Contacts of the strand formed by residues 222 - 230 (chain B) in PDB entry 2Q4E
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 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B ARG 4.9 0.2 - - - +
181B GLY 5.0 0.2 + - - -
182B LEU 3.9 14.1 + - - +
183B GLY* 3.3 6.8 - - - -
184B ALA* 3.0 23.8 + - + +
185B LEU* 3.9 33.9 - - + +
214B ALA* 6.0 0.9 - - + -
215B VAL 4.0 2.0 - - - +
216B LEU* 3.3 22.7 - - + -
220B GLY 5.0 0.4 - - - +
221B VAL* 1.3 75.6 - - - +
223B LEU* 1.3 65.2 + - - +
224B SER* 3.5 26.7 - - - +
225B CYS* 3.9 18.4 - - + -
243B PHE* 4.3 0.7 - - - -
347B LYS* 4.2 27.4 - - + -
350B VAL* 5.1 9.0 - - + -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 4.3 14.8 - - + +
175B VAL* 4.2 28.3 - - + -
184B ALA* 3.3 7.6 - - - +
215B VAL* 2.9 30.3 + - + +
217B ASN* 4.4 22.0 - - + +
221B VAL* 4.2 8.5 - - + +
222B ILE* 1.3 78.9 - - - +
224B SER* 1.3 61.9 + - - +
243B PHE* 2.8 36.2 + - + +
244B LEU* 3.2 32.5 - - + +
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ALA* 4.3 1.1 - - - -
213B GLY 4.9 0.3 - - - +
214B ALA* 3.9 0.5 - - - -
215B VAL* 3.2 41.7 + - - +
222B ILE* 3.5 6.8 - - - +
223B LEU* 1.3 83.7 - - - +
225B CYS* 1.3 65.6 + - - +
240B TYR* 4.2 8.9 + - - -
241B CYS 2.9 17.3 - - - -
242B SER* 3.5 18.8 - - - +
244B LEU* 4.1 5.9 - - - +
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Residues in contact with CYS 225 (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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185B LEU* 4.2 7.2 - - - -
211B PHE 6.2 0.2 - - - +
214B ALA* 4.1 21.1 - - + +
222B ILE* 3.9 20.2 - - + -
224B SER* 1.3 77.0 - - - +
226B GLY* 1.3 63.3 + - - +
239B ILE* 4.4 0.7 - - - +
240B TYR* 3.6 10.9 - - - -
241B CYS* 2.8 52.7 + - - -
346B VAL* 3.8 27.4 - - - -
350B VAL* 4.8 3.6 - - + -
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Residues in contact with GLY 226 (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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210B ALA* 3.6 5.5 - - - +
211B PHE* 2.9 33.0 + - - +
225B CYS* 1.3 80.4 - - - +
227B ALA* 1.3 68.1 + - - +
239B ILE* 3.1 22.0 - - - -
240B TYR* 4.3 5.0 - - - -
346B VAL* 4.7 2.5 - - - +
350B VAL* 5.4 0.2 - - - +
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Residues in contact with ALA 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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208B VAL* 4.8 1.8 - - + -
209B THR 3.1 18.8 - - - +
210B ALA* 3.3 9.2 - - - -
211B PHE* 3.0 31.7 - - - -
226B GLY* 1.3 77.9 - - - +
228B SER* 1.3 63.4 + - - +
229B LEU* 5.4 2.4 - - + +
238B THR* 3.3 1.6 - - - -
239B ILE* 3.2 29.5 + - + +
346B VAL* 4.2 18.4 - - + -
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Residues in contact with SER 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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211A PHE* 3.3 33.8 - - - +
212A PRO* 3.9 12.9 - - - +
208B VAL* 4.1 0.3 - - - -
209B THR* 3.5 23.2 + - - -
211B PHE* 3.3 12.8 - - - -
227B ALA* 1.3 75.7 - - - +
229B LEU* 1.3 77.3 + - - +
236B THR* 6.1 1.3 - - - -
237B ALA 3.2 12.1 - - - -
238B THR* 3.8 6.1 - - - -
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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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212A PRO 5.4 0.7 - - - +
193B ILE* 5.4 3.4 - - + -
196B THR* 4.3 20.6 - - + +
197B LEU* 5.8 2.0 - - + -
205B PRO* 3.7 24.2 - - + -
207B THR 4.0 2.2 - - - -
208B VAL* 3.3 37.5 - - + -
227B ALA* 5.4 4.0 - - + +
228B SER* 1.3 89.6 - - - +
230B SER* 1.3 62.3 + - - +
231B TRP* 3.7 21.3 - - + -
236B THR* 3.3 28.2 - - - +
237B ALA* 3.0 13.8 + - + +
238B THR* 5.9 0.9 - - - -
239B ILE* 5.7 11.2 - - + -
342B VAL* 4.6 13.7 - - + -
346B VAL* 5.9 1.6 - - + -
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Residues in contact with SER 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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212A PRO* 4.6 15.3 - - - -
213A GLY* 3.8 18.3 + - - -
205B PRO* 3.4 1.4 - - - +
206B LYS* 2.6 38.2 + - - +
207B THR* 3.6 18.1 + - - -
229B LEU* 1.3 77.4 - - - +
231B TRP* 1.3 62.7 + - - +
232B GLU* 3.4 11.8 + - - +
235B ARG 3.9 2.5 - - - -
236B THR* 4.3 4.2 - - - +
356B GLN* 5.0 6.1 - - - -
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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