Contacts of the helix formed by residues 214 - 233 (chain B) in PDB entry 5Y7G
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 LEU 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LEU* 3.6 8.0 - - - +
212B PHE* 4.0 3.1 - - - +
213B ARG* 1.3 109.5 - - + +
215B ARG* 1.3 63.4 + - - +
216B ALA* 3.9 13.7 - - + +
217B ASP* 3.3 48.8 + - - +
218B VAL 3.5 4.0 + - - -
251B ASN* 5.4 0.9 - - - +
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Residues in contact with ARG 215 (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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39B ASP 5.5 0.4 - - - +
40B LEU* 2.4 63.7 + - + +
41B LEU 5.3 0.7 - - - -
42B ASP* 3.4 22.5 + - - +
45B GLU* 2.4 43.5 + - - -
174B ARG* 3.7 19.1 - - - +
178B MET* 4.1 12.7 - - + +
214B LEU* 1.3 68.7 - - - +
216B ALA* 1.3 62.2 + - - +
217B ASP 3.0 1.8 - - - -
218B VAL* 2.9 22.7 + - - +
219B ASP* 2.9 27.1 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.3 17.4 - - + +
215B ARG* 1.3 77.9 - - - +
217B ASP* 1.3 59.0 + - - +
219B ASP* 3.5 16.2 - - + +
220B ALA* 2.9 25.1 + - - +
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Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PHE* 3.6 19.0 - - + -
213B ARG* 4.5 4.0 + - - +
214B LEU* 3.3 45.9 + - - +
215B ARG 3.0 1.0 - - - -
216B ALA* 1.3 77.6 - - - +
218B VAL* 1.3 65.4 + - - +
220B ALA* 3.1 3.6 + - - +
221B TYR* 2.9 19.6 + - - +
250B ALA* 5.9 2.1 - - - +
251B ASN* 3.2 27.1 + - - +
253B TRP* 6.5 0.2 - - + -
254B LEU* 3.6 27.8 - - + +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.7 2.2 - - + -
174B ARG* 3.5 35.7 - - + +
177B LEU* 4.4 9.6 - - + +
178B MET* 3.5 36.6 - - + +
212B PHE* 3.3 41.2 - - + -
214B LEU 3.5 3.3 + - - +
215B ARG* 2.9 12.2 + - + +
217B ASP* 1.3 71.9 - - - +
219B ASP* 1.3 65.1 + - - +
220B ALA 3.1 0.5 + - - -
221B TYR* 3.1 3.5 + - - +
222B LEU* 3.0 23.7 + - + +
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Residues in contact with ASP 219 (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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174B ARG* 2.2 41.3 + - - +
215B ARG* 2.9 33.8 + - - +
216B ALA* 3.5 18.6 - - + +
218B VAL* 1.3 74.3 - - - +
220B ALA* 1.3 57.1 + - - +
222B LEU* 3.9 4.0 - - - +
223B HIS* 3.0 29.3 + - - +
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Residues in contact with ALA 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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216B ALA 2.9 15.8 + - - +
217B ASP* 3.3 8.7 - - - +
218B VAL 3.0 0.6 - - - -
219B ASP* 1.3 73.3 - - - +
221B TYR* 1.3 66.9 + - - +
223B HIS* 2.8 16.2 + - - +
224B LEU* 2.9 19.5 + - + +
249B TYR* 4.1 29.1 + - + -
254B LEU* 3.6 22.2 - - + -
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Residues in contact with TYR 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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177B LEU* 4.0 21.3 - - + -
181B GLY 4.1 9.6 - - - -
182B ASN* 3.8 9.3 - - - +
183B LEU* 3.6 27.7 + - + +
184B TRP* 5.2 1.6 - - - -
212B PHE* 3.9 23.6 - + + -
217B ASP 2.9 13.4 + - - +
218B VAL 3.8 5.6 - - - +
220B ALA* 1.3 75.4 - - - +
222B LEU* 1.3 64.4 + - - +
224B LEU* 3.4 6.6 + - - +
225B PHE* 2.9 34.0 + + + +
253B TRP* 4.0 19.5 - + - -
254B LEU* 4.4 13.8 - - + +
257B ARG* 2.5 42.6 + - + -
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Residues in contact with LEU 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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170B ALA* 5.3 4.3 - - + +
173B ASP* 4.8 5.8 - - + -
174B ARG* 3.5 57.2 - - + +
177B LEU* 3.5 26.0 - - + +
183B LEU* 4.9 7.6 - - + -
218B VAL* 3.0 15.3 + - + +
219B ASP* 3.9 4.3 - - - +
221B TYR* 1.3 77.2 - - - +
223B HIS* 1.3 58.8 + - - +
225B PHE* 3.4 4.6 + - - +
226B ASP* 2.9 30.5 + - - +
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Residues in contact with HIS 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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219B ASP 3.0 18.0 + - - +
220B ALA* 2.8 9.7 + - - +
