Contacts of the helix formed by residues 221 - 232 (chain B) in PDB entry 2VSH
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 THR 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B LYS* 3.7 11.3 - - - +
219B ILE* 4.3 1.0 - - - +
220B THR* 1.3 91.6 - - + +
222B VAL* 1.3 65.6 + - - +
223B THR* 3.4 12.0 + - - +
224B ASP* 3.1 31.8 + - - +
225B LEU* 3.1 17.7 + - - +
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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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22B LYS* 4.0 15.4 - - - +
221B THR* 1.3 74.3 - - - +
223B THR* 1.3 73.9 + - + +
225B LEU* 3.2 9.2 + - - +
226B LYS* 3.0 24.4 + - - +
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Residues in contact with THR 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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227A ILE* 4.9 17.9 - - + +
230A SER* 5.0 12.8 - - - +
231A MET* 6.3 2.5 - - + -
221B THR* 3.3 9.3 + - - +
222B VAL* 1.3 84.8 - - + +
224B ASP* 1.3 64.9 + - - +
226B LYS* 3.1 13.2 + - + +
227B ILE* 2.8 35.8 + - - +
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Residues in contact with ASP 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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227A ILE* 6.2 0.5 - - - +
217B LEU* 3.4 24.0 - - + +
218B LYS 3.1 12.7 - - - +
219B ILE* 3.7 19.1 - - - -
220B THR* 3.0 22.7 + - - -
221B THR* 3.1 28.8 + - - +
223B THR* 1.3 78.9 + - - +
225B LEU* 1.3 57.6 + - - +
227B ILE* 3.4 4.6 + - - +
228B ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 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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22B LYS* 4.8 4.7 - - + -
25B LEU* 3.8 31.4 - - + -
26B GLU 4.2 5.6 - - - +
27B LEU* 4.8 2.2 - - + -
32B ILE* 3.8 26.7 - - + -
219B ILE* 3.9 13.4 - - + +
221B THR 3.1 11.2 + - - +
222B VAL* 3.4 11.9 - - - +
223B THR 3.1 0.6 - - - -
224B ASP* 1.3 77.2 - - - +
226B LYS* 1.3 57.1 + - - +
228B ALA* 3.2 7.6 + - + +
229B LYS* 2.9 66.5 + - + +
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Residues in contact with LYS 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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230A SER* 3.5 40.1 + - - +
233A GLU 5.4 2.6 + - - -
222B VAL 3.0 13.1 + - - +
223B THR* 3.4 14.4 - - + +
225B LEU* 1.3 74.8 - - - +
227B ILE* 1.3 68.5 + - + +
229B LYS* 3.3 15.7 + - + +
230B SER* 3.2 20.4 + - - -
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Residues in contact with ILE 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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223A THR* 3.9 13.7 - - + +
226A LYS* 3.8 31.2 - - + +
227A ILE* 3.7 35.2 - - + +
230A SER* 5.9 0.4 - - - +
217B LEU* 4.2 11.0 - - + -
223B THR* 2.8 25.7 + - - +
224B ASP* 3.7 7.2 - - - +
226B LYS* 1.3 76.0 - - + +
228B ALA* 1.3 67.3 + - - +
230B SER* 2.8 24.9 + - - +
231B MET* 3.1 36.1 + - + +
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Residues in contact with ALA 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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27B LEU* 3.7 13.0 - - + +
117B PHE* 3.7 25.4 - - + -
217B LEU* 4.0 3.8 - - + +
219B ILE* 3.6 29.2 - - + -
224B ASP 2.8 21.1 + - - +
225B LEU* 3.5 6.7 - - + +
227B ILE* 1.3 71.0 - - - +
229B LYS* 1.3 63.4 + - - +
231B MET* 3.0 16.4 + - - +
232B ILE* 3.3 8.1 + - - +
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Residues in contact with LYS 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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26B GLU* 3.0 30.3 + - - +
27B LEU* 3.7 16.3 - - + +
28B GLY 5.1 5.8 - - - +
225B LEU* 2.9 43.2 + - + +
226B LYS* 3.5 13.5 - - + +
227B ILE 3.2 0.2 - - - -
228B ALA* 1.3 76.5 - - - +
230B SER* 1.3 59.7 + - - +
232B ILE* 3.2 23.3 + - + +
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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
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226A LYS* 2.9 39.4 + - - +
226B LYS 3.2 8.5 + - - -
227B ILE* 2.8 18.7 + - - -
229B LYS* 1.3 78.1 - - - +
231B MET* 1.3 58.3 + - - +
232B ILE 3.2 2.6 + - - -
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Residues in contact with MET 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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223A THR* 3.9 20.0 - - + +
226A LYS* 4.5 8.1 - - - +
117B PHE* 4.0 35.0 - - + -
214B TYR 5.7 0.9 - - - +
215B SER* 4.8 21.5 - - - +
217B LEU* 4.4 10.1 - - + -
227B ILE* 3.1 34.7 + - + +
228B ALA* 3.0 10.1 + - - +
230B SER* 1.3 83.6 + - - +
232B ILE* 1.3 61.3 + - - +
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Residues in contact with ILE 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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27B LEU* 3.7 23.3 - - + -
28B GLY* 4.0 21.5 - - - +
30B ARG* 5.7 2.0 - - - +
35B HIS* 4.4 24.9 - - + +
39B LYS* 6.0 3.4 - - - +
117B PHE* 3.5 30.5 - - + -
228B ALA 3.3 4.9 + - - +
229B LYS* 3.2 20.3 + - - +
230B SER 3.2 2.0 - - - -
231B MET* 1.3 82.4 - - - +
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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