Contacts of the helix formed by residues 211 - 231 (chain B) in PDB entry 2G5W
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 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLY 3.7 2.8 + - - -
210B GLY* 1.3 75.3 - - - +
212B ILE* 1.3 64.3 + - - +
213B ALA* 3.7 9.6 + - - +
214B ASN* 2.9 36.4 + - - +
215B ARG* 3.1 22.3 + - - +
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Residues in contact with ILE 212 (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 SER* 1.3 71.2 - - - +
213B ALA* 1.3 65.1 + - - +
215B ARG* 3.2 29.3 + - - +
216B CYS* 3.1 23.5 + - - -
255B SER* 3.6 28.0 - - - +
256B LEU* 4.2 24.2 - - + -
259B ALA* 3.6 27.8 - - + -
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER* 3.2 9.7 + - - +
212B ILE* 1.3 77.8 - - - +
214B ASN* 1.3 61.9 + - - +
216B CYS* 3.1 17.2 + - - +
217B ARG* 3.2 16.2 + - - +
259B ALA* 5.6 1.3 - - - +
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Residues in contact with ASN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 5.8 0.3 - - - -
206B ASP 4.5 1.0 - - - +
207B GLN* 2.7 32.9 + - - +
208B TYR* 3.4 14.6 - - - +
209B GLY 3.1 28.8 - - - +
210B GLY* 4.7 0.2 - - - -
211B SER* 2.9 27.5 + - - +
213B ALA* 1.3 78.5 - - - +
215B ARG* 1.3 61.3 + - - +
217B ARG* 3.2 37.7 + - - +
218B PHE 4.5 0.3 + - - -
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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
----------------------------------------------------------
196B PHE* 3.3 34.3 - - - +
197B LEU* 3.3 27.3 + - - +
199B ASP* 3.4 32.5 + - - +
202B ASN* 3.4 26.0 - - - +
208B TYR 4.0 5.6 - - - +
209B GLY* 4.4 5.4 - - - -
210B GLY 3.8 15.7 + - - +
211B SER 3.1 11.6 + - - +
212B ILE* 3.2 53.5 + - + +
214B ASN* 1.3 76.7 - - - +
216B CYS* 1.3 60.8 + - - +
217B ARG 3.6 0.3 + - - -
218B PHE* 4.4 2.4 + - - +
219B LEU 5.0 0.3 + - - -
250B ASP* 3.0 28.7 + - - -
256B LEU* 4.4 2.5 - - + +
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Residues in contact with CYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 4.0 12.8 - - - -
212B ILE 3.1 15.1 + - - +
213B ALA* 3.1 11.4 + - - +
215B ARG* 1.3 75.0 - - - +
217B ARG* 1.3 59.2 + - - +
218B PHE 3.2 1.6 - - - -
219B LEU* 3.2 4.7 + - - +
220B LYS* 2.8 30.3 + - + +
256B LEU* 4.8 5.6 - - - -
259B ALA* 4.1 24.7 - - - -
260B VAL* 3.9 28.7 - - - -
263B MET* 4.8 17.0 - - + -
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Residues in contact with ARG 217 (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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98A ALA* 5.8 5.9 - - - +
207B GLN* 2.9 40.3 + - - +
208B TYR* 3.7 17.3 - - + -
213B ALA* 3.2 12.0 + - - +
214B ASN* 3.2 33.4 + - - +
216B CYS* 1.3 77.2 - - - +
218B PHE* 1.3 57.3 + - - +
220B LYS* 3.3 16.1 + - + +
221B GLN* 3.0 45.9 + - + +
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Residues in contact with PHE 218 (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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156B LEU* 5.5 0.9 - - + -
161B ILE* 3.3 44.6 - - + -
164B VAL* 4.0 14.6 - - + -
165B VAL* 4.4 3.8 - - + -
168B TYR* 4.7 1.6 - + - -
192B LEU* 3.9 33.2 - - + -
193B ILE* 3.6 32.5 - - + -
196B PHE* 3.6 46.2 - + + -
208B TYR* 4.1 8.4 - - + -
214B ASN 4.5 0.4 + - - -
215B ARG 4.4 1.4 + - - +
216B CYS 3.2 0.8 - - - -
217B ARG* 1.3 76.6 - - - +
219B LEU* 1.3 65.3 + - - +
221B GLN* 3.3 5.1 + - - +
222B VAL* 3.1 43.0 + - + +
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Residues in contact with LEU 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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185B ILE* 4.5 13.2 - - + -
187B GLY* 5.2 1.1 - - - -
193B ILE* 4.0 26.9 - - + +
196B PHE* 5.7 0.2 - - - +
197B LEU* 4.1 28.7 - - + -
215B ARG 5.0 1.0 + - - -
216B CYS* 3.2 7.9 + - - +
218B PHE* 1.3 78.7 - - - +
220B LYS* 1.3 58.8 + - - +
222B VAL* 3.2 6.3 + - + +
223B VAL* 2.9 49.4 + - + +
237B VAL* 4.4 13.7 - - + -
239B VAL* 4.5 7.2 - - + -
260B VAL* 4.0 21.5 - - + -
263B MET* 3.6 24.2 - - + -
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Residues in contact with LYS 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 CYS 2.8 13.8 + - - +
217B ARG* 3.3 20.3 - - + +
218B PHE 3.2 0.2 - - - -
219B LEU* 1.3 77.5 - - - +
221B GLN* 1.3 52.3 - - + +
223B VAL* 3.3 2.0 + - - +
224B GLU* 2.7 69.0 + - - +
263B MET* 3.9 38.3 - - + +
266B LYS* 6.2 4.3 - - - -
267B LEU* 4.1 6.0 - - + +
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Residues in contact with GLN 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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98A ALA* 3.7 27.7 - - + +
99A LYS* 6.1 0.4 - - - +
161B ILE* 3.9 12.1 - - - +
