Contacts of the helix formed by residues 163 - 181 (chain B) in PDB entry 4OE4
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 ILE 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ILE* 3.5 26.9 - - + +
136B SER* 3.9 18.4 - - - +
140B ARG* 3.8 52.3 - - + +
143B MET* 4.4 1.6 - - + -
144B LEU* 3.8 20.0 - - + -
159B GLU* 3.2 19.6 + - + +
161B ASP 3.2 0.2 - - - -
162B CYS* 1.3 92.4 - - - +
164B THR* 1.3 66.1 + - - +
165B GLU 3.6 0.7 - - - -
167B SER* 2.9 36.8 + - - -
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Residues in contact with THR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 5.8 0.7 + - - -
159B GLU* 3.0 17.0 + - - +
160B ILE* 3.7 19.9 - - + +
163B ILE* 1.3 80.0 - - - +
165B GLU* 1.3 61.3 + - + +
167B SER* 3.9 2.4 - - - -
168B ASP* 2.9 47.2 + - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 2.9 42.0 + - + +
161B ASP* 3.5 4.3 + - - +
164B THR* 1.3 72.5 - - + +
166B LEU* 1.3 60.5 + - - +
168B ASP* 3.1 9.2 + - + +
169B PHE* 2.8 40.1 + - + -
213B PHE* 3.7 27.3 - - - -
215B ALA* 3.8 12.0 - - + +
216B ILE* 6.2 0.3 - - - +
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 4.7 2.2 - - - -
135B ILE* 3.6 35.0 - - + -
143B MET* 4.7 1.8 - - + -
161B ASP 3.1 11.7 + - - +
162B CYS 3.6 25.8 - - - +
164B THR 3.4 0.4 - - - -
165B GLU* 1.3 77.7 - - - +
167B SER* 1.3 69.0 + - - +
169B PHE* 3.1 12.7 + - - +
170B PHE* 3.3 31.7 + - + -
214B THR* 4.0 26.5 - - + +
215B ALA* 3.4 11.6 - - + +
218B ALA* 3.7 22.2 - - + -
246B LEU* 4.3 6.7 - - + -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 3.2 22.7 + - - +
135B ILE* 5.0 1.0 - - - +
136B SER* 2.9 23.1 + - - -
163B ILE* 2.9 19.8 + - - -
164B THR* 3.9 3.4 - - - -
166B LEU* 1.3 78.9 - - - +
168B ASP* 1.3 57.9 + - - +
170B PHE* 3.4 1.7 + - - +
171B ARG* 3.0 62.2 + - - +
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Residues in contact with ASP 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B THR* 2.9 34.6 + - - +
165B GLU* 3.1 10.0 + - + +
167B SER* 1.3 76.8 - - - +
169B PHE* 1.3 66.7 + - - +
171B ARG* 4.6 9.9 + - - +
172B TYR* 2.9 50.8 + - + +
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 2.8 30.1 + - + -
166B LEU* 3.1 7.4 + - - +
168B ASP* 1.3 72.4 - - - +
170B PHE* 1.3 62.7 + - + +
172B TYR* 4.0 1.7 - - - -
173B TYR* 2.9 57.5 + + + -
215B ALA* 3.3 39.7 - - + +
216B ILE* 4.5 9.0 - - + -
218B ALA* 5.4 0.2 - - + -
219B ASN* 3.7 37.5 - - + +
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Residues in contact with PHE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 3.2 66.0 - + + +
129B LEU* 4.5 1.1 - - - +
131B ALA* 4.2 13.0 - - + -
132B ALA* 4.1 15.3 - - + -
166B LEU* 3.3 22.4 + - + +
167B SER 3.9 5.8 - - - +
168B ASP 3.3 0.4 - - - -
169B PHE* 1.3 82.4 - - + +
171B ARG* 1.3 64.0 + - + +
173B TYR* 3.8 7.4 - + + +
174B VAL* 3.0 29.9 + - - +
218B ALA* 3.4 45.5 - - + -
221B ILE* 5.4 0.7 - - + -
222B GLY* 4.2 7.4 - - - -
246B LEU* 4.5 9.4 - - + -
250B LEU* 4.3 5.8 - - + -
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.8 22.7 - - + +
132B ALA* 4.3 4.5 - - + -
133B ASP* 2.9 44.2 + - - +
136B SER* 3.8 18.8 + - - -
167B SER* 3.0 43.5 + - - +
168B ASP* 4.3 8.8 + - - +
170B PHE* 1.3 73.7 - - - +
172B TYR* 1.3 71.5 + - + +
