Contacts of the helix formed by residues 220 - 236 (chain B) in PDB entry 2XH7
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 THR 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B LEU* 3.8 11.8 - - - +
218B ILE* 3.7 0.9 - - - +
219B GLN* 1.3 89.8 - - + +
221B ALA* 1.3 64.6 - - - +
222B GLU* 3.9 14.8 - - - +
223B GLU* 3.0 33.3 + - - +
224B ALA* 3.4 14.6 + - - +
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Residues in contact with ALA 221 (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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164B LEU* 4.3 1.9 - - - +
166B LEU* 4.1 15.0 - - + -
169B PHE* 4.0 25.6 - - + -
220B THR* 1.3 71.0 - - - +
222B GLU* 1.3 61.6 + - - +
224B ALA* 3.1 2.6 + - - +
225B LEU* 2.7 40.5 + - - +
281B LEU* 5.1 4.5 - - + -
285B LEU* 3.9 26.0 - - + -
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B THR* 3.9 13.3 - - - +
221B ALA* 1.3 85.2 + - - +
223B GLU* 1.3 56.1 + - - +
225B LEU* 3.5 0.4 + - - -
226B ASP* 2.9 29.4 + - - +
281B LEU* 5.1 13.1 - - - +
284B SER* 5.3 5.4 + - - -
285B LEU* 3.7 26.3 - - + +
289B TYR* 3.1 24.7 + - + +
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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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200B ARG* 4.8 1.6 + - - +
201B TYR* 2.8 33.3 + - - +
218B ILE* 3.5 24.2 - - + +
219B GLN* 3.7 7.4 + - - +
220B THR* 3.0 37.3 + - - +
222B GLU* 1.3 77.7 - - - +
224B ALA* 1.3 63.7 + - - +
226B ASP* 3.7 10.8 - - + +
227B LEU* 3.0 29.8 + - - +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.9 19.9 - - + +
164B LEU* 4.5 1.1 - - + -
169B PHE* 3.8 25.6 - - + -
218B ILE* 3.7 20.6 - - + -
220B THR 3.4 8.2 + - - +
221B ALA 3.1 9.3 + - - +
223B GLU* 1.3 78.3 - - - +
225B LEU* 1.3 57.9 + - - +
227B LEU* 3.2 5.7 + - - +
228B ILE* 3.1 31.5 + - - +
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Residues in contact with LEU 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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169B PHE* 3.9 22.0 - - + -
221B ALA 2.7 23.5 + - - +
224B ALA* 1.3 71.0 - - - +
226B ASP* 1.3 59.8 + - - +
228B ILE* 3.3 5.9 + - + +
229B VAL* 3.0 33.6 + - - +
243B ILE* 3.8 38.8 - - + -
245B LEU* 4.2 4.5 - - + -
285B LEU* 3.9 28.5 - - + -
289B TYR* 3.6 42.2 - - + -
291B ILE* 4.2 9.0 - - + -
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Residues in contact with ASP 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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200B ARG* 4.4 8.3 - - - +
222B GLU* 2.9 23.7 + - - +
223B GLU* 3.7 11.0 - - + +
224B ALA 3.3 0.2 - - - -
225B LEU* 1.3 74.5 - - - +
227B LEU* 1.3 59.2 + - - +
229B VAL* 3.9 2.8 - - - +
230B ASP* 2.9 40.2 + - - +
289B TYR* 2.7 31.1 + - - -
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.8 20.9 - - + -
193B LEU* 3.8 10.0 - - + +
196B LEU* 3.9 28.6 - - + +
197B THR* 3.6 32.8 - - - +
200B ARG* 3.9 17.6 - - - +
201B TYR* 3.7 29.8 - - + -
216B PRO* 4.0 10.8 - - + -
218B ILE* 4.9 1.6 - - + -
223B GLU 3.0 13.3 + - - +
224B ALA 3.3 8.7 - - - +
226B ASP* 1.3 75.7 - - - +
228B ILE* 1.3 57.1 + - - +
230B ASP* 3.3 3.8 + - - +
231B ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.4 13.9 - - + -
154B LEU* 4.5 11.9 - - + -
169B PHE* 3.4 43.5 - - + -
171B ILE* 3.6 29.2 - - + -
189B VAL* 5.5 1.1 - - + -
193B LEU* 4.5 5.4 - - + -
224B ALA 3.1 16.0 + - - +
