Contacts of the helix formed by residues 165 - 178 (chain X) 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 LEU 165 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9X LEU* 4.0 6.0 - - + +
12X PHE* 3.6 33.4 - - + -
60X TYR* 3.5 24.8 - - + -
161X PRO 3.2 13.0 - - - +
162X ILE* 3.0 40.6 + - + +
164X THR* 1.3 82.0 - - + +
166X GLY* 1.3 64.2 + - - +
168X VAL* 3.1 19.6 + - + +
169X ARG* 3.5 6.6 + - - +
200X LEU* 4.9 0.2 - - + -
234X ALA* 4.6 6.7 - - + -
237X LEU* 4.3 7.2 - - + -
238X LEU* 3.7 31.6 - - + -
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Residues in contact with GLY 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ARG* 3.6 33.9 + - - +
57X LYS* 4.7 0.2 - - - -
59X GLU* 5.8 0.2 - - - +
60X TYR* 3.8 9.4 - - - -
163X GLY 3.2 10.8 + - - -
164X THR 2.8 4.2 - - - -
165X LEU* 1.3 84.5 - - - +
167X TYR* 1.3 59.8 + - - -
169X ARG* 3.2 7.1 + - - +
170X ALA* 3.1 18.7 + - - +
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Residues in contact with TYR 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X LYS* 6.3 0.2 - - - -
43X ASP* 2.5 30.9 + - - +
53X ASN* 2.9 54.0 - - + +
56X ARG* 3.3 17.3 - - + -
57X LYS* 5.0 7.9 - - + -
163X GLY 4.7 0.6 + - - -
164X THR* 3.4 5.2 + - - +
166X GLY* 1.3 72.5 - - - +
168X VAL* 1.3 62.0 + - - +
170X ALA* 3.0 32.0 - - + +
171X VAL* 3.1 17.5 + - - +
193X GLY 5.3 0.2 - - - +
194X THR* 3.8 34.3 - - + +
197X GLY* 3.2 7.6 - - - +
198X LEU* 3.7 21.8 - - + +
306X ILE* 4.3 25.2 - - + +
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Residues in contact with VAL 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ILE* 3.7 16.7 - - + +
9X LEU* 4.1 7.4 - - + -
164X THR 3.2 7.4 - - - +
165X LEU* 3.1 41.1 - - + +
167X TYR* 1.3 71.0 - - - +
169X ARG* 1.3 66.7 + - - +
171X VAL* 3.3 8.3 + - - +
172X GLY 3.0 17.0 + - - -
197X GLY* 3.4 12.3 - - - +
200X LEU* 4.3 8.1 - - + -
201X GLY* 3.6 25.1 - - - +
204X ILE* 3.8 21.5 - - + -
238X LEU* 4.1 9.2 - - + -
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Residues in contact with ARG 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET* 4.1 29.5 - - + +
5X ILE* 4.1 4.5 + - - -
6X PHE* 5.5 10.3 + - - +
9X LEU* 3.6 33.6 + - + +
14X ARG* 2.7 48.4 - - - +
56X ARG* 5.2 5.6 - - - +
59X GLU* 4.7 4.3 - - - -
60X TYR* 2.7 34.7 + - + +
165X LEU 3.5 4.1 + - - +
166X GLY 3.2 10.9 + - - +
168X VAL* 1.3 80.9 - - - +
170X ALA* 1.3 50.9 + - - +
172X GLY* 2.9 3.3 + - - -
173X GLU* 2.7 35.8 + - + +
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Residues in contact with ALA 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X LYS* 4.5 3.0 - - - -
56X ARG* 3.9 21.9 - - - +
166X GLY 3.1 4.0 + - - +
167X TYR* 3.0 50.7 - - + +
169X ARG* 1.3 79.3 - - - +
171X VAL* 1.3 63.9 + - + +
173X GLU* 2.9 14.8 + - - +
174X ILE* 3.1 20.9 + - + +
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Residues in contact with VAL 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ILE* 4.8 4.7 - - + -
167X TYR 3.1 16.3 + - - +
168X VAL 3.5 7.6 - - - +
170X ALA* 1.3 74.9 - - + +
172X GLY* 1.3 60.6 + - - +
173X GLU 2.8 0.3 + - - -
174X ILE* 2.9 16.2 + - + +
