Contacts of the helix formed by residues 191 - 202 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112F SER* 4.3 17.1 + - - +
177F VAL* 4.7 0.2 - - - +
178F ASP 4.0 9.1 + - - -
181F SER* 3.0 55.2 + - - +
182F GLU 5.1 0.6 + - - -
183F LYS* 3.6 23.8 - - + +
184F TYR 3.4 25.4 + - - -
185F ARG* 3.8 12.6 + - - +
190F MET* 1.3 72.4 - - + +
192F PHE* 1.3 90.9 + - + +
193F THR 3.4 0.4 - - - -
194F LEU* 4.1 10.9 - - + +
195F GLY* 2.7 32.8 + - - -
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Residues in contact with PHE 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F SER* 3.5 20.2 - - - -
113F GLY* 4.4 16.2 - - - -
177F VAL* 3.7 9.8 - - + +
178F ASP* 3.3 24.2 - - - -
181F SER* 5.1 0.4 - - - -
190F MET* 3.0 17.9 + - + -
191F ARG* 1.3 114.8 - - + +
193F THR* 1.3 51.7 + - - +
195F GLY 3.7 0.2 - - - -
196F THR* 2.5 43.6 + - - -
272F MET* 4.2 25.6 - - + -
303F PHE* 4.6 2.9 - - + -
1001F UUL 3.7 26.5 - + + -
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Residues in contact with THR 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F MET* 3.0 17.4 + - - +
192F PHE* 1.3 78.8 - - - +
194F LEU* 1.3 52.9 + - - +
196F THR* 3.4 2.6 + - - +
197F PHE* 2.8 34.7 + - + +
300F LEU* 6.1 0.7 - - + +
303F PHE* 3.3 32.4 - - + -
304F LEU* 5.7 4.9 - - + -
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Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F LYS* 4.2 21.1 - - + -
190F MET 3.5 5.0 + - - +
191F ARG* 4.1 12.1 - - + +
192F PHE 3.4 0.2 - - - -
193F THR* 1.3 76.4 - - - +
195F GLY* 1.3 61.7 + - - +
197F PHE* 3.2 12.0 + - + +
198F LEU* 2.8 61.9 + - + +
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Residues in contact with GLY 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F VAL* 3.6 16.6 - - - -
180F GLU 5.6 1.8 - - - -
181F SER* 5.0 0.7 - - - -
183F LYS* 3.9 15.9 - - - +
191F ARG 2.7 23.9 + - - -
192F PHE 3.7 0.7 - - - -
194F LEU* 1.3 72.5 - - - +
196F THR* 1.3 51.4 + - - +
198F LEU* 3.3 5.3 + - - +
199F ARG* 2.8 39.0 + - - +
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Residues in contact with THR 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 3.5 24.1 - - + -
177F VAL* 3.6 0.8 - - - +
192F PHE 2.5 28.1 + - - -
193F THR* 3.4 8.3 - - - +
194F LEU 3.2 0.2 - - - -
195F GLY* 1.3 70.4 - - - +
197F PHE* 1.3 57.1 + - - +
200F LEU* 2.7 39.0 + - + +
299F LEU 6.5 0.2 - - - -
300F LEU* 5.0 9.0 - - + -
303F PHE* 3.7 18.1 - - + -
1001F UUL 3.0 42.9 + - - +
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Residues in contact with PHE 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F THR* 2.8 21.2 + - + +
194F LEU* 3.2 12.1 + - + +
196F THR* 1.3 72.6 - - - +
198F LEU* 1.3 79.6 + - + +
200F LEU* 3.2 38.9 - - + +
201F ALA* 3.5 6.2 + - - +
300F LEU* 5.4 14.8 - - + +
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F LYS* 3.9 22.2 - - - +
194F LEU* 2.8 45.3 + - + +
195F GLY* 3.4 4.9 - - - +
197F PHE* 1.3 88.9 - - + +
199F ARG* 1.3 64.9 + - + +
201F ALA* 3.2 9.8 + - - +
202F ALA* 3.1 20.0 + - - +
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Residues in contact with ARG 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 3.6 27.6 - - + -
176F ASP* 3.8 26.3 + - - +
177F VAL* 3.7 25.4 - - + +
180F GLU* 5.3 14.3 + - - +
195F GLY 2.8 17.4 + - - +
198F LEU* 1.3 71.5 - - + +
200F LEU* 1.3 64.7 + - - +
202F ALA* 2.8 62.0 + - + +
203F LEU* 3.1 5.1 + - - +
204F ARG* 3.2 30.1 - - - +
206F TYR* 4.0 15.6 + - - -
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Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 3.8 8.7 - - + -
196F THR* 2.7 17.2 + - + +
197F PHE* 3.2 31.9 - - + +
199F ARG* 1.3 78.6 - - - +
201F ALA* 1.3 78.7 + - + +
203F LEU* 3.3 24.1 - - - +
296F ARG* 3.6 38.7 - - + +
297F ALA* 5.4 0.2 - - - -
299F LEU* 5.6 1.8 - - + -
300F LEU* 3.6 46.9 - - + +
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Residues in contact with ALA 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F PHE* 3.5 7.4 + - + +
198F LEU* 3.2 10.3 + - - +
200F LEU* 1.3 87.5 - - + +
202F ALA* 1.3 56.6 + - - +
203F LEU 3.1 4.4 + - - -
296F ARG* 4.4 18.2 + - - +
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Residues in contact with ALA 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F LEU 3.1 15.4 + - - +
199F ARG* 2.8 47.5 + - + +
201F ALA* 1.3 75.3 - - - +
203F LEU* 1.3 62.2 + - - +
204F ARG* 3.8 1.6 - - - +
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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