Contacts of the helix formed by residues 221 - 235 (chain B) in PDB entry 2XAR
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 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A GLN* 4.3 15.5 + - - -
329A PRO 4.8 3.2 + - - -
331A PRO* 3.9 15.5 - - - -
219B SER* 3.1 16.4 + - - -
220B GLY* 1.3 77.6 - - - +
222B LYS* 1.3 65.3 + - - +
223B GLU* 3.1 19.9 + - - -
224B ARG* 3.2 20.4 + - - +
225B VAL* 3.0 25.1 + - - +
296B TYR* 4.0 1.6 - - - -
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Residues in contact with LYS 222 (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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329A PRO* 6.0 4.0 - - + +
331A PRO* 5.6 0.6 - - - +
335A GLU* 3.4 28.3 + - + -
221B SER* 1.3 72.7 + - - +
223B GLU* 1.3 69.5 + - + +
225B VAL* 3.4 3.8 + - - +
226B LEU* 3.3 19.1 + - - +
289B GLN* 4.1 9.3 - - - +
292B SER* 4.1 4.1 + - - +
293B ASP* 2.8 31.5 + - - +
296B TYR* 3.7 41.4 + - + +
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Residues in contact with GLU 223 (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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328A GLN* 5.4 3.0 - - - +
329A PRO* 2.8 42.8 - - - +
221B SER* 3.1 17.0 + - - -
222B LYS* 1.3 75.2 + - + +
224B ARG* 1.3 61.0 + - + +
225B VAL 3.2 0.7 - - - -
226B LEU* 3.3 14.1 + - + +
227B GLU* 2.9 33.2 + - - +
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Residues in contact with ARG 224 (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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328A GLN* 5.5 5.8 - - - +
417A GLU* 5.6 3.2 + - - -
213B ASP* 5.1 1.6 + - - -
215B LEU* 3.4 29.5 + - - +
216B ASP* 2.7 43.4 + - - +
219B SER* 3.3 34.5 - - - +
221B SER* 3.2 17.6 + - - +
223B GLU* 1.3 79.5 - - + +
225B VAL* 1.3 62.8 + - - +
227B GLU* 3.4 13.1 - - - +
228B ALA* 3.1 17.0 + - - +
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Residues in contact with VAL 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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216B ASP 3.9 6.1 - - - +
217B LEU* 3.6 25.8 - - + +
219B SER* 4.8 0.2 - - - +
220B GLY* 4.9 1.8 - - - +
221B SER 3.0 24.6 + - - +
222B LYS 3.6 8.5 - - - +
223B GLU 3.2 0.2 - - - -
224B ARG* 1.3 74.7 - - - +
226B LEU* 1.3 63.9 + - - +
228B ALA* 3.1 7.9 + - - +
229B ILE* 3.0 21.1 + - + +
292B SER* 3.5 31.2 - - - +
295B VAL* 3.7 22.0 - - + -
296B TYR* 4.2 17.9 - - + -
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Residues in contact with LEU 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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222B LYS 3.3 9.1 + - - +
223B GLU* 3.3 15.5 + - + +
225B VAL* 1.3 74.3 - - - +
227B GLU* 1.3 57.4 + - - +
229B ILE* 3.1 2.7 + - + -
230B LYS* 2.8 68.0 + - + +
285B GLU 5.7 0.4 - - - +
288B LEU* 4.3 4.9 - - + +
289B GLN* 3.9 38.6 - - + +
292B SER* 3.1 34.7 + - - +
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Residues in contact with GLU 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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216B ASP* 5.0 15.9 - - - +
223B GLU* 2.9 21.4 + - - +
224B ARG* 3.4 15.8 - - - +
226B LEU* 1.3 76.1 - - - +
228B ALA* 1.3 57.7 + - - +
230B LYS* 3.4 10.3 + - - +
231B ALA* 2.9 29.0 + - - +
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Residues in contact with ALA 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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212B TYR* 4.2 10.9 - - + -
213B ASP 4.8 1.3 - - - +
216B ASP* 4.1 7.1 - - + +
