Contacts of the helix formed by residues 164 - 178 (chain V) in PDB entry 1J0B
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 164 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57V LYS* 4.9 4.9 - - - +
158V GLY 4.6 1.4 + - - -
159V ALA* 5.6 1.5 - - - +
160V SER 3.3 10.1 + - - -
161V PRO 3.0 17.9 + - - +
162V ILE 3.0 0.2 + - - -
163V GLY* 1.3 74.5 - - - +
165V LEU* 1.3 60.1 + - + +
166V GLY 3.2 2.1 + - - -
167V TYR* 3.7 2.3 + - - -
168V VAL* 3.1 4.2 + - - +
193V GLY* 3.7 8.2 + - - -
196V ALA* 3.0 30.4 - - - +
197V GLY* 2.9 27.8 + - - +
200V LEU* 3.8 12.6 - - + -
230V LEU* 3.7 7.2 - - - +
234V ALA* 3.3 27.4 - - + -
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Residues in contact with LEU 165 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V LEU* 3.7 19.4 - - + +
12V PHE* 4.1 23.6 - - + -
60V TYR* 3.5 19.7 + - + -
161V PRO 4.0 3.6 - - - +
162V ILE* 2.7 35.3 + - + +
163V GLY 2.7 0.8 + - - -
164V THR* 1.3 84.1 - - + +
166V GLY* 1.3 63.2 + - - +
167V TYR 3.2 2.5 - - - -
168V VAL* 3.6 12.7 - - + +
169V ARG* 3.1 22.9 + - - +
200V LEU* 4.4 1.3 - - + -
234V ALA* 5.0 2.0 - - + +
237V LEU* 4.8 4.3 - - + -
238V LEU* 3.5 44.4 - - + -
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Residues in contact with GLY 166 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V ARG* 3.3 46.6 - - - +
60V TYR* 3.9 6.7 - - - -
163V GLY 2.7 13.2 + - - -
165V LEU* 1.3 80.0 - - - +
167V TYR* 1.3 62.8 + - - +
169V ARG* 3.5 6.5 - - - +
170V ALA 3.2 14.7 + - - -
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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
----------------------------------------------------------
43V ASP* 2.5 32.5 + - - +
53V ASN* 2.9 53.6 - - + +
56V ARG* 3.9 9.1 - - + -
57V LYS* 3.8 15.7 - - + -
164V THR 3.7 3.4 + - - +
166V GLY* 1.3 77.9 - - - +
168V VAL* 1.3 61.0 + - - +
169V ARG 2.9 5.4 - - - -
170V ALA* 3.4 16.4 - - + +
171V VAL* 3.1 23.9 + - - +
194V THR* 3.2 33.0 - - + +
197V GLY* 3.9 8.4 - - - +
198V LEU* 3.7 24.6 - - + +
306V ILE* 3.9 23.3 - - + -
308V THR* 3.9 1.4 - - + +
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Residues in contact with VAL 168 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V ILE* 3.0 21.0 - - + +
9V LEU* 4.1 15.0 - - + -
164V THR 3.1 19.7 - - - +
165V LEU* 3.4 16.1 + - + +
167V TYR* 1.3 79.1 - - - +
169V ARG* 1.3 58.3 + - - +
171V VAL* 2.8 21.0 - - - +
197V GLY 3.5 15.9 - - - +
200V LEU* 3.5 23.3 - - + -
201V GLY* 3.9 17.9 - - - +
204V ILE* 4.1 18.8 - - + -
238V LEU* 4.1 6.7 - - + -
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Residues in contact with ARG 169 (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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1V MET* 4.3 25.0 - - - +
5V ILE* 4.2 2.2 + - - -
6V PHE* 5.6 10.1 - - - +
9V LEU* 4.1 20.5 + - + +
14V ARG* 2.6 54.9 - - - +
18V ILE* 6.3 1.1 - - - -
56V ARG* 5.8 7.4 - - - +
59V GLU* 4.3 6.5 - - - -
60V TYR* 3.2 21.9 + - - +
165V LEU 3.1 17.1 + - - +
166V GLY* 3.5 8.1 - - - +
168V VAL* 1.3 79.7 - - - +
170V ALA* 1.3 59.3 + - - +
172V GLY* 3.1 4.7 + - - -
173V GLU* 3.0 24.1 + - - +
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Residues in contact with ALA 170 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V LYS* 5.1 1.3 - - - -
43V ASP* 5.0 0.2 - - - +
56V ARG* 3.8 22.2 - - - +
166V GLY 3.2 6.6 + - - +
167V TYR* 3.2 39.0 + - + +
169V ARG* 1.3 74.6 - - - +
171V VAL* 1.3 54.6 + - - +
172V GLY 3.0 1.6 - - - -
173V GLU* 2.9 10.0 + - - +
174V ILE* 2.7 47.9 + - + +
306V ILE* 5.5 0.2 - - + -
