Contacts of the helix formed by residues 165 - 183 (chain B) in PDB entry 4OE5
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 GLU 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASP* 3.1 23.7 + - + +
164B ALA* 1.3 79.4 - - - +
166B LEU* 1.3 71.4 + - + +
169B PHE* 3.0 49.6 + - - +
216B GLY* 5.6 4.7 - - - +
217B GLY 5.6 2.4 + - - +
218B ASN* 4.1 19.6 + - - +
525B ALA* 3.8 19.0 - - + +
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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
----------------------------------------------------------
135B LEU* 3.8 36.3 - - + -
143B ILE* 4.0 14.4 - - + -
161B ASP 3.2 6.8 + - - +
162B ALA* 3.5 14.6 - - - +
165B GLU* 1.3 85.5 - - + +
167B ILE* 1.3 63.7 + - + +
169B PHE* 4.1 1.1 - - - +
170B PHE* 3.3 39.8 + - + -
215B ILE* 5.0 7.9 - - + -
217B GLY* 4.8 14.4 - - - +
218B ASN 5.8 0.2 - - - +
245B VAL* 3.9 36.6 - - + -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.7 21.1 - - + -
132B ALA* 4.1 10.5 - - + +
135B LEU* 3.9 25.6 - - + +
136B SER* 3.8 26.0 - - - +
140B ARG* 4.2 7.0 - - - +
143B ILE* 6.2 0.4 - - + -
162B ALA* 2.9 35.2 + - + +
163B ALA* 3.7 3.8 - - - +
166B LEU* 1.3 74.5 - - + +
168B ASP* 1.3 67.5 + - - +
170B PHE* 3.1 15.1 + - - +
171B ARG* 3.1 50.6 + - - +
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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
----------------------------------------------------------
33B ALA 4.5 1.0 - - - +
34B ASN* 2.9 22.0 + - - +
35B GLU* 2.8 29.8 + - - +
163B ALA 3.0 23.0 + - - +
164B ALA* 3.3 13.9 - - - +
165B GLU 3.9 0.2 + - - -
166B LEU 3.6 0.2 - - - -
167B ILE* 1.3 74.5 - - - +
169B PHE* 1.3 57.8 + - - +
171B ARG* 4.7 3.5 + - - +
172B PHE* 2.8 40.5 + - - +
523B ALA* 3.7 11.4 - - + -
524B ARG* 2.9 30.7 + - - +
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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
----------------------------------------------------------
164B ALA 4.0 1.8 - - - -
165B GLU* 3.0 53.7 + - - +
166B LEU* 4.2 2.2 - - - +
168B ASP* 1.3 74.0 - - - +
170B PHE* 1.3 68.9 + - + +
172B PHE* 6.3 0.4 - - + -
173B ASN* 2.9 46.0 + - - +
218B ASN* 3.5 41.3 - - + +
523B ALA* 3.7 20.2 - - + -
525B ALA 4.1 3.4 - - - -
526B SER* 4.0 18.8 - - - -
530B ASP* 3.3 40.8 - - + -
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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* 3.6 51.0 - + - +
129B LEU* 4.8 0.2 - - - +
131B ALA* 4.3 3.8 - - + -
132B ALA* 3.9 22.2 - - + -
135B LEU* 3.9 24.0 - - + -
166B LEU* 3.3 29.2 + - + -
167B ILE 3.1 8.1 + - - +
169B PHE* 1.3 82.8 - - + +
171B ARG* 1.3 62.3 + - - +
173B ASN* 4.1 5.5 - - - +
174B ALA* 3.2 21.7 + - - +
217B GLY 4.8 9.6 - - - -
218B ASN* 5.4 2.7 - - - -
221B GLY* 4.5 13.9 - - - -
245B VAL* 4.2 11.7 - - + -
248B ILE* 6.2 0.2 - - + -
249B LEU* 4.0 24.5 - - + -
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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
----------------------------------------------------------
32B VAL* 3.7 28.3 - - + +
33B ALA 4.3 15.5 + - - +
34B ASN 4.9 0.2 - - - -
35B GLU* 2.8 37.4 + - - +
129B LEU* 4.0 19.7 + - + +
132B ALA* 3.6 20.3 + - + +
133B ASP* 3.0 29.7 + - - -
136B SER* 3.5 21.0 + - - -
167B ILE* 3.1 25.6 + - - +
168B ASP* 4.0 4.6 + - - +
170B PHE* 1.3 76.9 - - - +
172B PHE* 1.3 61.7 + - + +
174B ALA* 3.3 4.3 + - - +
175B LYS 3.0 22.3 + - - -
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 3.4 33.2 - - + -
33B ALA 3.9 2.9 - - - -
34B ASN* 3.5 47.1 - - - -
168B ASP* 2.8 35.4 + - - +
169B PHE* 4.7 0.7 - - + +
171B ARG* 1.3 73.7 - - + +
173B ASN* 1.3 60.5 + - - +
175B LYS* 3.6 16.3 - - + +
176B TYR* 2.9 30.3 + - - +
522B GLY* 3.6 32.8 - - - -
523B ALA* 3.6 20.2 - - + +
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Residues in contact with ASN 173 (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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169B PHE* 2.9 37.3 + - - +
