Contacts of the helix formed by residues 222 - 237 (chain B) in PDB entry 2VKZ
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 GLY 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B GLU* 3.6 24.7 - - - -
220B ALA* 3.1 11.0 - - - +
221B LEU* 1.3 80.3 - - - +
223B LYS* 1.3 60.3 + - - -
224B GLN 3.6 1.8 - - - -
226B SER* 2.7 33.8 + - - -
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Residues in contact with LYS 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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192B LYS* 3.2 44.5 + - + +
193B GLU* 3.7 1.8 + - - -
222B GLY* 1.3 71.4 - - - +
224B GLN* 1.3 61.9 + - - +
226B SER* 3.5 4.6 + - - -
227B SER* 3.2 22.9 + - - -
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Residues in contact with GLN 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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154B LEU* 4.3 12.3 - - + -
158B LYS* 6.0 0.4 - - - +
189B ASP* 3.7 54.6 + - + +
192B LYS* 4.0 24.2 + - + +
193B GLU* 3.2 9.9 + - + +
223B LYS* 1.3 76.6 - - - +
225B SER* 1.3 61.9 + - - +
227B SER* 3.8 8.6 + - - -
228B LEU* 3.3 40.4 + - - +
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Residues in contact with SER 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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150B LEU* 3.6 5.6 - - - +
154B LEU* 4.4 8.7 - - - -
193B GLU* 2.9 18.3 + - - -
221B LEU* 3.0 23.5 + - - +
222B GLY 3.9 0.2 + - - -
223B LYS 3.3 0.2 - - - -
224B GLN* 1.3 74.6 - - - +
226B SER* 1.3 58.3 + - - +
227B SER 3.2 2.2 - - - -
228B LEU* 3.2 6.6 + - - +
229B LEU* 3.0 35.6 + - - +
266B LEU* 3.1 32.1 - - - +
269B LEU* 4.7 1.2 - - - +
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.9 20.1 + - - +
222B GLY 2.7 23.7 + - - -
223B LYS* 3.8 5.4 - - - -
225B SER* 1.3 77.0 - - - +
227B SER* 1.3 59.4 + - - +
229B LEU* 4.1 6.5 - - - +
230B SER* 3.6 23.6 + - - -
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139A GLU* 3.2 30.2 + - - -
223B LYS 3.2 16.3 + - - -
224B GLN* 4.0 13.9 - - - -
225B SER 3.2 0.6 - - - -
226B SER* 1.3 77.9 - - - +
228B LEU* 1.3 58.5 + - - +
230B SER* 3.7 3.1 + - - -
231B ARG* 3.2 32.3 + - - +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.5 32.1 - - + +
157B HIS* 3.4 38.4 - - + +
189B ASP* 5.7 0.7 - - - +
224B GLN* 3.3 28.4 + - - +
225B SER 3.2 6.1 + - - +
227B SER* 1.3 82.4 - - - +
229B LEU* 1.3 57.5 + - - +
230B SER 3.5 0.2 - - - -
231B ARG* 3.8 21.0 - - - +
232B LEU* 3.2 26.2 + - - +
269B LEU* 3.5 23.6 - - + +
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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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221B LEU* 4.4 25.6 - - + -
225B SER* 3.0 27.5 + - - +
226B SER* 3.9 4.9 + - - +
227B SER 3.3 0.2 - - - -
228B LEU* 1.3 76.0 - - - +
230B SER* 1.3 61.0 + - - +
231B ARG 3.3 0.4 - - - -
232B LEU* 3.8 8.5 - - + +
233B ILE* 3.1 32.9 + - - +
243B ILE* 4.4 13.7 - - + -
247B ARG* 5.4 0.4 - - - +
262B ASP 5.0 0.4 - - - +
265B LEU* 3.2 54.7 - - + +
266B LEU* 4.2 5.2 - - + +
269B LEU* 3.5 28.7 - - + -
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137A SER* 3.8 24.7 + - - -
1162A GLU* 3.4 22.2 + - - -
226B SER 3.6 17.7 + - - -
227B SER* 3.7 3.3 + - - -
228B LEU 3.5 0.2 - - - -
