Contacts of the helix formed by residues 173 - 192 (chain B) in PDB entry 1JG0
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 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ASP 3.0 10.6 + - - -
172B LEU* 1.3 76.5 - - - +
174B LEU* 1.3 64.0 + - - +
175B PRO* 3.4 1.1 - - - -
176B PHE* 3.0 9.4 + - - +
177B ASN* 3.0 28.4 + - - -
305B UMP 4.0 4.0 - - - -
306B DDT 2.9 33.3 + - - -
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Residues in contact with LEU 174 (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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4B TYR* 3.7 20.4 - - + -
7B LEU* 3.4 32.5 - - + -
34B MET* 3.9 5.8 - - + -
165B GLN* 4.3 2.5 - - - +
168B CYS* 3.6 22.4 - - - -
169B ASP 3.0 5.6 + - - +
170B VAL* 3.4 17.5 - - + +
173B GLY* 1.3 74.3 - - - +
175B PRO* 1.3 63.6 - - - +
177B ASN* 3.7 7.4 + - + -
178B ILE* 3.0 48.1 + - + +
201B TRP* 3.6 33.4 - - + +
305B UMP 4.5 0.4 + - - -
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Residues in contact with PRO 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.5 25.1 - - + +
43B PRO 5.0 1.9 - - - +
44B LEU* 4.7 7.0 - - + +
45B VAL* 3.9 25.4 + - + +
48B LYS* 4.4 10.8 - - - +
50B CYS* 4.1 20.0 - - - -
170B VAL 3.6 7.4 - - - +
171B PHE 3.7 13.7 - - - +
172B LEU 3.9 4.0 - - - +
173B GLY 3.4 5.4 - - - -
174B LEU* 1.3 92.6 - - + +
176B PHE* 1.3 63.2 + - + +
178B ILE* 3.7 7.2 + - + +
179B ALA* 3.3 21.0 + - - +
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Residues in contact with PHE 176 (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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48B LYS* 5.9 4.3 - - - -
50B CYS* 4.3 24.0 - - + -
51B HIS 3.4 25.8 - - - -
52B LEU* 4.5 5.2 - - + -
55B ILE* 3.6 19.4 - - + +
172B LEU* 3.4 26.0 - - + -
173B GLY 3.0 5.0 + - - +
175B PRO* 1.3 80.5 - - + +
177B ASN* 1.3 65.4 + - - +
179B ALA* 3.2 4.4 + - - +
180B SER* 2.9 28.1 + - - -
306B DDT 3.4 79.2 - + - -
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Residues in contact with ASN 177 (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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147B HIS* 4.6 10.7 + - + +
163B LEU* 5.0 5.8 - - + +
165B GLN* 2.9 30.7 + - - +
173B GLY 3.0 16.2 + - - +
174B LEU* 3.2 8.4 + - + +
176B PHE* 1.3 77.2 - - - +
178B ILE* 1.3 61.3 + - - +
180B SER* 3.5 5.4 + - - -
181B TYR* 3.3 31.1 + - + +
199B PHE* 4.9 1.2 - - - -
201B TRP* 5.1 1.3 - - - +
305B UMP 2.8 45.2 + - - -
306B DDT 3.9 9.9 - - - -
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Residues in contact with ILE 178 (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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1B CXM 4.2 12.3 - - + -
4B TYR* 4.7 6.5 - - + -
34B MET* 4.1 7.2 - - + -
36B PHE* 4.1 25.8 - - + -
43B PRO* 3.6 36.1 - - + +
174B LEU* 3.0 46.9 + - + +
175B PRO* 3.9 6.1 - - + +
177B ASN* 1.3 75.1 - - - +
179B ALA* 1.3 58.4 + - - +
181B TYR* 3.5 0.7 + - - -
182B ALA* 2.9 27.4 + - - +
199B PHE* 4.1 27.1 - - + -
201B TRP* 4.7 3.8 - - + -
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Residues in contact with ALA 179 (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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42B PHE* 3.4 26.0 - - + -
43B PRO 4.7 2.7 + - - +
44B LEU* 4.1 5.8 - - + -
52B LEU* 3.7 30.3 - - + -
55B ILE* 4.5 2.7 - - + -
175B PRO 3.3 12.1 + - - +