162B PRO* 4.6 2.6 - - - +
165B VAL* 3.7 22.7 - - + +
208B TYR* 2.7 44.3 + - - -
217B ARG* 3.0 29.4 + - + +
218B PHE* 3.7 5.4 - - - +
219B LEU 3.3 0.2 - - - -
220B LYS* 1.3 75.4 - - + +
222B VAL* 1.3 58.5 + - - +
224B GLU* 3.3 13.9 + - - +
225B GLY* 2.9 28.1 + - - -
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Residues in contact with VAL 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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165B VAL* 4.0 22.7 - - + +
168B TYR* 3.7 44.9 - - + -
185B ILE* 3.8 23.8 - - + -
193B ILE* 4.5 3.8 - - + -
218B PHE* 3.1 38.5 + - + +
219B LEU* 3.6 8.3 - - - +
221B GLN* 1.3 74.9 - - - +
223B VAL* 1.3 65.1 + - + +
225B GLY* 3.9 0.5 - - - -
226B VAL* 3.1 25.3 + - - +
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Residues in contact with VAL 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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185B ILE* 4.8 9.2 - - + -
219B LEU* 2.9 40.7 + - + +
220B LYS* 3.7 3.4 - - - +
222B VAL* 1.3 76.2 - - - +
224B GLU* 1.3 65.3 + - - +
225B GLY 3.3 0.2 + - - -
226B VAL* 4.0 3.0 - - - +
227B VAL* 2.9 36.8 + - + +
235B VAL* 5.2 2.0 - - + -
237B VAL* 3.9 21.1 - - + -
264B LEU* 3.9 20.2 - - + -
267B LEU* 3.8 27.1 - - + -
275B LEU* 4.6 7.0 - - + -
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Residues in contact with GLU 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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220B LYS* 2.7 60.4 + - - +
221B GLN* 3.6 15.1 - - - +
223B VAL* 1.3 72.2 - - - +
225B GLY* 1.3 58.6 + - - +
227B VAL* 3.8 5.3 - - - +
228B SER* 3.0 32.3 + - - -
267B LEU* 3.8 20.3 - - + +
270B VAL* 6.0 2.3 - - - +
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Residues in contact with GLY 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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165B VAL* 4.7 4.9 - - - -
169B CYS* 3.5 26.9 - - - -
221B GLN 2.9 19.0 + - - -
222B VAL 3.9 0.9 - - - -
224B GLU* 1.3 73.2 - - - +
226B VAL* 1.3 62.8 + - - +
228B SER* 3.3 9.8 + - - -
229B ALA* 3.0 17.8 + - - +
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Residues in contact with VAL 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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107B LEU* 4.5 0.4 - - + -
168B TYR* 3.9 32.8 - - + +
169B CYS* 4.0 2.0 - - - +
172B ALA* 3.9 14.1 - - + -
183B ILE* 3.7 19.7 - - + -
185B ILE* 4.0 19.3 - - + -
222B VAL 3.1 20.0 + - - +
223B VAL* 4.0 3.1 - - - +
225B GLY* 1.3 72.1 - - - +
227B VAL* 1.3 65.3 + - - +
229B ALA* 3.0 8.2 + - - +
230B ILE* 3.0 24.9 + - + +
235B VAL* 3.7 24.7 - - + -
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Residues in contact with VAL 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 VAL* 2.9 30.7 + - + +
224B GLU* 3.8 5.4 - - - +
226B VAL* 1.3 75.9 - - - +
228B SER* 1.3 59.6 + - - +
231B GLY* 2.7 30.1 + - - +
232B ALA* 3.7 12.8 - - + +
235B VAL* 4.0 16.4 - - + -
267B LEU* 4.4 8.7 - - + -
271B ASN* 3.6 37.2 - - - +
275B LEU* 3.8 28.5 - - + -
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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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224B GLU 3.0 16.5 + - - -
225B GLY* 3.3 13.6 + - - -
227B VAL* 1.3 77.1 - - - +
229B ALA* 1.3 60.9 + - - +
231B GLY 4.8 0.5 + - - -
271B ASN* 5.9 1.1 - - - -
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Residues in contact with ALA 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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387A PRO* 4.3 15.4 - - - +
169B CYS* 4.4 12.8 - - + +
172B ALA* 5.0 0.9 - - + -
173B LEU* 3.9 36.8 - - + +
225B GLY 3.0 11.5 + - - +
226B VAL* 3.0 13.1 + - - +
228B SER* 1.3 79.7 - - - +
230B ILE* 1.3 67.3 + - + +
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Residues in contact with ILE 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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20B ARG* 5.6 0.3 + - - -
172B ALA* 3.8 19.7 - - + +
173B LEU* 4.1 8.7 - - + +
176B ILE* 3.7 34.5 - - + -
183B ILE* 3.8 24.0 - - + -
226B VAL* 3.0 20.0 + - + +
229B ALA* 1.3 85.1 - - + +
231B GLY* 1.3 65.2 + - - +
234B LYS* 3.2 55.9 + - + +
235B VAL* 3.9 5.8 - - + -
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Residues in contact with GLY 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 VAL* 2.7 23.6 + - - -
228B SER 4.7 0.4 - - - -
229B ALA 3.8 0.4 - - - -
230B ILE* 1.3 75.9 - - - +
232B ALA* 1.3 66.3 + - - -
233B SER* 3.4 4.0 - - - -
234B LYS* 3.2 12.7 + - - +
235B VAL* 3.3 13.0 - - - +
271B ASN* 5.7 0.9 - - - -
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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