229B LEU* 1.3 78.8 - - - +
231B ARG* 1.3 58.3 + - - +
232B LEU 3.5 0.2 - - - -
233B ILE* 3.9 8.6 - - - +
234B SER* 3.3 26.3 + - - -
243B ILE* 3.9 11.2 - - - +
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Residues in contact with ARG 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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1267A ASP* 3.7 32.5 + - - -
1268A GLU 4.8 0.6 + - - -
1269A PRO* 4.5 26.1 - - - +
157B HIS* 6.3 0.4 - - - -
227B SER* 3.2 22.1 + - - +
228B LEU* 3.8 22.1 - - - +
230B SER* 1.3 76.9 - - - +
232B LEU* 1.3 60.5 + - - +
233B ILE 3.3 0.2 - - - -
234B SER* 4.1 3.4 - - - -
235B SER* 2.8 33.7 + - - +
272B GLU* 5.9 1.8 - - - +
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Residues in contact with LEU 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 LEU 3.2 16.2 + - - +
229B LEU* 3.8 11.0 - - + +
230B SER 3.5 0.2 - - - -
231B ARG* 1.3 76.1 - - - +
233B ILE* 1.3 63.2 + - + +
235B SER* 4.5 1.8 - - - -
236B LYS* 3.2 32.5 + - + +
237B MET* 4.0 9.4 + - + +
265B LEU* 4.1 7.6 - - + +
268B ALA* 3.6 14.1 - - + +
269B LEU* 3.5 36.1 - - + +
272B GLU* 3.3 46.0 - - + +
273B PRO* 4.0 11.9 - - + -
286B PHE* 5.1 4.7 - - + -
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Residues in contact with ILE 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 LEU 3.1 20.5 + - - +
230B SER* 4.1 8.3 - - - +
231B ARG 3.3 0.2 - - - -
232B LEU* 1.3 81.6 - - + +
234B SER* 1.3 62.6 + - - +
237B MET* 3.0 55.4 - - + +
241B PHE 3.9 5.0 - - - +
242B THR* 3.7 23.3 - - + +
243B ILE* 3.4 41.3 - - + +
246B ALA* 4.1 8.7 - - + -
265B LEU* 5.6 6.7 - - + -
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Residues in contact with SER 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 SER 3.3 17.5 + - - -
231B ARG* 3.6 5.4 + - - -
232B LEU 3.4 0.4 - - - -
233B ILE* 1.3 83.4 - - - +
235B SER* 1.3 53.5 + - - +
237B MET 4.4 2.5 - - - +
276B ARG* 2.7 25.3 + - - -
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Residues in contact with SER 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 ARG* 2.8 21.7 + - - +
234B SER* 1.3 77.5 - - - +
236B LYS* 1.3 84.6 + - - +
276B ARG* 3.1 40.8 + - - +
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Residues in contact with LYS 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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1269A PRO* 5.0 14.1 - - - +
232B LEU* 3.2 19.3 + - + +
235B SER* 1.3 108.4 + - - +
237B MET* 1.3 61.9 - - + +
272B GLU* 3.7 29.4 + - - +
273B PRO* 3.0 48.2 - - + +
274B ALA* 4.6 4.2 - - - +
275B ALA* 3.8 17.9 - - - +
276B ARG* 3.9 6.7 - - - +
277B LEU* 3.0 33.6 + - - +
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Residues in contact with MET 237 (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 LEU* 4.0 11.8 + - + +
233B ILE* 3.0 55.8 + - + +
234B SER 4.4 2.9 - - - +
236B LYS* 1.3 85.6 - - + +
238B PRO* 1.3 76.3 - - + +
239B GLY* 4.7 0.2 - - - -
241B PHE* 3.2 50.7 - - + +
246B ALA* 5.0 2.2 - - + -
268B ALA* 6.4 0.4 - - + -
273B PRO* 6.4 0.2 - - - -
276B ARG* 3.2 16.6 + - - -
277B LEU* 4.4 9.0 - - - -
283B ALA* 4.2 9.9 - - - +
286B PHE* 4.5 20.4 - - + -
287B LEU* 5.2 6.7 - - + -
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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