222B LEU* 1.3 76.4 - - - +
224B LEU* 1.3 64.4 + - + +
226B ASP* 3.2 8.3 + - - +
227B CYS* 3.0 45.4 + - - -
230B ARG* 4.7 10.8 - - - -
243B GLY 3.8 20.1 + - - -
245B PRO* 4.5 11.0 - - + +
249B TYR* 3.8 19.1 - - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ALA* 2.9 19.2 + - + +
221B TYR* 3.9 6.1 - - + +
223B HIS* 1.3 76.0 - - + +
225B PHE* 1.3 58.4 + - - +
227B CYS* 2.9 20.0 + - - +
228B ARG* 3.0 13.2 + - - +
244B LEU* 4.9 1.3 - - + -
245B PRO* 4.6 14.4 - - + -
249B TYR* 4.0 27.4 - - + +
254B LEU* 3.9 14.4 - - + +
257B ARG* 4.0 13.0 - - + -
258B ARG* 3.7 35.9 - - + +
261B LEU* 3.9 25.6 - - + +
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 3.5 42.2 - - + -
221B TYR* 2.9 29.3 + + + +
222B LEU 3.9 2.9 - - - +
224B LEU* 1.3 78.4 - - - +
226B ASP* 1.3 66.6 + - - +
228B ARG* 3.3 17.5 + - + +
229B GLN* 3.0 54.9 + - + +
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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
----------------------------------------------------------
222B LEU 2.9 18.1 + - - +
223B HIS* 3.7 8.6 + - - +
225B PHE* 1.3 79.8 - - - +
227B CYS* 1.3 57.6 + - - +
229B GLN* 3.2 11.5 + - - +
230B ARG* 2.9 61.7 + - - +
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Residues in contact with CYS 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 HIS* 3.0 45.9 + - - -
224B LEU* 2.9 11.0 + - - +
226B ASP* 1.3 73.9 - - - +
228B ARG* 1.3 66.6 + - - +
230B ARG* 3.1 31.0 + - - +
231B PHE 3.1 9.4 + - - -
240B LEU* 4.7 3.4 - - + +
243B GLY 5.0 3.4 - - - -
244B LEU* 3.5 24.5 - - + -
261B LEU* 3.7 15.5 - - + -
265B PHE* 3.8 10.4 - - + -
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Residues in contact with ARG 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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224B LEU 3.0 10.0 + - - +
225B PHE* 4.0 18.2 - - + +
227B CYS* 1.3 75.5 - - - +
229B GLN* 1.3 67.2 + - + +
231B PHE* 3.0 17.2 + - + +
232B ASP* 3.3 27.0 + - - +
260B LYS* 5.8 4.0 - - - +
261B LEU* 3.6 22.2 - - + +
264B GLN* 3.7 36.8 + - + +
265B PHE* 4.5 3.6 - - + -
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Residues in contact with GLN 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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225B PHE* 3.0 49.9 + - + +
226B ASP* 3.4 15.7 - - - +
228B ARG* 1.3 79.5 - - + +
230B ARG* 1.3 62.8 + - - +
232B ASP* 3.1 25.8 + - - +
233B LEU* 3.3 24.3 + - + +
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Residues in contact with ARG 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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223B HIS* 4.7 9.3 - - - -
226B ASP* 2.9 40.4 + - - +
227B CYS* 3.1 27.2 + - - +
229B GLN* 1.3 74.7 - - - +
231B PHE* 1.3 62.4 + - - +
233B LEU* 3.7 11.9 + - - +
234B GLY 3.8 0.2 + - - -
235B GLU* 3.1 54.3 + - - +
240B LEU* 3.8 12.0 - - + +
243B GLY* 5.5 7.9 + - - -
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Residues in contact with PHE 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 CYS 3.1 4.4 + - - -
228B ARG* 3.0 12.0 + - + +
230B ARG* 1.3 76.6 - - - +
232B ASP* 1.3 79.9 + - - +
233B LEU 3.1 2.0 - - - -
234B GLY* 3.0 20.3 + - - -
235B GLU 4.5 1.9 + - - +
237B LEU* 4.2 19.1 - - + -
240B LEU* 3.9 7.4 - - + +
264B GLN* 5.3 4.7 - - + -
265B PHE* 3.3 40.8 - + + -
268B HIS* 3.1 60.8 - + + -
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 3.3 23.6 + - - +
229B GLN* 3.1 19.6 + - - +
231B PHE* 1.3 101.2 - - - +
233B LEU* 1.3 67.8 + - + +
234B GLY 3.5 0.4 - - - -
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Residues in contact with LEU 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 GLN* 3.3 20.3 + - + +
230B ARG* 3.7 7.8 + - - +
231B PHE 3.1 1.6 - - - -
232B ASP* 1.3 86.0 - - + +
234B GLY* 1.3 58.5 + - - +
235B GLU 3.8 1.1 - - - +
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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
------------------------------------------------------------
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