225B LEU* 3.7 12.8 - - + +
226B ASP 3.3 0.2 - - - -
227B LEU* 1.3 73.6 - - - +
229B VAL* 1.3 65.6 + - - +
231B ALA* 3.0 8.3 + - - +
232B ILE* 2.9 26.9 + - + +
243B ILE* 3.8 22.2 - - + -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU 3.0 19.9 + - - +
226B ASP* 4.0 6.1 - - - +
228B ILE* 1.3 74.2 - - - +
230B ASP* 1.3 62.9 + - - +
232B ILE* 3.3 11.4 + - + +
233B LYS* 3.0 32.1 + - + +
238B ASP* 4.8 3.2 - - - +
243B ILE* 4.4 6.5 - - + -
288B ARG 5.4 0.4 - - - +
289B TYR* 3.6 24.2 - - + -
290B PRO* 4.2 19.3 - - + -
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Residues in contact with ASP 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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196B LEU* 3.2 25.0 - - + +
200B ARG* 2.7 31.7 + - - -
226B ASP* 2.9 30.3 + - - +
227B LEU 3.5 0.9 - - - +
228B ILE 3.2 0.2 - - - -
229B VAL* 1.3 79.4 - - - +
231B ALA* 1.3 58.2 + - - +
233B LYS* 3.4 31.2 + - - +
234B ALA* 2.9 27.9 + - - +
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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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189B VAL* 3.8 12.7 - - + +
192B ASN* 3.8 6.3 - - - +
193B LEU* 3.7 41.1 - - + +
196B LEU* 4.2 4.2 - - + +
227B LEU 2.9 13.5 + - - +
228B ILE* 3.0 8.9 + - - +
230B ASP* 1.3 76.0 - - - +
232B ILE* 1.3 64.5 - - - +
234B ALA* 3.3 6.7 + - - +
235B ALA* 3.0 24.9 + - - +
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Residues in contact with ILE 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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189B VAL* 3.9 18.2 - - + -
228B ILE* 2.9 37.5 + - + +
229B VAL* 3.7 12.6 - - + +
231B ALA* 1.3 76.1 - - - +
233B LYS* 1.3 62.3 + - - +
235B ALA* 3.4 1.4 + - - +
236B GLY 3.1 16.6 + - - -
237B HIS 3.1 21.3 + - - +
238B ASP* 3.6 29.8 - - - +
239B GLY 5.1 0.2 - - - +
241B ILE* 3.7 44.9 - - + +
243B ILE* 4.5 10.1 - - + -
290B PRO* 5.2 3.4 - - + -
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Residues in contact with LYS 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 VAL* 3.0 19.5 + - + +
230B ASP* 3.4 32.1 + - - +
232B ILE* 1.3 76.2 - - - +
234B ALA* 1.3 58.5 + - - +
236B GLY* 2.9 21.0 + - - -
238B ASP* 3.4 23.0 + - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN* 3.5 26.6 + - + +
196B LEU* 5.8 3.8 - - + -
230B ASP 2.9 18.3 + - - +
231B ALA* 3.3 6.3 + - - +
233B LYS* 1.3 77.2 - - - +
235B ALA* 1.3 61.5 + - - +
236B GLY 3.5 0.5 + - - -
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Residues in contact with ALA 235 (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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188B GLU* 4.0 5.3 - - + +
189B VAL* 4.0 17.7 - - + +
192B ASN* 3.5 21.7 - - - +
231B ALA 3.0 15.7 + - - +
232B ILE 3.9 3.1 - - - +
233B LYS 3.2 0.2 - - - -
234B ALA* 1.3 75.9 - - - +
236B GLY* 1.3 61.4 + - - +
237B HIS* 3.5 33.0 + - + +
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Residues in contact with GLY 236 (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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232B ILE 3.1 0.2 + - - -
233B LYS 2.9 16.7 + - - -
234B ALA 3.2 1.4 + - - -
235B ALA* 1.3 79.1 - - - +
237B HIS* 1.3 67.7 + - - +
238B ASP* 3.6 8.2 + - - -
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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