Contacts of the helix formed by residues 186 - 202 (chain B) in PDB entry 5W4A
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 THR 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B TYR* 3.7 27.1 - - + -
157B PHE* 3.6 37.2 - - + -
181B LEU 2.8 26.4 + - - +
182B GLU* 3.3 4.0 - - - -
183B ASP* 2.9 23.3 + - - +
185B ASP* 1.3 75.9 - - - +
187B ALA* 1.3 65.8 + - - +
188B ASP 3.3 2.5 - - - -
189B GLU* 3.1 11.3 + - - +
190B VAL* 2.9 20.5 + - - +
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 4.2 24.7 - - + +
183B ASP 2.9 18.2 + - - +
184B GLU* 4.0 9.4 + - - +
185B ASP 3.6 2.2 - - - -
186B THR* 1.3 75.5 - - - +
188B ASP* 1.3 66.9 + - - +
190B VAL* 3.3 3.0 + - - +
191B GLU* 3.0 22.9 + - - +
194B ARG* 5.4 0.3 + - - -
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Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU 5.4 0.6 + - - -
185B ASP 5.2 1.7 + - - +
186B THR 3.3 0.8 - - - -
187B ALA* 1.3 80.8 - - - +
189B GLU* 1.3 64.7 + - + +
191B GLU* 3.3 15.4 + - - +
192B VAL* 3.3 25.4 + - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 4.6 12.9 + - - -
157B PHE* 3.4 28.2 - - + -
158B THR* 5.6 1.6 + - - -
161B SER* 5.1 1.8 + - - +
185B ASP 4.5 11.3 - - - +
186B THR* 3.1 10.7 + - - +
188B ASP* 1.3 75.7 - - + +
190B VAL* 1.3 66.9 + - - +
192B VAL* 3.1 10.8 + - - +
193B ILE* 3.1 27.6 + - + +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PHE* 3.7 26.0 - - + -
173B TYR* 4.8 8.2 - - + -
176B THR* 3.8 24.5 - - + +
182B GLU* 3.7 30.1 - - + +
186B THR* 2.9 28.4 + - - +
187B ALA 3.6 7.9 - - - +
189B GLU* 1.3 75.2 - - - +
191B GLU* 1.3 57.9 + - - +
193B ILE* 3.2 6.6 + - + +
194B ARG* 2.8 42.4 + - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA 3.0 12.5 + - - +
188B ASP* 3.5 17.8 - - - +
189B GLU 3.2 0.4 - - - -
190B VAL* 1.3 77.8 - - - +
192B VAL* 1.3 58.2 + - + +
194B ARG* 3.4 22.0 + - - +
195B ASP* 2.9 50.4 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASP 3.3 14.8 + - - +
189B GLU* 3.1 10.6 + - - +
191B GLU* 1.3 79.3 - - + +
193B ILE* 1.3 58.6 + - + +
195B ASP* 3.3 6.9 + - + +
196B ASN* 2.8 45.8 + - - +
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Residues in contact with ILE 193 (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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157B PHE* 3.9 19.5 - - + -
161B SER* 3.8 23.6 - - - +
164B CYS* 3.7 23.1 - - - -
169B ASP* 3.5 23.8 - - - +
172B ALA* 3.9 13.5 - - + -
173B TYR* 3.8 19.7 - - + +
176B THR* 5.2 2.0 - - - +
189B GLU* 3.1 16.2 + - + +
190B VAL* 3.2 7.6 + - + +
192B VAL* 1.3 76.3 - - + +
194B ARG* 1.3 65.0 + - - +
196B ASN* 3.2 11.2 + - - +
197B PHE* 3.1 20.3 + - - +
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TYR* 3.2 45.9 + - + -
177B LYS* 5.4 3.2 - - - +
182B GLU* 3.2 29.7 + - - -
187B ALA 5.4 0.2 + - - -
190B VAL* 2.8 27.2 + - - +
191B GLU* 3.6 37.9 - - - +
193B ILE* 1.3 77.3 - - - +
195B ASP* 1.3 62.8 + - - +
197B PHE* 3.1 7.2 + - + +
198B LEU* 2.8 47.8 + - + +
212B ILE* 4.1 20.1 + - + +
213B ARG* 5.6 2.7 - - - +
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Residues in contact with ASP 195 (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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191B GLU* 2.9 38.9 + - - +
192B VAL* 3.7 6.7 - - + +
194B ARG* 1.3 78.9 - - - +
196B ASN* 1.3 62.6 + - - +
198B LEU* 3.7 18.0 - - - +
199B ASN* 2.9 40.7 + - - +
213B ARG* 5.2 5.0 + - - +
