Contacts of the helix formed by residues 191 - 202 (chain B) in PDB entry 3VZC
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 ARG 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 3.7 28.2 + - - -
178B ASP 4.0 6.9 + - - -
181B SER* 3.0 57.3 + - - +
183B LYS* 3.3 26.9 - - + +
184B TYR* 3.7 24.4 + - - +
185B ARG 4.9 2.5 + - - -
190B MET* 1.3 89.4 - - + +
192B PHE* 1.3 87.4 + - + +
193B THR 3.2 0.2 - - - -
194B LEU* 4.0 7.2 - - - +
195B GLY* 3.0 23.9 + - - -
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Residues in contact with PHE 192 (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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112B SER* 4.1 8.5 - - - -
113B GLY* 4.0 27.6 - - - -
177B VAL* 3.9 6.6 - - + +
178B ASP* 3.3 29.2 - - - -
181B SER* 4.1 8.3 - - - -
190B MET* 3.2 17.8 - - + -
191B ARG* 1.3 116.9 - - - +
193B THR* 1.3 56.2 + - - +
196B THR* 2.5 36.3 + - - -
272B MET* 5.0 18.6 - - + -
303B PHE* 4.2 2.4 - - - -
1001B UUL 4.1 20.9 - + + -
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Residues in contact with THR 193 (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 MET* 2.9 20.0 + - - +
192B PHE* 1.3 77.8 - - - +
194B LEU* 1.3 64.9 + - - +
196B THR* 3.6 0.3 + - - -
197B PHE* 3.1 56.5 + - + -
303B PHE* 3.6 23.4 - - - -
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 3.8 36.3 - - + +
190B MET 3.4 8.4 + - - +
191B ARG* 4.2 7.2 - - - +
193B THR* 1.3 79.4 - - - +
195B GLY* 1.3 60.5 + - - +
196B THR 3.3 0.2 + - - -
197B PHE* 3.3 9.9 + - + +
198B LEU* 3.2 41.7 + - + +
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Residues in contact with GLY 195 (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 VAL* 3.3 27.7 - - - +
180B GLU* 5.1 4.3 - - - +
181B SER* 5.2 0.9 - - - -
183B LYS* 4.4 15.4 - - - +
191B ARG 3.0 18.2 + - - -
194B LEU* 1.3 77.6 - - - +
196B THR* 1.3 59.0 + - - +
198B LEU* 4.1 5.6 - - - +
199B ARG* 3.4 15.4 + - - +
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Residues in contact with THR 196 (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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173B PHE* 3.6 20.4 - - + -
177B VAL* 4.0 6.1 - - - -
192B PHE 2.5 24.4 + - - -
193B THR 3.9 4.3 - - - -
194B LEU 3.2 0.2 - - - -
195B GLY* 1.3 75.2 - - - +
197B PHE* 1.3 58.8 + - + +
198B LEU 3.1 0.3 + - - -
199B ARG 3.1 1.4 + - - -
200B LEU* 2.8 42.3 + - + +
300B LEU* 6.3 0.2 - - + -
303B PHE* 3.7 30.3 - - + -
1001B UUL 3.1 33.7 + - - +
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Residues in contact with PHE 197 (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 THR* 3.1 38.9 + - + +
194B LEU* 3.3 10.1 + - + +
196B THR* 1.3 81.9 - - + +
198B LEU* 1.3 60.3 + - + +
200B LEU* 3.7 10.5 - - + +
201B ALA* 3.0 28.4 + - - +
300B LEU* 3.5 31.9 - - + -
303B PHE* 4.0 18.8 - + - -
304B LEU* 4.2 14.8 - - + -
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Residues in contact with LEU 198 (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 LYS* 3.6 27.6 - - - +
194B LEU* 3.2 35.2 + - + +
195B GLY* 4.2 4.7 - - - +
196B THR 3.1 0.4 - - - -
197B PHE* 1.3 79.8 - - + +
199B ARG* 1.3 63.6 + - - +
201B ALA* 3.5 6.3 + - - +
202B ALA* 3.2 23.6 + - - +
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Residues in contact with ARG 199 (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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173B PHE* 3.8 21.7 - - + -
176B ASP* 2.5 39.6 + - + +
177B VAL* 3.8 14.6 - - + -
180B GLU* 3.5 29.8 + - - +
195B GLY 3.4 15.8 + - - +
196B THR 3.1 2.8 + - - +
198B LEU* 1.3 78.2 - - - +
200B LEU* 1.3 59.0 + - - +
202B ALA* 3.1 18.4 + - - +
203B LEU* 2.9 27.0 + - - -
204B ARG* 3.2 38.0 - - - +
206B TYR* 3.0 9.0 + - - -
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Residues in contact with LEU 200 (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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173B PHE* 3.8 12.5 - - + -
196B THR* 2.8 22.5 + - + +
197B PHE* 3.7 12.8 - - + +
199B ARG* 1.3 77.0 - - - +
201B ALA* 1.3 66.5 + - + +
202B ALA 3.2 0.2 - - - -
203B LEU* 3.1 13.2 + - + +
296B ARG* 3.3 36.6 - - + +
299B LEU* 3.7 21.1 - - + -
300B LEU* 3.4 62.1 - - + +
303B PHE* 5.7 0.2 - - + -
1001B UUL 5.7 1.1 - - - -
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Residues in contact with ALA 201 (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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197B PHE 3.0 19.1 + - - +
198B LEU* 3.8 6.5 - - - +
199B ARG 3.5 0.2 - - - -
200B LEU* 1.3 79.4 - - + +
202B ALA* 1.3 57.1 + - + +
203B LEU 3.4 0.2 - - - -
296B ARG* 3.5 19.4 + - - +
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Residues in contact with ALA 202 (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 3.2 15.4 + - - +
199B ARG* 3.1 22.4 + - - +
201B ALA* 1.3 76.3 - - + +
203B LEU* 1.3 67.3 + - - +
204B ARG* 3.6 1.4 + - - +
296B ARG* 4.0 4.7 - - - +
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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