176B PHE 3.2 8.1 + - - +
178B ILE* 1.3 80.6 - - - +
180B SER* 1.3 63.2 + - - +
182B ALA* 4.3 0.7 - - - -
183B LEU* 2.9 26.5 + - - +
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Residues in contact with SER 180 (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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55B ILE* 3.1 37.6 + - - +
58B GLU* 4.4 7.2 + - - -
59B LEU* 3.8 15.6 - - - +
62B PHE* 5.9 4.7 - - - -
147B HIS* 6.2 0.7 - - - -
176B PHE 2.9 16.1 + - - -
177B ASN* 3.7 8.5 + - - -
179B ALA* 1.3 78.5 - - - +
181B TYR* 1.3 67.6 + - - +
183B LEU* 3.3 5.2 - - - +
184B LEU* 3.1 25.3 + - - +
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Residues in contact with TYR 181 (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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62B PHE* 6.2 0.9 - + - -
98B TRP* 3.5 18.3 + + - -
147B HIS* 2.6 52.4 + + + +
150B PHE* 3.7 37.1 - + + -
161B CYS* 5.0 4.3 - - - -
163B LEU* 3.9 26.7 - - + -
177B ASN* 3.3 18.1 + - - +
180B SER* 1.3 86.4 - - - +
182B ALA* 1.3 66.9 + - - +
183B LEU 3.1 0.2 - - - -
184B LEU* 3.2 21.9 + - + +
185B VAL* 3.0 27.9 + - + +
199B PHE* 3.7 26.7 - + + -
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Residues in contact with ALA 182 (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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38B LEU* 4.4 10.7 - - + +
42B PHE* 3.6 17.3 - - + -
43B PRO* 3.5 30.7 - - + -
178B ILE* 2.9 19.8 + - + +
179B ALA 3.7 1.1 - - - +
181B TYR* 1.3 76.2 - - - +
183B LEU* 1.3 62.7 + - - +
185B VAL* 3.3 9.0 + - - +
186B HIS* 3.1 26.9 + - - -
199B PHE* 4.9 6.1 - - + -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.7 15.1 - - + -
52B LEU* 5.8 3.4 - - + -
55B ILE* 4.7 8.3 - - + -
56B ILE* 3.7 38.8 - - + -
59B LEU* 4.0 14.8 - - + -
179B ALA 2.9 19.1 + - - +
180B SER 3.3 4.9 - - - +
182B ALA* 1.3 76.7 - - - +
184B LEU* 1.3 62.8 + - - +
186B HIS* 3.1 9.6 + - + +
187B MET* 3.0 26.7 + - + +
230B LEU* 5.2 8.5 - - + -
247B PHE* 3.3 37.5 - - + -
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Residues in contact with LEU 184 (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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59B LEU* 3.9 17.0 - - + +
63B LEU* 4.5 26.0 - - + -
98B TRP* 4.0 21.1 - - + -
112B ILE* 5.7 4.0 - - + -
150B PHE* 3.8 29.6 - - + -
152B PHE* 4.8 4.9 - - + -
180B SER 3.1 10.6 + - - +
181B TYR* 3.2 21.7 + - + +
183B LEU* 1.3 78.3 - - - +
185B VAL* 1.3 63.1 + - + +
187B MET* 3.2 4.3 + - - +
188B MET* 2.9 40.7 + - + +
239B ILE* 4.8 7.0 - - + -
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Residues in contact with VAL 185 (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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38B LEU* 3.4 28.3 - - + -
152B PHE* 4.5 5.2 - - + -
159B LEU* 3.8 28.7 - - + +
160B SER 5.3 0.2 - - - -
161B CYS* 3.4 35.4 - - + +
181B TYR 3.0 20.9 + - - +
182B ALA* 3.5 7.6 - - - +
183B LEU 3.2 0.2 - - - -
184B LEU* 1.3 75.6 - - + +
186B HIS* 1.3 54.0 + - - +
188B MET* 3.2 5.9 + - - +
189B ALA* 2.7 33.4 + - - +
196B VAL* 4.3 6.3 - - + -
198B ASP 5.5 0.4 - - - +
199B PHE* 4.7 7.0 - - + -
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Residues in contact with HIS 186 (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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38B LEU* 4.0 27.3 + - + +
42B PHE* 4.3 21.5 - + - -
