Contacts of the helix formed by residues 217 - 235 (chain B) in PDB entry 2PKG
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 GLN 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B PRO* 3.1 32.2 - - - +
182B ARG* 4.8 4.2 - - - +
183B ARG* 3.8 0.7 + - - -
215B ASP* 2.6 17.9 + - - +
216B GLU* 1.3 79.6 + - + +
218B ASP* 1.3 70.6 + - - +
219B SER* 3.2 23.0 + - - +
220B VAL* 2.9 19.1 + - + +
221B ARG* 2.9 15.6 + - - +
147D TRP* 3.2 15.5 - - - +
148D PHE* 3.0 42.4 - - + +
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Residues in contact with ASP 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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216B GLU 3.9 0.2 + - - -
217B GLN* 1.3 71.0 - - - +
219B SER* 1.3 63.0 + - - -
220B VAL 2.6 11.1 + - - -
221B ARG* 3.3 30.8 - - - +
222B LEU* 2.6 36.7 + - + +
256B SER* 3.1 30.4 + - - +
258B ARG* 4.1 22.5 + - + -
259B VAL* 4.4 3.8 - - + -
148D PHE 5.2 1.0 - - - +
150D LEU* 5.6 5.8 - - - +
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ARG* 3.6 26.3 - - - -
217B GLN* 3.2 23.1 + - - +
218B ASP* 1.3 79.2 + - - +
220B VAL* 1.3 58.1 + - - +
222B LEU* 4.2 11.2 - - - +
223B LEU* 3.5 22.0 - - - +
258B ARG* 6.6 0.2 - - - +
148D PHE 3.0 27.0 + - - -
149D GLY* 4.7 6.5 - - - -
150D LEU* 5.8 0.7 - - - -
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PRO* 4.3 5.4 - - + +
182B ARG* 4.1 20.9 - - + +
183B ARG* 3.5 25.4 - - + -
186B ALA* 4.7 3.5 - - + +
212B LEU* 3.7 27.7 - - + +
215B ASP* 3.4 37.2 - - + +
217B GLN* 2.9 14.6 + - + +
218B ASP 2.6 4.8 + - - -
219B SER* 1.3 74.2 - - - +
221B ARG* 1.3 56.2 + - - +
222B LEU 2.9 2.0 - - - -
223B LEU* 2.6 32.1 + - - +
224B ALA 3.2 6.6 + - - -
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU 3.5 10.3 - - - -
213B ALA* 3.1 24.6 - - - +
214B SER* 3.5 7.4 - - - +
215B ASP 3.1 42.5 + - - +
216B GLU 3.2 16.4 + - - -
217B GLN 2.9 5.8 + - - +
218B ASP* 2.9 31.1 + - - +
220B VAL* 1.3 75.6 - - - +
222B LEU* 1.3 62.7 + - - +
224B ALA* 2.9 19.6 + - - +
225B VAL* 3.5 7.8 + - - +
254B ASP* 2.9 35.9 + - - +
255B LYS* 5.0 5.5 - - - +
256B SER* 3.9 6.7 - - - +
259B VAL* 4.3 7.9 - - + +
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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
----------------------------------------------------------
218B ASP* 2.6 22.6 + - + +
219B SER* 4.2 10.3 - - - +
221B ARG* 1.3 73.3 - - - +
223B LEU* 1.3 85.1 + - + +
225B VAL* 3.2 20.6 + - - +
226B GLU 4.0 1.4 + - - -
258B ARG* 4.3 29.8 - - + +
259B VAL* 4.0 17.4 - - + +
262B MET* 3.3 35.6 - - + +
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Residues in contact with LEU 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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183B ARG* 3.6 33.9 - - + +
186B ALA* 3.6 19.4 - - + +
187B SER* 4.3 17.5 - - - +
219B SER 3.5 19.7 - - - +
220B VAL* 2.6 13.0 + - - +
222B LEU* 1.3 93.8 - - + +
224B ALA* 1.3 67.6 + - - +
226B GLU* 3.1 22.6 + - + +
227B ALA* 3.5 4.5 + - - +
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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
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186B ALA* 4.9 4.3 - - - +
189B LEU* 6.0 1.1 - - - -
209B PHE* 3.6 12.8 - - + -
212B LEU* 3.8 12.6 - - + +
213B ALA* 3.2 41.3 - - + +
220B VAL 3.2 4.4 + - - -
221B ARG 2.9 14.8 + - - +
223B LEU* 1.3 76.5 - - - +
225B VAL* 1.3 63.4 + - + +
227B ALA* 2.9 19.4 + - - +
228B CYS 3.0 9.2 + - - -
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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
----------------------------------------------------------
209B PHE* 5.4 0.2 - - - -
221B ARG 3.5 3.1 + - - +
222B LEU 3.2 11.4 + - - +
223B LEU 3.1 0.4 - - - -
224B ALA* 1.3 77.1 - - + +
226B GLU* 1.3 67.4 + - - +
228B CYS* 2.8 25.2 + - + +
229B VAL* 3.6 4.9 + - - +
248B LEU* 6.4 0.4 - - + -
251B ALA* 4.1 20.0 - - + -
259B VAL* 3.8 28.3 - - + -
262B MET* 3.6 26.7 - - + -
263B VAL* 3.8 22.0 - - + +
266B LYS* 4.8 6.7 - - + -
270B LEU* 4.9 5.1 - - + +
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Residues in contact with GLU 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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187B SER* 5.9 7.2 - - - +
222B LEU 4.0 1.4 + - - -
223B LEU* 3.1 14.7 + - + +
225B VAL* 1.3 79.3 - - - +
227B ALA* 1.3 65.8 + - - +
229B VAL* 3.0 17.9 + - - +
230B ASN* 3.0 23.0 + - - +
