Contacts of the helix formed by residues 219 - 235 (chain B) in PDB entry 2I91
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 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A GLN* 3.9 8.7 - - - +
275A ASP* 2.9 23.7 + - - -
218B LEU* 1.3 78.0 - - - +
220B PRO* 1.3 73.7 - - - +
221B GLU* 3.2 7.7 + - - +
222B THR* 3.2 18.3 + - - -
223B GLU* 2.9 28.1 + - - +
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Residues in contact with PRO 220 (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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249A ASP* 3.9 43.1 - - + +
274A GLN* 3.3 37.0 - - + +
275A ASP* 4.8 4.5 - - + +
218B LEU 4.6 0.7 - - - +
219B SER* 1.3 90.9 - - - +
221B GLU* 1.3 61.9 + - + +
223B GLU* 3.6 7.1 + - + +
224B LYS* 3.3 25.5 + - - +
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Residues in contact with GLU 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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252A ARG* 3.0 49.4 + - - +
275A ASP* 2.5 31.6 - - - +
160B ASP* 6.2 0.3 - - - +
161B ALA* 5.6 2.1 - - - +
162B LEU* 4.6 18.0 + - - +
219B SER* 3.2 3.0 + - - +
220B PRO* 1.3 79.2 - - - +
222B THR* 1.3 64.1 + - - +
224B LYS* 3.3 32.2 + - - +
225B VAL* 3.5 12.0 + - - +
14D A 5.8 1.2 - - - +
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Residues in contact with THR 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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193B GLU* 3.9 30.2 - - + +
194B GLY* 4.4 15.1 + - - -
197B MET* 3.6 12.0 - - + +
218B LEU* 3.2 28.0 - - + -
219B SER* 3.2 25.0 + - - -
221B GLU* 1.3 76.1 - - - +
223B GLU* 1.3 67.3 + - - +
225B VAL* 3.0 17.3 + - - +
226B LEU* 3.1 12.0 + - - +
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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
----------------------------------------------------------
218B LEU* 4.0 23.0 - - + +
219B SER 2.9 17.2 + - - +
220B PRO* 3.7 8.3 - - + +
222B THR* 1.3 75.5 - - - +
224B LYS* 1.3 53.9 + - - +
226B LEU* 3.1 29.7 + - - +
227B LYS* 2.8 52.6 + - + +
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Residues in contact with LYS 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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249A ASP 5.8 2.0 + - - +
250A GLU* 4.1 20.6 + - - +
251A TYR* 5.8 1.0 - - - +
252A ARG* 5.6 6.1 - - - +
162B LEU* 3.9 25.3 - - + +
220B PRO 3.3 15.1 + - - +
221B GLU* 3.3 27.1 + - - +
223B GLU* 1.3 80.0 - - - +
225B VAL* 1.3 60.7 + - + +
227B LYS* 3.4 11.2 - - + +
228B TYR* 3.2 23.2 + - - +
251B TYR* 5.5 1.5 - - + -
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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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161B ALA* 3.4 28.5 - - + +
162B LEU* 3.5 23.6 - - + +
165B ALA* 4.5 4.5 - - + -
194B GLY* 4.2 5.8 - - - +
197B MET* 4.0 14.1 - - - -
198B VAL* 3.7 30.3 - - + -
221B GLU* 3.6 15.9 - - - +
222B THR* 3.0 11.7 + - - +
224B LYS* 1.3 74.2 - - - +
226B LEU* 1.3 65.1 + - - +
228B TYR* 3.5 3.1 + - - +
229B LEU* 3.1 25.2 + - + +
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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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197B MET* 3.6 31.5 - - + -
206B TRP* 3.6 33.7 - - + -
209B VAL* 4.6 7.4 - - + +
210B GLN* 5.4 2.7 - - + -
213B TYR* 4.8 21.5 - - + +
218B LEU* 4.9 4.7 - - + -
222B THR 3.1 6.0 + - - +
223B GLU* 3.1 29.0 + - - +
225B VAL* 1.3 73.4 - - - +
227B LYS* 1.3 58.0 + - - +
229B LEU* 3.1 4.8 + - - +
230B GLU* 2.7 36.0 + - + +
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Residues in contact with LYS 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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223B GLU* 2.8 31.1 + - + +
224B LYS* 3.4 16.2 - - + +
226B LEU* 1.3 77.4 - - - +
228B TYR* 1.3 52.6 + - - +
230B GLU* 3.1 26.1 + - - +
231B ALA* 2.8 32.2 + - - +
250B GLU* 5.4 1.6 + - - -
251B TYR* 3.7 32.6 + - + +