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Residues in contact with ASN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B CYS* 4.8 5.5 - - - +
169B ASP* 2.9 33.1 + - - +
192B VAL* 2.8 40.1 + - - +
193B ILE* 3.2 7.3 + - - +
195B ASP* 1.3 76.2 - - - +
197B PHE* 1.3 62.2 + - - +
199B ASN* 3.3 23.1 + - - +
200B ARG* 3.6 10.9 + - - +
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Residues in contact with PHE 197 (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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13B GLY 4.5 5.8 - - - -
14B ILE* 4.1 19.3 - - + -
15B ARG 5.9 0.4 - - - -
47B VAL* 6.2 0.2 - - + -
48B PHE* 4.2 5.8 - + - -
169B ASP* 4.1 5.7 - - + +
170B PHE* 3.3 63.5 - + + +
173B TYR* 4.7 14.8 - + + -
193B ILE 3.1 11.4 + - - +
194B ARG* 3.6 8.3 - - + +
196B ASN* 1.3 74.6 - - - +
198B LEU* 1.3 68.6 + - + +
200B ARG* 3.0 18.5 + - + +
201B LEU* 3.0 36.5 + - + +
212B ILE* 3.8 30.1 - - + -
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Residues in contact with LEU 198 (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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194B ARG* 2.8 38.7 + - + +
195B ASP* 3.3 14.3 + - - +
197B PHE* 1.3 78.8 - - + +
199B ASN* 1.3 58.2 + - - +
201B LEU* 4.2 6.1 - - + +
202B ASP* 2.8 37.7 + - - -
209B ALA* 3.8 21.8 - - + -
212B ILE* 3.8 35.9 - - + -
213B ARG* 3.7 48.7 - - + +
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Residues in contact with ASN 199 (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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195B ASP* 2.9 26.6 + - - +
196B ASN* 3.6 17.2 + - - +
197B PHE 3.2 0.4 - - - -
198B LEU* 1.3 77.3 - - - +
200B ARG* 1.3 63.4 + - + +
202B ASP* 4.3 9.8 + - - +
203B GLN* 3.7 19.2 + - - +
213B ARG* 5.1 3.3 + - - -
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Residues in contact with ARG 200 (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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7A GLU* 5.2 8.2 + - - -
8A ILE 4.8 9.5 + - - -
9A VAL* 5.8 0.2 - - - +
10B GLU* 2.9 36.7 + - - -
13B GLY* 3.4 33.7 - - - +
15B ARG* 4.4 19.4 - - - +
167B ASP* 5.6 4.9 + - - +
196B ASN 3.6 10.3 + - - +
197B PHE* 3.0 12.1 + - + +
199B ASN* 1.3 79.8 - - + +
201B LEU* 1.3 64.1 + - - +
203B GLN* 3.3 18.9 + - - +
204B THR* 3.9 9.7 + - - +
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Residues in contact with LEU 201 (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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13B GLY 4.9 1.8 - - - +
14B ILE* 3.9 33.2 - - + -
48B PHE* 4.2 3.4 - - + -
197B PHE* 3.0 39.3 + - + +
198B LEU* 4.1 6.1 - - + +
200B ARG* 1.3 74.9 - - - +
202B ASP* 1.3 59.9 + - - +
204B THR* 3.0 8.9 + - - +
205B LYS* 2.7 61.8 + - + +
208B LEU* 4.0 11.7 - - + -
209B ALA* 3.7 28.0 - - + +
212B ILE* 4.0 10.1 - - + -
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Residues in contact with ASP 202 (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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198B LEU 2.8 25.8 + - - +
199B ASN* 4.4 10.8 - - - +
200B ARG 3.3 0.2 - - - -
201B LEU* 1.3 73.4 - - - +
203B GLN* 1.3 67.0 + - - +
204B THR 3.5 0.5 + - - -
206B PRO* 3.7 29.6 - - + +
209B ALA* 3.1 12.1 - - - +
213B ARG* 2.9 42.9 + - - -
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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