Contacts of the helix formed by residues 169 - 186 (chain B) in PDB entry 4O46
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 HIS 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 3.3 27.7 + - + -
165B MET* 3.4 32.7 - - + +
166B GLN* 3.0 23.1 + - + +
167B PRO 3.4 0.4 - - - -
168B THR* 1.3 79.0 + - - +
170B PRO* 1.4 78.0 - - + +
171B ILE* 3.1 42.8 + - + -
172B ARG* 3.0 11.0 + - + +
173B LEU* 2.9 21.5 + - - +
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Residues in contact with PRO 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B THR 3.3 0.6 - - - +
169B HIS* 1.4 96.8 - - + +
171B ILE* 1.4 53.9 + - + +
173B LEU* 4.5 2.7 - - + -
174B GLY* 2.8 30.7 + - - -
215B SER* 3.7 33.7 - - - +
218B ASP* 4.1 17.3 - - + -
219B SER* 3.4 22.2 - - - +
222B ILE* 3.3 20.6 - - + +
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.5 28.7 - - - +
118B GLU* 3.8 21.5 - - + +
121B VAL* 3.8 24.7 - - + -
122B PHE* 3.9 31.6 - - + +
125B LYS* 4.9 6.3 - - + +
165B MET* 3.7 6.3 - - + -
169B HIS* 3.1 26.2 + - + +
170B PRO* 1.4 76.9 - - + +
172B ARG* 1.4 57.6 + - - +
174B GLY* 3.5 1.7 + - - -
175B LEU* 3.0 29.1 + - - +
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B HIS* 6.0 2.2 + - + -
161B SER* 3.6 42.0 + - - +
162B LYS* 4.0 32.0 + - - +
165B MET* 2.8 32.6 + - + +
166B GLN 3.4 18.8 - - - +
167B PRO* 3.3 34.6 + - + +
169B HIS* 3.0 14.6 + - + +
171B ILE* 1.4 75.1 - - - +
173B LEU* 1.3 63.0 + - - +
175B LEU* 3.4 6.2 + - - +
176B ALA* 3.1 22.5 + - + +
200B ALA* 6.3 1.0 - - - +
203B ASP* 4.1 18.2 + - - +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO 3.5 20.0 - - - +
168B THR* 3.4 29.2 - - - +
169B HIS 2.9 10.1 + - - +
170B PRO* 3.8 2.5 - - + +
172B ARG* 1.3 74.4 - - - +
174B GLY* 1.3 57.7 + - - +
176B ALA* 3.2 8.5 + - - +
177B LEU* 2.9 25.3 + - - +
200B ALA* 3.9 11.2 - - + +
204B ALA* 3.9 14.8 - - + -
219B SER* 3.6 30.5 - - - +
222B ILE* 3.6 19.6 - - + +
223B MET* 4.0 10.5 - - + -
226B LEU* 3.9 23.0 - - + +
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Residues in contact with GLY 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 3.7 19.8 - - - -
170B PRO 2.8 21.5 + - - -
171B ILE* 3.8 2.2 - - - -
173B LEU* 1.3 72.4 - - - +
175B LEU* 1.3 59.6 + - - +
177B LEU* 3.5 5.7 + - - +
178B ASN* 3.2 20.3 + - - +
222B ILE* 3.8 17.0 - - - +
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 3.9 8.1 - - + -
125B LYS* 3.8 22.4 - - + +
154B TYR* 3.7 31.9 - - + +
157B ALA* 3.5 48.5 - - + +
158B HIS* 3.5 18.2 - - + +
161B SER* 3.6 12.1 - - - +
171B ILE 3.0 16.9 + - - +
172B ARG 3.6 4.0 - - - +
173B LEU 3.2 0.2 - - - -
174B GLY* 1.3 73.2 - - - +
176B ALA* 1.3 56.2 + - - +
178B ASN* 3.3 1.6 + - - +
179B TYR* 2.8 40.6 + - + +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B HIS* 5.4 5.4 - - + +
172B ARG* 3.1 14.1 + - + +
173B LEU* 3.2 9.6 + - - +
175B LEU* 1.3 76.6 - - - +
177B LEU* 1.4 56.9 + - - +
179B TYR* 4.5 4.9 - - - -
180B SER* 3.0 31.6 + - - -
196B LEU* 3.9 17.8 - - + +
197B ALA 5.1 0.2 + - - -
200B ALA* 3.5 32.3 - - + -
226B LEU* 4.3 3.7 - - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU 2.9 13.6 + - - +
174B GLY* 3.5 9.4 - - - +
175B LEU 3.2 0.2 - - - -
176B ALA* 1.4 75.0 - - - +
178B ASN* 1.3 68.4 + - - +
180B SER* 2.7 20.6 + - - +
181B VAL* 3.1 20.4 + - + +
222B ILE* 3.9 18.8 - - + -
225B LEU* 3.8 48.0 - - + -
226B LEU* 3.9 15.2 - - + +
229B ASN* 3.4 28.9 - - - +
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Residues in contact with ASN 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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50B LYS* 6.2 0.6 - - - +