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Residues in contact with TYR 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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162B LEU* 4.1 15.7 - - + -
165B ALA* 3.7 20.6 - - + -
166B MET* 3.1 55.4 - - + +
169B THR* 3.7 7.6 - - + -
224B LYS 3.2 13.1 + - - +
225B VAL 3.6 3.6 - - - +
226B LEU 3.2 0.2 - - - -
227B LYS* 1.3 76.4 - - - +
229B LEU* 1.3 71.6 + - + +
231B ALA* 2.8 18.8 + - - +
232B THR* 2.8 18.8 + - + +
251B TYR* 3.5 45.4 + + + -
252B ARG 5.1 2.1 + - - -
253B LEU* 3.8 12.5 - - + +
257B HIS* 3.4 18.5 + - - -
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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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165B ALA* 4.6 16.4 - - + -
168B VAL* 5.4 1.1 - - + -
169B THR* 4.3 11.9 - - + -
197B MET* 4.1 26.9 - - + +
198B VAL* 4.5 5.4 - - + -
201B TYR* 3.4 54.9 - - + -
206B TRP* 3.7 18.2 - - + -
209B VAL* 5.2 0.7 - - + -
225B VAL* 3.1 21.5 + - + +
226B LEU 3.1 6.1 + - - +
228B TYR* 1.3 78.7 - - - +
230B GLU* 1.3 62.1 + - - +
232B THR* 2.5 19.5 + - - -
233B GLU* 3.0 15.1 + - - +
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Residues in contact with GLU 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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206B TRP* 3.4 30.1 - - + +
210B GLN* 5.5 2.8 - - - +
226B LEU* 2.7 18.5 + - + +
227B LYS* 3.1 32.4 + - - +
229B LEU* 1.3 73.2 - - - +
231B ALA* 1.3 57.8 + - - +
233B GLU* 3.1 3.8 + - - +
234B ARG* 2.8 36.7 + - + +
251B TYR* 5.5 0.3 + - - -
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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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227B LYS 2.8 8.9 + - - +
228B TYR 2.8 14.1 + - - +
230B GLU* 1.3 71.9 - - - +
232B THR* 1.3 60.9 + - - +
234B ARG* 3.0 16.0 + - - +
235B VAL* 2.8 24.6 + - - +
247B LEU* 4.0 9.6 - - + +
251B TYR* 3.3 46.2 - - + -
253B LEU* 4.6 4.7 - - + -
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Residues in contact with THR 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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169B THR* 4.0 22.2 - - - +
201B TYR* 4.5 4.9 + - - -
228B TYR* 2.8 17.1 + - + +
229B LEU* 2.5 32.6 + - - +
231B ALA* 1.3 73.0 - - - +
233B GLU* 1.3 61.6 + - - +
235B VAL* 3.4 17.0 - - - +
236B LYS* 3.6 20.6 - - - +
253B LEU* 3.6 15.9 - - + -
257B HIS* 3.5 37.6 - - + +
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Residues in contact with GLU 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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172B LYS* 5.1 2.9 + - - -
201B TYR* 2.7 32.2 + - + -
206B TRP* 3.3 52.3 - - + +
207B LYS* 5.6 1.9 + - - -
229B LEU 3.0 12.2 + - - +
230B GLU 3.1 7.2 + - - +
232B THR* 1.3 76.7 - - - +
234B ARG* 1.3 63.8 + - - +
236B LYS* 3.1 27.6 + - - +
237B ARG* 3.6 34.0 + - + +
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Residues in contact with ARG 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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230B GLU* 2.8 21.2 + - + +
231B ALA* 3.0 11.0 + - - +
233B GLU* 1.3 71.7 - - - +
235B VAL* 1.3 58.0 + - - +
236B LYS 2.9 10.2 + - - -
237B ARG* 3.1 22.0 + - - +
238B THR* 3.2 18.9 + - - +
243B GLU* 3.2 32.8 + - - +
247B LEU* 3.8 14.4 - - + -
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Residues in contact with VAL 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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231B ALA 2.8 19.6 + - - +
232B THR* 3.4 14.6 - - - +
234B ARG* 1.3 70.9 - - - +
236B LYS* 1.3 56.8 + - - +
237B ARG 3.6 0.7 - - - -
238B THR* 4.0 14.3 - - - +
244B ILE* 4.4 14.0 - - + +
247B LEU* 4.0 12.1 - - + +
248B ILE* 5.9 0.4 - - + -
253B LEU* 3.5 25.6 - - + -
257B HIS* 3.7 21.3 - - + +
258B LEU* 3.7 24.9 - - + -
259B LEU* 4.6 1.0 - - - +
262B HIS* 3.9 19.1 - - - -
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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