170B PHE* 4.1 5.3 - - - +
172B PHE* 1.3 77.3 - - - +
174B ALA* 1.3 56.9 + - - +
176B TYR* 3.1 5.8 + - - +
177B ALA* 2.8 26.2 + - - +
218B ASN* 2.7 28.1 + - - +
221B GLY 4.8 1.4 - - - -
222B ALA* 3.6 21.8 - - - +
225B LEU* 3.4 21.9 - - + +
538B ILE* 3.5 20.1 - - + +
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.6 10.8 - - + -
125B ALA* 3.9 25.1 - - + +
128B PHE* 5.0 1.3 - - + -
129B LEU* 4.1 13.5 - - + -
170B PHE 3.2 17.1 + - - +
171B ARG 3.5 4.5 - - - +
173B ASN* 1.3 77.6 - - - +
175B LYS* 1.3 62.3 + - - +
177B ALA* 3.3 1.6 + - - +
178B VAL* 3.0 29.3 + - - +
225B LEU* 3.6 14.7 - - + +
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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
----------------------------------------------------------
30B LEU* 3.4 36.4 + - - +
31B LYS* 4.6 4.0 - - - +
32B VAL* 3.8 35.7 - - + +
171B ARG 3.0 13.5 + - - +
172B PHE* 3.6 18.2 - - + +
174B ALA* 1.3 76.4 - - - +
176B TYR* 1.3 65.0 + - - +
178B VAL* 3.8 1.4 - - - +
179B GLU* 2.9 32.3 + - + +
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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 PHE 2.9 18.3 + - - +
173B ASN* 3.5 6.7 - - - +
175B LYS* 1.3 78.0 - - - +
177B ALA* 1.3 56.9 + - - +
179B GLU* 3.9 4.9 - - - +
180B LEU* 2.9 32.2 + - - +
538B ILE* 4.5 20.0 - - + -
539B LEU* 6.0 1.1 - - + +
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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 ILE* 3.6 31.6 - - + +
125B ALA* 5.9 0.2 - - + -
173B ASN 2.8 17.0 + - - +
174B ALA* 3.7 4.3 - - - +
175B LYS 3.2 0.2 - - - -
176B TYR* 1.3 75.3 - - - +
178B VAL* 1.3 64.3 + - - +
180B LEU* 3.4 7.4 + - - +
181B GLU* 3.1 22.5 + - - +
225B LEU* 4.0 7.0 - - + -
226B MET* 4.0 24.5 - - + -
538B ILE* 6.2 0.4 - - - -
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 6.1 0.3 - - - +
28B SER* 3.5 36.6 - - - +
29B SER* 3.9 13.0 - - - -
30B LEU* 3.9 24.5 - - + +
121B ILE* 4.5 7.2 - - + -
122B ALA* 4.5 14.4 - - - +
125B ALA* 4.0 18.4 - - + -
174B ALA 3.0 19.3 + - - +
175B LYS 3.9 2.7 - - - +
177B ALA* 1.3 75.7 - - - +
179B GLU* 1.3 62.8 + - - +
181B GLU* 3.3 19.5 - - + +
182B GLY* 3.5 5.5 + - - -
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Residues in contact with GLU 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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30B LEU 6.0 0.7 - - - +
175B LYS* 2.9 28.5 + - + +
176B TYR* 3.9 5.4 - - - +
178B VAL* 1.3 75.3 - - - +
180B LEU* 1.3 59.8 + - - +
182B GLY* 2.8 22.9 + - - +
183B GLN* 3.2 9.9 + - - +
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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
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176B TYR 2.9 19.5 + - - +
177B ALA* 3.5 7.2 - - - +
179B GLU* 1.3 75.5 - - - +
181B GLU* 1.3 58.3 + - - +
183B GLN* 2.9 33.2 + - + +
197B TYR* 3.4 46.8 + - + +
226B MET* 4.2 21.3 - - + -
539B LEU* 3.6 44.6 - - + -
542B THR* 4.4 0.7 - - + -
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 5.2 13.5 - - + +
121B ILE* 3.7 28.6 - - + +
177B ALA 3.1 10.0 + - - +
178B VAL 3.3 13.9 - - - +
180B LEU* 1.3 80.1 - - - +
182B GLY* 1.3 54.7 + - - +
184B GLN* 2.8 34.8 + - - +
195B THR 5.1 1.8 - - - +
196B VAL* 6.1 0.3 - - - -
197B TYR* 3.9 26.9 + - - +
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Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 5.5 9.6 - - - +
178B VAL 3.5 5.8 + - - -
179B GLU* 2.8 15.8 + - - -
181B GLU* 1.3 71.9 - - - +
183B GLN* 1.3 60.8 + - - +
184B GLN* 3.0 14.3 + - - +
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Residues in contact with GLN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLU 3.2 6.2 + - - +
180B LEU* 2.9 21.8 + - + +
182B GLY* 1.3 72.5 - - - +
184B GLN* 1.3 65.4 + - - +
185B PRO* 4.4 2.8 - - - +
195B THR* 4.6 0.7 + - - -
197B TYR* 3.0 23.6 + - - +
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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