217B LEU* 3.8 37.5 - - + +
224B ARG 3.1 11.3 + - - +
225B VAL 3.1 9.2 + - - +
227B GLU* 1.3 76.8 - - - +
229B ILE* 1.3 61.1 + - - +
231B ALA* 3.1 8.2 + - - +
232B LEU* 2.8 33.8 + - - +
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Residues in contact with ILE 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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167B ILE* 4.2 10.8 - - + -
217B LEU* 3.9 21.5 - - + -
225B VAL* 3.0 14.8 + - + +
226B LEU 3.8 4.9 - - - +
228B ALA* 1.3 75.2 - - - +
230B LYS* 1.3 63.7 + - - +
232B LEU* 3.4 14.3 + - + +
233B TYR* 3.0 22.9 + - - +
240B PHE* 4.3 7.9 - - + -
288B LEU* 3.8 33.4 - - + +
291B VAL* 3.7 31.9 - - + -
292B SER* 3.8 20.4 - - - -
295B VAL* 4.2 5.6 - - + -
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Residues in contact with LYS 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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226B LEU* 2.8 52.8 + - + +
227B GLU* 3.6 8.7 - - - +
229B ILE* 1.3 76.4 - - - +
231B ALA* 1.3 63.4 + - - +
233B TYR* 3.4 4.9 + - - +
234B SER* 3.1 25.1 + - - -
285B GLU* 6.3 3.1 - - - -
288B LEU* 4.3 23.3 - - + -
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Residues in contact with ALA 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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211B GLU* 3.6 43.5 - - + +
212B TYR* 3.7 9.0 - - - -
213B ASP 5.2 0.2 - - - +
227B GLU* 2.9 14.8 + - + +
228B ALA* 3.2 10.8 - - - +
230B LYS* 1.3 76.7 - - - +
232B LEU* 1.3 63.4 + - - +
234B SER* 2.9 14.4 + - - -
235B THR* 3.0 18.3 + - - -
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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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167B ILE* 4.3 13.7 - - + -
212B TYR* 3.6 36.1 - - + -
217B LEU* 4.6 3.1 - - + -
228B ALA 2.8 30.1 + - - +
229B ILE* 3.6 21.3 - - + +
231B ALA* 1.3 72.0 - - - +
233B TYR* 1.3 62.4 + - - +
235B THR 4.4 5.4 - - - +
236B PRO* 3.0 30.6 - - - +
239B ASN* 3.7 41.3 - - + +
240B PHE* 3.3 22.4 - - + -
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Residues in contact with TYR 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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229B ILE 3.0 6.6 + - - +
230B LYS 3.5 10.3 - - - +
232B LEU* 1.3 75.9 - - - +
234B SER* 1.3 63.4 + - - +
236B PRO* 3.3 5.7 - - - +
240B PHE* 4.4 11.3 - - + -
250B LEU* 3.7 23.0 - - + +
260B THR* 2.7 48.3 + - + +
265B GLY* 3.5 25.2 + - - -
268B PHE* 4.0 17.3 - + - -
284B THR* 3.7 27.7 + - + +
288B LEU* 3.6 38.8 - - + -
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Residues in contact with SER 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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211B GLU* 3.4 27.9 + - - -
230B LYS 3.1 11.9 + - - -
231B ALA 2.9 10.6 + - - -
233B TYR* 1.3 85.9 - - - +
235B THR* 1.3 60.8 + - - +
259B ARG* 3.5 12.5 + - - +
260B THR* 2.8 33.8 + - - -
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Residues in contact with THR 235 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B GLU* 4.7 6.7 - - + +
209B GLU 4.3 2.9 - - - +
210B SER* 3.1 24.8 + - - -
211B GLU* 2.8 30.6 + - - +
212B TYR* 5.3 0.5 - - - +
231B ALA 3.0 9.5 + - - +
232B LEU* 3.3 8.9 - - - +
234B SER* 1.3 81.9 - - - +
236B PRO* 1.3 65.2 - - - +
237B GLN* 3.3 11.2 + - - +
239B ASN* 5.2 1.2 - - - +
258B GLY 5.4 0.4 - - - -
259B ARG* 3.6 43.3 - - + +
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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