Contacts of the helix formed by residues 178 - 194 (chain B) in PDB entry 3UGV
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 ASP 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B ARG* 3.2 8.1 - - - +
177B ASP* 1.3 78.4 - - + +
179B PRO* 1.3 65.6 - - - +
180B ALA* 2.9 26.3 + - - +
181B VAL* 2.9 46.8 + - + +
182B ASP 3.5 3.3 + - - -
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Residues in contact with PRO 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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177B ASP 3.5 9.6 - - - +
178B ASP* 1.3 92.0 - - - +
180B ALA* 1.3 61.4 + - - +
182B ASP* 3.0 19.7 + - + +
183B ILE* 3.2 14.4 + - - +
215B ARG* 3.7 37.9 - - + +
218B GLN* 3.5 33.7 - - - +
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Residues in contact with ALA 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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178B ASP* 2.9 20.3 + - - +
179B PRO* 1.3 78.8 - - - +
181B VAL* 1.3 57.5 + - + +
183B ILE* 3.4 12.7 + - - +
184B GLU* 2.9 29.6 + - - +
218B GLN* 4.6 1.5 + - - -
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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
----------------------------------------------------------
147B SER* 5.7 0.4 - - - -
148B PRO* 4.1 24.9 - - + -
176B ARG* 3.5 23.6 - - + +
178B ASP* 2.9 36.2 + - + +
180B ALA* 1.3 76.2 - - + +
182B ASP* 1.3 59.0 + - - +
184B GLU* 3.3 14.6 + - - +
185B THR* 2.8 34.2 + - - -
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Residues in contact with ASP 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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172B LEU* 5.0 0.3 - - - +
174B MET* 3.6 33.1 - - - +
175B GLY 3.0 28.3 + - - -
176B ARG* 2.8 49.8 + - - +
178B ASP 3.5 1.2 + - - -
179B PRO* 3.0 12.5 + - + +
181B VAL* 1.3 78.7 - - - +
183B ILE* 1.3 63.3 + - + +
185B THR* 3.4 3.5 + - - -
186B ALA 3.2 16.5 + - - -
203B PHE* 4.3 2.8 - - + -
215B ARG* 3.2 17.5 + - - -
219B ILE* 5.7 1.6 - - + -
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Residues in contact with ILE 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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174B MET* 5.0 0.2 - - - -
179B PRO 3.2 9.2 + - - +
180B ALA* 3.6 11.0 - - - +
182B ASP* 1.3 74.3 - - - +
184B GLU* 1.3 67.3 + - - +
186B ALA* 3.0 17.7 + - - +
187B GLU* 3.0 21.7 + - + +
218B GLN* 3.8 43.3 - - + +
219B ILE* 4.0 19.1 - - + -
222B LEU* 4.3 22.7 - - + -
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Residues in contact with GLU 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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148B PRO* 3.7 24.1 - - + +
180B ALA* 2.9 14.5 + - - +
181B VAL* 3.3 24.0 + - - +
183B ILE* 1.3 77.0 - - - +
185B THR* 1.3 55.5 + - - +
187B GLU* 3.3 6.9 + - - +
188B ALA* 2.9 30.0 + - - +
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Residues in contact with THR 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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148B PRO* 3.6 24.9 - - + +
151B VAL* 3.6 36.3 - - + -
172B LEU* 3.9 11.4 - - + -
176B ARG* 3.6 29.7 + - - +
181B VAL 2.8 20.9 + - - -
182B ASP 3.5 5.6 - - - -
184B GLU* 1.3 71.2 - - - +
186B ALA* 1.3 59.8 + - - +
188B ALA* 3.4 1.8 + - - +
189B VAL* 3.0 28.1 + - - +
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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
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172B LEU* 3.8 25.7 - - + +
174B MET* 4.0 9.9 - - + -
182B ASP 3.2 7.2 + - - +
183B ILE 3.0 9.1 + - - +
185B THR* 1.3 78.3 - - - +
187B GLU* 1.3 64.5 + - + +
189B VAL* 3.4 3.0 + - - +
190B TRP* 3.2 34.6 + - + -
199B LEU* 4.0 9.3 - - + +
222B LEU* 4.4 15.5 - - + -
224B LEU* 5.1 2.0 - - + -
