Contacts of the helix formed by residues 158 - 167 (chain V) in PDB entry 4ADV
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 158 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147V ARG* 5.9 4.5 - - - -
156V ALA 3.2 3.1 + - - -
157V TYR* 1.3 75.3 - - - +
159V ARG* 1.3 67.7 + - - -
160V LEU* 3.1 4.6 + - - -
161V SER* 2.9 17.5 + - - -
162V VAL* 3.1 14.6 + - - +
218V PHE* 3.6 19.5 - - - -
221V ARG* 3.8 6.7 - - - -
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Residues in contact with ARG 159 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124V PHE* 3.9 27.5 - - - -
158V GLY* 1.3 72.3 - - - -
160V LEU* 1.3 58.9 + - - +
162V VAL* 3.3 2.0 + - - +
163V MET* 2.9 40.7 + - + +
211V SER* 2.6 34.9 + - - -
214V THR* 3.3 25.3 + - - +
215V THR* 3.1 34.0 + - - +
218V PHE* 3.5 24.5 - - + +
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Residues in contact with LEU 160 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120V THR* 4.5 15.3 - - + +
123V MET* 5.1 3.8 - - + -
124V PHE* 3.8 31.9 - - + -
127V PHE* 5.2 3.1 - - + -
144V VAL* 4.3 14.6 - - + -
147V ARG* 3.8 47.4 - - + +
148V LEU* 3.7 32.8 - - + -
158V GLY* 3.1 1.0 - - - -
159V ARG* 1.3 77.4 - - - +
161V SER* 1.3 60.6 + - - +
163V MET* 4.8 1.8 - - - -
164V ALA* 2.9 39.4 + - + +
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Residues in contact with SER 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147V ARG* 2.5 28.8 + - - +
148V LEU 3.8 6.3 - - - -
150V ALA 3.8 8.1 - - - -
156V ALA 3.4 1.9 + - - -
157V TYR* 3.4 27.9 - - - -
158V GLY* 2.9 25.0 + - - -
160V LEU* 1.3 77.5 - - - +
162V VAL* 1.3 58.0 + - - -
164V ALA* 4.0 0.2 - - - +
165V GLN* 2.8 37.9 + - - +
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Residues in contact with VAL 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157V TYR* 3.5 30.3 - - + +
158V GLY 3.1 12.8 + - - +
159V ARG 3.8 5.4 - - - +
161V SER* 1.3 79.6 - - - +
163V MET* 1.3 59.5 + - - +
165V GLN* 3.7 0.7 - - - +
166V TYR* 2.8 29.3 + - - +
210V LEU* 4.3 9.6 - - + -
214V THR* 3.6 23.8 - - + -
218V PHE* 4.1 7.4 - - + -
254V VAL* 4.0 19.3 - - + +
257V TYR* 3.8 31.6 - - + -
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Residues in contact with MET 163 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124V PHE* 3.7 24.0 - - + -
127V PHE* 5.0 0.4 - - - -
159V ARG* 2.9 47.0 + - + +
160V LEU 4.2 0.2 - - - +
162V VAL* 1.3 71.1 - - - +
164V ALA* 1.3 63.8 + - - +
166V TYR* 3.2 12.5 + - + +
167V TYR* 3.2 44.4 + - + +
207V VAL* 4.4 7.6 - - + +
210V LEU* 3.9 24.2 - - + -
211V SER* 3.7 38.8 - - - +
214V THR* 3.8 9.6 - - - -
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Residues in contact with ALA 164 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127V PHE* 4.0 23.7 - - + -
148V LEU* 3.6 28.5 - - + +
160V LEU* 2.9 25.6 + - + +
161V SER 4.0 1.3 - - - +
163V MET* 1.3 72.8 - - - +
165V GLN* 1.3 58.0 + - - +
167V TYR* 3.3 2.8 + - - +
168V CYS* 2.8 33.1 + - - +
170V VAL* 4.4 11.4 - - + -
194V LEU* 5.5 0.4 - - + -
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Residues in contact with GLN 165 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148V LEU 3.0 18.2 + - - -
149V VAL* 3.4 9.7 + - - +
150V ALA 2.9 28.5 + - - +
151V GLY* 5.3 1.9 - - - -
157V TYR* 4.9 1.2 - - - -
161V SER* 2.8 21.5 + - - +
162V VAL 3.9 2.2 - - - +
164V ALA* 1.3 74.9 - - - +
166V TYR* 1.3 60.1 + - - +
167V TYR 3.3 0.2 - - - -
168V CYS 3.3 8.1 - - - +
170V VAL* 3.9 18.6 - - + +
197V HIS* 2.9 26.0 + - - -
201V PRO* 5.2 2.4 - - - +
254V VAL* 3.5 27.5 - - + +
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Residues in contact with TYR 166 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162V VAL 2.8 14.0 + - - +
163V MET* 3.4 8.5 - - - +
165V GLN* 1.3 75.6 - - - +
167V TYR* 1.3 85.2 + + - +
197V HIS* 3.1 18.5 - - - -
200V MET* 3.3 35.8 - - + +
201V PRO* 4.7 3.4 - - - +
202V HIS* 3.3 28.3 - - + -
203V PRO* 4.5 0.3 - - - +
204V VAL* 3.3 32.6 + - + +
207V VAL* 3.4 32.7 - - + +
210V LEU* 3.7 19.7 - - + -
254V VAL* 4.3 7.1 - - + +
258V CYS* 3.7 16.4 - - - -
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Residues in contact with TYR 167 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124V PHE* 5.0 6.3 - + - -
127V PHE* 3.5 58.1 - + + -
128V SER* 4.9 6.0 - - - -
130V THR* 4.6 14.4 - - + -
163V MET* 3.2 38.6 + - + +
164V ALA 3.8 4.0 - - - +
166V TYR* 1.3 107.4 - + - +
168V CYS* 1.3 67.6 + - - +
196V PRO* 3.3 8.0 - - + +
197V HIS* 3.2 23.5 + - - -
200V MET* 4.5 9.0 - - + +
207V VAL* 3.5 29.2 - - + +
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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
------------------------------------------------------------
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