262B MET* 4.3 8.9 - - + +
266B LYS* 3.2 37.7 - - - +
269B GLU* 5.3 3.5 - - - +
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA 5.0 2.9 - - - +
189B LEU* 4.2 21.1 - - + -
190B GLY* 4.1 24.5 - - - +
209B PHE* 4.6 2.0 - - + -
223B LEU 3.5 4.3 + - - +
224B ALA* 2.9 12.4 + - - +
226B GLU* 1.3 81.5 - - - +
228B CYS* 1.3 64.3 + - - +
229B VAL 2.8 0.9 + - - -
230B ASN* 3.1 9.1 + - - -
231B ILE* 2.7 34.6 + - + +
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Residues in contact with CYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 3.7 27.3 - - + -
224B ALA 3.0 5.2 + - - +
225B VAL* 2.8 20.7 + - + +
227B ALA* 1.3 76.3 - - - +
229B VAL* 1.3 63.1 + - - +
231B ILE* 4.0 3.5 - - - +
232B ALA* 3.0 24.3 + - - +
244B VAL* 3.6 27.9 - - - +
248B LEU* 3.7 33.7 - - + -
270B LEU* 4.3 5.6 - - + -
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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
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225B VAL 4.4 3.6 - - - +
226B GLU* 3.0 12.6 + - - +
227B ALA 2.8 1.8 + - - -
228B CYS* 1.3 73.7 - - - +
230B ASN* 1.3 71.9 + - - +
232B ALA* 2.8 17.8 + - - +
233B GLN* 3.0 30.6 + - - +
266B LYS* 4.5 12.6 - - + -
269B GLU* 4.4 25.4 - - + +
270B LEU* 3.2 39.3 - - + +
273B ALA* 4.1 10.7 - - + +
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Residues in contact with ASN 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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190B GLY* 4.2 27.3 - - - +
191B GLU* 4.9 1.4 - - - +
194B LYS* 3.7 33.8 - - + +
226B GLU* 3.0 31.6 + - - +
227B ALA* 3.6 7.3 - - - +
229B VAL* 1.3 75.1 - - - +
231B ILE* 1.3 65.4 + - - +
233B GLN* 3.0 30.0 + - - +
234B LEU* 3.5 13.7 - - - +
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Residues in contact with ILE 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 LEU* 4.4 3.4 - - + -
190B GLY* 5.2 1.6 - - - -
193B ALA* 4.6 9.2 - - + -
201B VAL* 4.9 6.1 - - + -
205B ILE* 3.6 22.9 - - + -
206B ILE* 3.8 26.0 - - + -
209B PHE* 3.5 42.8 - - + -
227B ALA* 2.7 33.5 + - + +
228B CYS* 4.0 4.0 - - - +
230B ASN* 1.3 71.8 - - + +
232B ALA* 1.3 58.7 + - - +
234B LEU* 2.9 34.8 + - - +
235B LEU* 3.6 12.6 + - + +
244B VAL* 4.7 5.2 - - + -
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Residues in contact with ALA 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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228B CYS* 3.0 21.2 + - - +
229B VAL* 2.8 10.8 + - - +
231B ILE* 1.3 71.7 - - - +
233B GLN* 1.3 58.0 + - - +
234B LEU 3.1 1.9 + - - -
235B LEU 3.7 15.6 - - - +
240B LEU* 3.8 24.9 - - + +
244B VAL* 4.4 14.1 - - + +
270B LEU* 6.1 1.1 - - + -
273B ALA* 3.9 21.9 - - + +
274B VAL* 4.7 12.6 - - + +
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Residues in contact with GLN 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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194B LYS* 4.6 12.8 + - - -
229B VAL* 3.0 22.1 + - - +
230B ASN* 3.0 26.0 + - - +
232B ALA* 1.3 76.7 - - - +
234B LEU* 1.3 62.8 + - + +
235B LEU 4.9 1.5 - - - +
269B GLU 5.6 1.0 + - - -
272B LYS* 5.6 8.9 - - - +
273B ALA* 3.4 31.4 - - + +
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Residues in contact with LEU 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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193B ALA* 3.9 18.8 - - + +
194B LYS* 3.9 46.9 - - + +
196B LEU 6.0 0.9 - - - +
198B LEU* 3.6 25.1 - - + +
201B VAL* 4.6 13.5 - - + -
230B ASN 3.5 15.7 - - - +
231B ILE* 2.9 12.9 + - - +
233B GLN* 1.3 84.4 - - + +
235B LEU* 1.3 67.1 + - + +
236B PRO* 3.8 3.5 - - - +
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Residues in contact with LEU 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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198B LEU* 3.8 21.5 - - + -
201B VAL* 3.9 23.8 - - + -
202B LYS* 4.3 11.2 - - + -
206B ILE* 4.1 9.6 - - + -
231B ILE* 3.6 10.9 + - + +
232B ALA 3.7 11.9 + - - +
233B GLN 4.9 1.0 - - - -
234B LEU* 1.3 78.1 - - - +
236B PRO* 1.3 73.7 - - + +
237B GLN 3.6 1.2 + - - -
239B ASP* 4.1 7.0 - - + -
240B LEU* 3.5 31.2 - - + +
243B LEU* 4.1 22.7 - - + -
244B VAL* 3.6 17.3 - - + -
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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
------------------------------------------------------------
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