Contacts of the helix formed by residues 172 - 187 (chain B) in PDB entry 2OJW
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 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 2.9 18.0 + - - -
9A LEU* 4.6 8.1 - - - -
139B LEU* 3.9 12.3 - - - +
147B PHE* 3.8 13.9 - - - -
170B ALA 3.8 0.6 + - - -
171B TYR* 1.3 72.7 - - - +
173B ARG* 1.3 65.2 + - - +
174B ASP* 3.0 4.8 + - - -
175B ILE* 3.1 22.5 + - - +
176B VAL* 3.7 3.1 + - - +
202B TRP* 4.3 3.6 - - - -
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 5.4 1.4 - - - -
29A MET* 4.2 18.8 - - - +
42A CYS* 4.4 7.8 - - - -
227A ARG* 3.7 35.6 - - - +
230A GLU* 2.7 46.3 + - - +
164B GLY 3.2 23.8 + - - -
165B VAL* 3.9 7.7 - - - +
170B ALA* 3.4 9.4 + - + +
171B TYR 3.8 1.6 - - - -
172B GLY* 1.3 76.4 - - - +
174B ASP* 1.3 63.6 + - - +
176B VAL* 3.0 9.5 + - + -
177B GLU* 2.9 42.7 + - + +
202B TRP* 3.9 33.8 - - + -
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Residues in contact with ASP 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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6A SER* 3.7 2.0 - - - +
9A LEU* 3.6 29.5 - - + +
11A LYS* 2.6 41.2 + - - +
14A LYS* 3.5 33.9 + - + +
231A ASP* 4.7 5.9 - - - +
172B GLY 3.0 0.6 + - - -
173B ARG* 1.3 77.0 - - - +
175B ILE* 1.3 62.4 - - - +
177B GLU* 3.6 2.8 + - - +
178B ALA* 3.1 25.8 + - - +
232B PHE* 4.0 18.8 - - + -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.6 29.2 - - + -
137B TYR* 4.7 2.5 - - - +
139B LEU* 4.1 16.4 - - + -
147B PHE* 5.8 0.7 - - + -
172B GLY* 3.1 15.1 + - - +
174B ASP* 1.3 79.2 - - - +
176B VAL* 1.3 59.8 + - - +
178B ALA* 3.5 0.9 + - - +
179B HIS* 3.0 30.0 + - - +
225B LEU* 4.0 16.6 - - + -
228B VAL* 4.0 12.7 - - + +
229B CYS* 3.9 21.5 - - - -
232B PHE* 3.7 31.2 - - + -
234B VAL* 4.1 22.9 - - + -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 6.1 0.9 - - - +
137B TYR* 3.4 22.4 - - + +
139B LEU* 5.3 0.2 - - + -
172B GLY 4.0 7.6 - - - +
173B ARG* 3.0 13.6 + - + +
175B ILE* 1.3 80.4 - - + +
177B GLU* 1.3 61.2 + - - +
179B HIS* 3.7 5.3 + - - +
180B TYR* 2.9 30.6 + - + +
193B THR* 4.2 29.9 - - + +
202B TRP* 3.4 50.5 - - + -
203B GLU 5.4 1.8 - - - +
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Residues in contact with GLU 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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14A LYS* 3.9 28.9 - - - +
18A MET* 4.0 14.4 - - - +
27A GLN* 4.8 3.3 + - - -
29A MET* 4.7 3.8 - - - +
89A PHE* 6.2 0.7 - - - -
90A ARG* 2.9 53.0 + - - +
227A ARG* 4.4 8.6 + - - +
173B ARG* 2.9 44.5 + - + +
174B ASP 3.9 3.6 - - - +
176B VAL* 1.3 79.7 - - - +
178B ALA* 1.3 61.5 + - - +
180B TYR* 3.5 5.7 + - - +
181B ARG* 3.2 24.6 + - - +
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Residues in contact with ALA 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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14A LYS* 4.9 5.1 - - + +
17A TYR* 3.6 43.4 - - + -
18A MET* 4.7 3.3 - - - -
174B ASP 3.1 18.2 + - - +
175B ILE 4.0 2.7 - - - +
177B GLU* 1.3 72.3 - - - +
179B HIS* 1.3 55.0 + - - +
181B ARG* 3.3 5.1 + - - +
182B ALA* 2.8 36.5 + - - +
228B VAL* 4.2 4.9 - - + -
232B PHE* 4.1 13.5 - - + -
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Residues in contact with HIS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 5.5 1.4 + - - -
175B ILE 3.0 19.3 + - - +
176B VAL* 3.7 5.6 + - - +
178B ALA* 1.3 72.9 - - - +
180B TYR* 1.3 66.6 + - - +
182B ALA* 3.3 1.7 + - - +
183B CYS* 2.9 44.4 + - - -
190B ILE* 4.3 7.0 - - + +
193B THR* 5.7 1.6 - - - +
204B PHE* 3.6 40.3 - + - +
221B ALA 3.0 21.9 + - - -
224B ILE* 3.8 11.7 - - + -
225B LEU* 3.4 43.2 - - + +
228B VAL* 4.1 12.8 - - + +