175X ALA* 2.5 36.4 + - - +
198X LEU* 3.4 42.2 - - + +
201X GLY* 3.5 26.7 - - - +
202X LEU* 3.8 16.2 - - + +
205X LEU* 4.9 7.2 - - + -
306X ILE* 6.3 0.2 - - + -
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Residues in contact with GLY 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET* 3.2 11.7 + - - -
2X HIS 3.1 22.4 + - - -
5X ILE* 3.8 25.4 - - - -
168X VAL 3.0 6.4 + - - -
169X ARG 2.9 10.1 + - - -
171X VAL* 1.3 82.3 - - - +
173X GLU* 1.3 57.0 + - - +
175X ALA* 3.3 15.2 - - - +
176X THR 3.7 0.2 + - - -
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Residues in contact with GLU 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET* 4.6 8.5 - - - +
18X ILE* 6.1 0.3 - - - +
20X TRP 5.1 1.6 - - - +
21X GLU* 3.2 35.6 - - + +
22X THR 2.8 31.3 + - - +
41X LYS* 3.2 9.6 + - - +
56X ARG* 2.8 33.7 + - - -
169X ARG* 2.7 9.6 + - + +
170X ALA 3.2 8.5 - - - +
171X VAL 2.9 0.2 - - - -
172X GLY* 1.3 76.9 - - - +
174X ILE* 1.3 65.8 + - - +
175X ALA 3.1 1.1 + - - -
176X THR* 3.3 2.3 + - - -
177X GLN* 3.0 30.4 + - - +
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Residues in contact with ILE 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X ILE* 4.1 9.4 - - + -
41X LYS* 3.5 31.6 - - + -
170X ALA* 3.3 9.2 - - + +
171X VAL* 2.9 26.9 + - + +
173X GLU* 1.3 75.7 - - - +
175X ALA* 1.3 66.1 + - - +
177X GLN* 3.2 9.8 + - - +
178X SER* 2.9 37.6 + - - -
182X PHE* 4.5 6.3 - - + -
185X ILE* 4.3 13.0 - - + -
198X LEU* 5.6 0.2 - - + -
304X LEU* 3.8 24.5 - - + -
306X ILE* 4.1 19.3 - - + -
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Residues in contact with ALA 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X HIS* 3.9 11.7 - - + -
171X VAL* 2.5 20.5 + - + +
172X GLY* 3.3 14.6 - - - +
174X ILE* 1.3 76.3 - - - +
176X THR* 1.3 60.4 + - - +
178X SER* 4.4 8.0 + - - +
205X LEU* 3.5 30.7 - - + -
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Residues in contact with THR 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET 2.6 46.5 + - - +
2X HIS* 3.1 6.4 + - - +
3X PRO* 5.3 0.3 - - - +
21X GLU* 5.2 0.9 - - - -
172X GLY 3.7 0.4 + - - -
173X GLU 3.3 3.0 + - - -
175X ALA* 1.3 76.4 - - - +
177X GLN* 1.3 66.8 + - - +
178X SER 4.6 1.9 - - - +
179X GLU* 5.4 1.0 - - - +
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Residues in contact with GLN 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X GLU* 4.3 20.8 + - - +
22X THR 3.1 17.8 - - - +
23X PRO* 4.1 4.2 - - - +
24X ILE* 3.4 25.5 + - + +
41X LYS* 2.6 30.3 - - - +
173X GLU* 3.0 20.2 + - - +
174X ILE* 3.2 22.8 - - - +
176X THR* 1.3 81.1 - - - +
178X SER* 1.3 76.1 + - - +
179X GLU* 3.3 16.3 + - - +
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Residues in contact with SER 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X ILE* 3.8 15.7 - - - +
174X ILE* 2.9 21.4 + - - -
175X ALA 4.6 7.2 - - - +
176X THR 3.6 1.8 - - - +
177X GLN* 1.3 78.7 - - - +
179X GLU* 1.3 59.4 + - - +
180X VAL* 2.7 34.9 + - - +
182X PHE* 2.9 20.9 - - - -
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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