125B LYS* 3.4 15.0 - - - +
129B ASP* 2.7 39.6 + - - +
132B ARG* 3.4 17.3 + - - +
133B TYR* 4.9 2.4 + - - -
154B TYR* 3.9 9.0 - - + +
174B GLY 3.2 15.8 + - - +
175B LEU 4.1 1.8 - - - +
177B LEU* 1.3 86.4 - - - +
179B TYR* 1.3 59.2 + - - +
181B VAL* 3.2 10.8 + - - +
182B PHE* 2.9 27.7 + - - +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLU* 2.7 26.9 + - - -
154B TYR* 3.5 56.0 - + + -
155B SER* 3.8 10.5 + - - -
158B HIS* 4.0 27.6 - + + -
175B LEU* 2.8 25.3 + - + +
176B ALA 4.1 0.2 - - - +
178B ASN* 1.3 73.1 - - - +
180B SER* 1.4 57.4 + - - +
182B PHE* 3.2 17.3 + + - +
183B TYR* 2.9 57.0 + + - -
196B LEU* 3.6 19.1 - - + -
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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
----------------------------------------------------------
176B ALA 3.0 16.5 + - - -
177B LEU* 2.7 24.1 + - - -
179B TYR* 1.4 72.4 - - - +
181B VAL* 1.4 63.4 + - - +
183B TYR* 3.2 2.1 + - - -
184B TYR 3.0 18.9 + - - -
193B ALA* 3.3 37.3 - - - +
196B LEU* 3.5 10.7 - - - +
197B ALA* 4.1 12.2 - - - +
226B LEU* 4.6 0.9 - - - +
229B ASN* 4.9 1.4 + - - -
233B TRP* 3.6 16.4 - - - -
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG* 3.8 24.7 - - - +
177B LEU* 3.1 22.9 + - + +
178B ASN* 3.2 11.9 + - - +
180B SER* 1.4 74.7 + - - +
182B PHE* 1.4 54.6 + - - +
184B TYR* 4.7 0.2 - - - -
185B GLU* 2.8 57.5 + - + +
229B ASN* 3.6 24.2 - - - +
233B TRP* 4.2 11.4 - - + -
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Residues in contact with PHE 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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132B ARG* 3.8 13.7 - - + +
135B ALA* 5.8 0.2 - - + -
147B VAL* 3.5 21.5 - - + -
150B SER* 3.4 26.2 - - - -
151B GLU* 3.7 25.8 - - + -
154B TYR* 3.7 15.3 - + + -
178B ASN 2.9 13.2 + - - +
179B TYR* 3.3 25.1 - + - +
181B VAL* 1.4 75.6 - - - +
183B TYR* 1.3 59.3 + + - +
186B ILE* 2.9 56.9 + - + +
187B GLN* 3.0 44.1 + - + -
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLU* 3.9 19.5 + - - -
179B TYR* 2.9 56.6 + + - -
180B SER* 3.2 7.8 + - - +
182B PHE* 1.3 76.9 - + - +
184B TYR* 1.3 52.0 + - - +
187B GLN* 3.4 18.8 - - + +
188B ASN 3.0 10.7 + - - -
189B ALA* 2.8 32.7 + - + +
192B GLN* 3.5 53.8 + - + -
193B ALA* 3.8 13.7 - - - +
196B LEU* 3.7 23.6 - - + -
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Residues in contact with TYR 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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180B SER 3.0 15.4 + - - +
181B VAL* 3.9 1.6 - - - +
183B TYR* 1.3 75.5 - - - +
185B GLU* 1.3 73.1 + - + +
188B ASN* 3.4 23.2 - - - +
189B ALA 4.3 2.9 - - - +
190B PRO* 3.6 35.2 - - + -
193B ALA* 3.6 7.8 - - + +
232B LEU* 5.3 2.1 + - + -
233B TRP* 3.4 67.2 + + + -
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 5.7 0.3 + - - -
132B ARG* 5.0 0.9 + - - -
136B GLU* 4.1 15.8 - - - +
143B ARG* 4.8 1.7 + - - -
181B VAL* 2.8 40.8 + - + +
184B TYR* 1.3 88.9 - - + +
186B ILE* 1.3 70.4 + - + +
188B ASN* 4.5 3.2 + - - +
233B TRP* 6.1 1.1 - - + -
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Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG* 3.7 31.6 - - + +
135B ALA* 4.1 5.6 - - + -
136B GLU* 3.8 37.7 - - + +
143B ARG* 2.8 37.8 + - - +
147B VAL* 3.6 26.0 - - + -
182B PHE* 2.9 37.4 + - + +
185B GLU* 1.3 82.8 - - + +
187B GLN* 1.3 60.9 - - - +
188B ASN* 3.3 2.4 + - - +
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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
------------------------------------------------------------
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