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Residues in contact with TYR 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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27A GLN* 3.4 31.5 - - + +
44A THR* 3.5 19.2 - - + +
45A ARG 3.5 5.0 - - - -
46A THR* 2.7 42.9 + - - -
90A ARG* 4.6 5.4 - - - -
176B VAL* 2.9 18.5 + - + +
177B GLU* 3.7 7.2 - - - +
178B ALA 3.4 0.4 - - - -
179B HIS* 1.3 76.0 + - - +
181B ARG* 1.3 57.6 + - - +
183B CYS* 3.4 2.6 + - - +
184B LEU* 3.1 31.5 + - + +
190B ILE* 3.8 30.5 - - + -
192B GLY* 3.5 11.1 - - - -
193B THR* 3.2 41.1 - - + -
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR 3.3 27.4 - - - +
18A MET* 2.9 51.8 + - - +
20A LEU* 3.0 28.0 + - + +
22A GLN* 3.4 40.6 + - - +
27A GLN* 4.5 10.7 + - - +
90A ARG* 3.1 26.5 + - - +
94A ASN* 4.1 3.0 - - - +
177B GLU 3.2 14.0 + - - +
178B ALA 3.7 3.6 - - - +
180B TYR* 1.3 74.8 - - - +
182B ALA* 1.3 59.6 + - - +
184B LEU* 3.3 8.5 + - - +
185B TYR* 2.9 30.0 + - - +
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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
----------------------------------------------------------
17A TYR* 4.3 14.8 - - + -
20A LEU* 4.2 6.2 - - - +
88B PRO* 3.6 27.7 - - + +
178B ALA 2.8 21.4 + - - +
179B HIS* 3.7 3.1 - - - +
181B ARG* 1.3 72.7 - - - +
183B CYS* 1.3 57.5 + - - +
185B TYR* 3.5 0.4 + - - -
186B ALA* 2.9 30.9 + - - +
224B ILE* 3.6 25.1 - - + -
228B VAL* 4.6 0.2 - - + -
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Residues in contact with CYS 183 (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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179B HIS* 2.9 52.4 + - - +
180B TYR 3.7 4.0 - - - +
182B ALA* 1.3 74.2 - - - +
184B LEU* 1.3 65.1 + - - +
186B ALA* 3.3 3.6 + - - +
187B GLY 3.1 4.5 + - - -
188B VAL* 3.0 52.7 + - + +
190B ILE* 3.8 20.0 - - + -
221B ALA* 4.3 8.7 - - - -
224B ILE* 4.2 8.7 - - - -
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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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22A GLN* 3.8 40.3 - - + +
25A LYS* 4.0 29.8 - - + +
27A GLN* 4.2 19.7 - - + +
46A THR* 4.3 11.0 - - + -
86B ARG* 5.1 0.9 + - - -
180B TYR* 3.1 35.3 + - + +
181B ARG* 3.6 11.0 - - - +
183B CYS* 1.3 76.6 - - - +
185B TYR* 1.3 63.4 + - - +
187B GLY* 3.4 9.5 + - - -
188B VAL 4.6 4.5 - - - +
190B ILE* 3.6 21.3 - - + +
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Residues in contact with TYR 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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20A LEU* 3.9 28.0 - - + -
21A PRO* 3.3 45.7 + - + +
22A GLN* 4.3 1.5 + - - +
86B ARG* 2.9 63.7 + - + +
87B ASP 3.6 20.6 - - - -
88B PRO* 3.8 16.6 - - + -
91B LYS* 3.5 14.1 + - + +
92B ASP* 2.9 34.6 + - - +
181B ARG 2.9 20.7 + - - +
182B ALA 3.8 3.6 - - - +
184B LEU* 1.3 74.5 - - - +
186B ALA* 1.3 62.5 + - - +
187B GLY 3.3 0.9 + - - -
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.6 14.0 - - + +
86B ARG* 3.0 46.8 + - - +
88B PRO* 4.4 2.7 - - + -
96B LEU* 5.0 0.4 - - + -
182B ALA 2.9 22.5 + - - +
183B CYS 3.3 5.4 + - - +
185B TYR* 1.3 73.9 - - - +
187B GLY* 1.3 57.3 + - - +
188B VAL* 4.1 8.3 - - + -
224B ILE* 3.8 22.7 - - + -
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Residues in contact with GLY 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.7 9.1 - - - -
86B ARG* 5.9 0.7 - - - -
183B CYS 3.1 4.5 + - - -
184B LEU 3.4 6.9 + - - -
185B TYR 3.3 4.2 - - - -
186B ALA* 1.3 77.3 - - - +
188B VAL* 1.3 62.9 + - - +
189B LYS* 3.7 0.7 + - - +
217B HIS* 3.5 16.1 - - - -
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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
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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