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Residues in contact with VAL 171 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V ILE* 4.6 2.5 - - + -
167V TYR 3.1 14.4 + - - +
168V VAL 2.8 25.6 - - - +
170V ALA* 1.3 73.6 - - - +
172V GLY* 1.3 57.1 + - - +
174V ILE* 3.7 14.8 - - + +
175V ALA* 2.8 27.7 + - - +
185V ILE* 5.8 1.1 - - + -
197V GLY 5.0 0.2 - - - +
198V LEU* 4.8 9.2 - - + +
201V GLY* 3.4 26.5 - - - +
202V LEU* 3.7 24.9 - - + +
205V LEU* 3.2 26.0 - - + -
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Residues in contact with GLY 172 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1V MET* 3.4 24.5 - - - -
2V HIS 3.6 3.9 + - - -
5V ILE* 4.1 12.6 - - - -
169V ARG 3.1 9.0 + - - -
170V ALA 3.0 0.6 - - - -
171V VAL* 1.3 83.2 - - - +
173V GLU* 1.3 62.4 - - - +
175V ALA* 3.5 5.6 + - - +
176V THR* 3.2 26.9 + - - -
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Residues in contact with GLU 173 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1V MET* 4.5 6.0 - - - +
18V ILE* 5.4 0.3 - - - +
20V TRP 4.3 3.1 - - - +
21V GLU* 3.7 43.2 - - + +
22V THR 3.5 7.8 + - - -
41V LYS* 2.6 27.0 + - - +
56V ARG* 3.1 30.9 + - - -
169V ARG 3.0 10.4 + - - +
170V ALA* 2.9 11.3 + - - +
172V GLY* 1.3 74.2 - - - +
174V ILE* 1.3 66.1 + - - +
176V THR* 3.1 4.6 + - - -
177V GLN* 3.0 29.5 + - - +
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Residues in contact with ILE 174 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V ILE* 4.4 6.3 - - + -
41V LYS* 3.5 33.4 - - + -
170V ALA* 2.7 29.0 + - + +
171V VAL* 3.7 11.9 - - + +
173V GLU* 1.3 75.4 - - - +
175V ALA* 1.3 56.5 + - - +
177V GLN* 3.6 8.5 - - - +
178V SER* 3.0 43.1 + - - +
182V PHE* 4.9 2.9 - - + -
185V ILE* 4.6 13.7 - - + -
198V LEU* 5.5 2.2 - - + -
304V LEU* 3.5 31.0 - - + -
306V ILE* 4.4 16.8 - - + -
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Residues in contact with ALA 175 (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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2V HIS* 4.4 16.6 - - + -
171V VAL 2.8 22.1 + - - +
172V GLY* 3.6 9.2 - - - +
174V ILE* 1.3 76.6 - - - +
176V THR* 1.3 60.1 + - - +
178V SER* 4.3 7.4 + - - +
205V LEU* 3.8 21.3 - - + -
207V GLU* 5.5 5.4 - - - +
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Residues in contact with THR 176 (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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1V MET* 2.8 34.7 + - - +
2V HIS* 3.0 20.8 + - - +
21V GLU* 5.1 5.6 - - - +
172V GLY 3.2 3.5 + - - -
173V GLU* 3.1 4.9 + - - -
175V ALA* 1.3 80.1 - - - +
177V GLN* 1.3 58.8 + - - +
178V SER 3.5 2.2 + - - +
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Residues in contact with GLN 177 (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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21V GLU* 4.1 26.7 - - - +
22V THR 3.2 15.6 - - - +
23V PRO* 4.6 4.3 - - - +
24V ILE* 3.8 18.3 + - + +
41V LYS* 2.4 35.7 - - - +
173V GLU* 3.0 17.5 + - - +
174V ILE* 3.6 16.7 - - - +
176V THR* 1.3 76.7 - - - +
178V SER* 1.3 67.1 + - - +
179V GLU* 3.8 12.8 + - - +
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Residues in contact with SER 178 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V ILE* 4.8 6.9 - - - +
174V ILE* 3.0 28.7 + - - -
175V ALA* 4.3 6.8 + - - +
176V THR 3.5 2.9 - - - +
177V GLN* 1.3 82.5 - - - +
179V GLU* 1.3 63.6 + - - +
180V VAL* 2.9 27.2 + - - +
182V PHE* 3.7 14.1 - - - -
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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
------------------------------------------------------------
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