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Residues in contact with GLU 187 (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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183B ILE* 3.0 30.8 + - + +
184B GLU* 3.7 6.5 - - - +
186B ALA* 1.3 78.5 - - - +
188B ALA* 1.3 58.2 + - - +
190B TRP* 3.5 8.0 + - - +
191B ASP* 3.1 35.7 + - - +
195B ARG* 2.9 37.2 + - - +
222B LEU* 3.5 23.9 - - + +
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Residues in contact with ALA 188 (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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148B PRO* 4.2 26.7 - - + +
149B ALA* 5.1 1.3 - - - +
152B ALA* 3.5 16.7 - - + +
184B GLU 2.9 17.6 + - - +
185B THR 3.9 4.5 - - - +
186B ALA 3.3 0.2 - - - -
187B GLU* 1.3 75.7 - - - +
189B VAL* 1.3 63.2 + - - +
191B ASP* 3.5 12.1 + - - +
192B ALA* 3.3 15.4 + - - +
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Residues in contact with VAL 189 (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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143B LEU* 4.6 7.4 - - + -
151B VAL* 3.6 29.4 - - + +
152B ALA* 4.2 14.8 - - - +
155B ALA* 4.0 17.0 - - + -
170B LEU* 4.6 2.9 - - + -
172B LEU* 4.7 4.3 - - + -
185B THR* 3.0 23.1 + - + +
186B ALA* 3.7 5.4 - - - +
187B GLU 3.3 0.2 - - - -
188B ALA* 1.3 76.8 - - - +
190B TRP* 1.3 58.1 + - - +
192B ALA* 3.3 2.9 + - - +
193B VAL* 3.0 34.2 + - + +
199B LEU* 3.9 30.7 - - + -
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Residues in contact with TRP 190 (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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186B ALA* 3.2 24.0 + - + +
187B GLU* 3.9 15.7 - - - +
189B VAL* 1.3 76.0 - - - +
191B ASP* 1.3 62.5 + - - +
192B ALA 3.1 0.4 - - - -
193B VAL* 4.8 0.9 - - + -
194B GLY* 2.8 51.8 + - - +
195B ARG* 3.6 53.5 + - - +
197B THR* 2.8 24.8 + - - -
198B ALA* 5.7 0.2 - - - -
199B LEU* 3.4 35.7 - - + +
222B LEU* 3.5 32.3 - - + -
223B GLY 3.7 22.7 - - - -
224B LEU* 4.0 13.7 - - + -
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Residues in contact with ASP 191 (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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187B GLU* 3.1 22.8 + - - +
188B ALA* 3.6 13.4 - - - +
189B VAL 3.3 0.2 - - - -
190B TRP* 1.3 77.3 - - - +
192B ALA* 1.3 59.8 + - - +
194B GLY* 4.3 2.3 + - - -
195B ARG* 4.2 11.6 + - - -
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Residues in contact with ALA 192 (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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152B ALA* 3.8 28.0 - - + +
156B VAL* 4.0 16.6 - - + +
188B ALA 3.3 13.2 + - - +
189B VAL 3.3 4.4 + - - +
190B TRP 3.1 0.4 - - - -
191B ASP* 1.3 81.9 - - + +
193B VAL* 1.3 61.9 + - + +
194B GLY 3.5 0.2 - - - -
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Residues in contact with VAL 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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155B ALA* 3.8 39.9 - - + +
156B VAL* 3.8 10.1 - - + +
159B LYS* 4.2 23.8 - - + +
170B LEU* 4.4 4.9 - - + -
189B VAL* 3.0 29.3 + - + +
190B TRP* 4.4 1.6 - - + -
192B ALA* 1.3 77.2 - - - +
194B GLY* 1.3 65.5 - - - +
196B ASP* 6.0 0.5 - - - +
197B THR* 3.6 33.1 + - + +
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Residues in contact with GLY 194 (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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190B TRP* 2.8 28.8 + - - -
191B ASP 4.3 2.0 + - - -
192B ALA 3.5 1.6 - - - -
193B VAL* 1.3 82.1 - - - +
195B ARG* 1.3 61.2 + - - -
196B ASP* 3.1 8.0 + - - -
197B THR* 3.2 13.2 + - - -
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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