174B VAL* 3.4 3.5 + - - +
175B LYS* 3.2 21.7 + - - +
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASP* 2.9 52.8 + - + +
169B PHE* 4.3 1.6 - - - +
171B ARG* 1.3 80.4 - - + +
173B TYR* 1.3 62.2 + - + +
175B LYS* 3.3 6.0 + - + +
176B TYR* 2.9 71.6 + + + -
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 2.9 47.8 + + + +
170B PHE* 3.8 7.9 - + - +
172B TYR* 1.3 77.8 - - + +
174B VAL* 1.3 57.6 + - - +
176B TYR* 4.3 14.6 - + - -
177B ALA* 2.8 34.1 + - - +
219B ASN* 2.4 36.8 + - - -
222B GLY 4.9 2.0 - - - -
223B ALA* 3.8 23.6 - - + -
226B LEU* 3.6 16.8 - - + -
547B ASN* 5.9 2.2 - - + -
548B ILE* 3.4 31.1 - - + +
549B LEU* 3.5 23.6 - - + +
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.4 6.5 - - + -
125B SER* 3.7 40.8 - - - +
128B PHE* 4.8 4.7 - - + -
129B LEU* 4.0 28.7 - - + -
170B PHE 3.0 21.1 + - - +
171B ARG 3.8 4.9 - - - +
172B TYR 3.2 0.2 - - - -
173B TYR* 1.3 76.4 - - - +
175B LYS* 1.3 57.1 + - - +
178B SER* 2.9 32.7 + - - -
226B LEU* 3.9 19.7 - - + -
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG 3.2 11.9 + - - +
172B TYR* 3.3 11.4 + - + +
174B VAL* 1.3 78.8 - - - +
176B TYR* 1.3 71.5 + - + +
178B SER* 3.2 8.5 + - - -
179B ASP* 3.1 32.8 + - - +
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 2.9 62.5 + + + +
173B TYR* 4.3 15.9 - + - -
175B LYS* 1.3 82.8 - - + +
177B ALA* 1.3 63.3 + - - +
179B ASP* 3.3 14.2 + - - +
180B LEU* 3.1 22.6 + - - +
547B ASN* 5.0 22.4 - - + +
549B LEU* 3.8 14.4 - - + -
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.5 24.7 - - + -
173B TYR 2.8 18.0 + - - +
176B TYR* 1.3 75.0 - - - +
178B SER* 1.3 66.4 + - - +
180B LEU* 3.0 10.2 + - - +
181B TYR* 2.9 26.8 + - + -
226B LEU* 4.0 2.9 - - + -
227B MET* 3.7 26.7 - - + -
549B LEU* 3.6 6.7 - - + +
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.5 21.9 - - - -
174B VAL* 2.9 20.4 + - - -
175B LYS* 3.3 9.2 - - - -
177B ALA* 1.3 78.9 - - - +
179B ASP* 1.3 64.1 + - - +
181B TYR* 3.4 4.8 + - - +
182B ALA* 3.4 19.2 + - - +
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Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LYS* 3.1 24.5 + - - +
176B TYR* 3.5 14.7 - - - +
177B ALA 3.2 0.2 - - - -
178B SER* 1.3 75.2 - - - +
180B LEU* 1.3 67.1 + - - +
182B ALA* 3.0 23.8 + - - +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR 3.1 11.5 + - - +
177B ALA* 3.0 10.9 + - - +
179B ASP* 1.3 79.2 - - - +
181B TYR* 1.3 57.6 + - + +
182B ALA 3.2 3.8 + - - -
183B GLN* 4.2 7.8 + - - +
198B TYR* 3.3 55.6 - - + +
227B MET* 3.8 26.7 - - + -
547B ASN 5.9 2.5 - - - +
549B LEU* 4.4 15.5 - - + -
550B SER* 4.6 18.2 - - - +
553B VAL* 4.9 5.2 - - + -
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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
----------------------------------------------------------
121B PHE* 3.4 48.2 - + + -
124B ARG* 2.9 23.2 + - - -
177B ALA* 2.9 20.2 + - + +
178B SER* 3.8 6.1 - - - +
179B ASP 3.2 0.2 - - - -
180B LEU* 1.3 73.0 - - - +
182B ALA* 1.3 55.5 + - - +
183B GLN* 3.1 14.8 + - - +
198B TYR* 3.9 40.4 + + + -
227B MET* 3.4 42.3 + - + +
553B VAL* 4.7 0.7 - - - +
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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