182B ALA 3.1 22.1 + - - -
183B LEU* 3.1 10.0 + - + +
185B VAL* 1.3 79.4 - - - +
187B MET* 1.3 56.5 + - - +
189B ALA* 3.6 1.6 - - - +
190B GLN* 2.9 30.5 + - - +
196B VAL* 3.6 32.9 - - + +
230B LEU* 4.1 26.8 - - + +
232B ILE* 4.3 16.6 - - + +
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Residues in contact with MET 187 (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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59B LEU* 3.7 26.7 - - - -
60B LEU* 4.3 5.4 - - + -
63B LEU* 3.5 29.2 - - + -
183B LEU* 3.0 16.6 + - + +
184B LEU* 3.6 7.4 - - - +
186B HIS* 1.3 75.5 - - - +
188B MET* 1.3 62.7 + - - +
190B GLN* 3.4 1.4 + - - -
191B GLN* 3.1 28.1 + - - +
232B ILE* 4.7 2.9 - - + -
239B ILE* 3.6 12.8 - - + +
242B TYR* 3.4 51.3 + - + -
247B PHE* 3.7 30.3 - - + -
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Residues in contact with MET 188 (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 ILE* 5.0 4.5 - - - -
115B VAL* 3.7 16.6 - - + -
116B LEU* 3.3 44.4 - - + -
119B LEU* 3.3 29.8 - - + -
152B PHE* 4.1 18.4 - - + -
159B LEU* 3.6 13.9 - - + -
184B LEU* 2.9 30.3 + - + +
185B VAL* 3.5 4.0 - - - +
187B MET* 1.3 74.7 - - - +
189B ALA* 1.3 66.8 + - - +
191B GLN* 3.2 4.1 + - - -
192B CYS* 3.1 27.4 + - - -
239B ILE* 4.1 11.4 - - + -
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Residues in contact with ALA 189 (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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159B LEU* 3.4 16.5 - - + +
185B VAL 2.7 20.8 + - - +
186B HIS 3.6 4.5 - - - +
188B MET* 1.3 71.8 - - - +
190B GLN* 1.3 62.3 + - - +
192B CYS* 3.0 3.2 + - - -
193B ASP 3.0 4.2 + - - -
194B LEU* 2.9 45.2 + - - +
195B GLU 4.1 6.5 - - - +
196B VAL* 3.8 21.5 - - + -
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Residues in contact with GLN 190 (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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186B HIS 2.9 18.4 + - - +
187B MET 3.6 4.0 - - - +
188B MET 3.2 0.2 - - - -
189B ALA* 1.3 75.2 - - - +
191B GLN* 1.3 58.3 + - - +
192B CYS 3.0 5.7 + - - -
193B ASP* 3.0 12.4 + - - +
194B LEU 4.9 1.8 - - - -
232B ILE* 3.4 26.6 + - + +
234B ARG 3.5 19.9 + - - +
235B LYS* 3.6 37.3 + - + +
236B PRO* 4.0 0.2 - - - +
242B TYR* 2.4 39.9 + - - +
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Residues in contact with GLN 191 (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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116B LEU* 4.1 16.6 - - + -
120B LYS* 3.3 22.7 + - - +
187B MET 3.1 20.2 + - - +
188B MET* 3.2 5.8 + - - +
190B GLN* 1.3 74.8 - - - +
192B CYS* 1.3 57.0 + - - +
193B ASP* 3.6 5.6 - - - +
235B LYS* 3.9 21.6 + - - +
236B PRO* 3.2 20.9 + - - +
237B GLU 3.9 2.9 - - - +
238B SER* 3.1 29.1 + - - -
239B ILE* 3.5 22.8 + - + +
242B TYR* 3.1 24.7 + - - +
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Residues in contact with CYS 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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116B LEU* 3.9 17.3 - - - -
119B LEU* 3.8 27.8 - - + +
120B LYS* 3.8 29.5 - - + +
188B MET 3.1 14.9 + - - +
189B ALA 3.0 3.6 + - - +
190B GLN 3.0 0.8 - - - -
191B GLN* 1.3 80.5 - - - +
193B ASP* 1.3 75.3 + - - +
194B LEU* 3.1 26.4 + - + +
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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