + +
328B PHE* 4.0 15.5 - - + -
330B LEU* 3.7 22.2 - - + -
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Residues in contact with LEU 232 (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 LEU* 4.2 14.6 - - + -
180B VAL* 4.2 29.4 - - + -
187B PHE* 5.0 4.3 - - + -
200B LEU* 3.7 29.4 - - + -
211B LEU* 4.5 5.8 - - + -
216B GLN 3.3 16.4 - - - +
217B PHE* 4.6 0.9 - - - -
218B ALA* 4.3 1.8 - - - +
230B VAL* 3.8 6.1 - - + -
231B LEU* 1.3 79.7 - - - +
233B ILE* 1.3 66.5 + - - +
238B HIS* 3.3 10.2 - - - -
239B ILE* 2.6 46.6 + - + +
241B ILE* 3.6 31.2 - - + -
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Residues in contact with ILE 233 (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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180B VAL* 4.9 0.4 - - - +
215B GLY 4.3 5.6 - - - +
216B GLN* 3.0 44.0 + - - +
218B ALA* 4.1 11.7 - - + -
232B LEU* 1.3 80.4 - - - +
234B ASN* 1.3 65.8 + - - +
236B GLY* 3.9 15.9 - - - +
237B LEU 3.3 25.4 - - - +
238B HIS* 3.8 26.5 - - + +
239B ILE* 5.0 2.0 - - - +
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Residues in contact with ASN 234 (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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179B SER* 3.3 26.9 + - - +
216B GLN* 3.3 13.2 + - - +
233B ILE* 1.3 79.5 - - - +
235B HIS* 1.3 78.1 + - - +
236B GLY 3.0 0.7 - - - -
237B LEU* 2.8 25.0 + - - +
239B ILE* 4.6 4.9 - - + -
556B HIS* 3.1 58.9 + - + +
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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