Contacts of the helix formed by residues 191 - 204 (chain B) in PDB entry 1URP
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 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ASN* 1.3 70.5 - - - +
192B GLU* 1.3 57.1 + - - +
194B ALA* 3.5 5.3 - - - +
195B LEU* 2.7 45.5 + - + +
213B GLY* 3.6 3.3 - - - -
214B PHE 2.9 23.0 + - - +
215B ASP* 4.2 1.0 + - - -
216B GLY* 3.0 8.5 + - - -
217B THR* 2.9 50.8 + - + +
220B GLY* 3.8 18.3 - - - +
229B LEU* 4.4 2.6 - - + +
232B THR* 2.7 24.8 + - - -
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Residues in contact with GLU 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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164B PHE 3.7 15.7 - - - +
165B ASP* 5.2 0.4 - - - -
166B ARG* 3.2 63.1 + - - +
190B ASN* 3.3 15.1 + - - +
191B ASP* 1.3 77.4 - - + +
193B MET* 1.3 58.1 + - - +
195B LEU* 3.2 6.7 + - - +
196B GLY 2.8 25.6 + - - -
217B THR* 5.2 4.4 + - - +
219B ASP* 4.7 4.3 - - - +
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Residues in contact with MET 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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129B LEU* 3.5 19.9 - - + +
130B GLN 3.1 25.8 - - - +
131B GLY 3.8 0.4 - - - +
162B ALA* 3.4 18.6 - - + -
164B PHE* 3.2 32.5 - - + -
165B ASP 3.4 27.4 - - - +
169B GLY* 4.2 3.2 - - - -
188B ALA* 3.8 8.7 - - + -
189B GLN* 3.5 25.8 - - + +
190B ASN* 2.7 25.4 + - - +
192B GLU* 1.3 71.5 - - - +
194B ALA* 1.3 52.8 + - - +
196B GLY* 3.2 0.7 + - - -
197B ALA* 2.7 36.0 + - - +
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Residues in contact with ALA 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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188B ALA* 3.3 12.5 - - + +
190B ASN 3.0 14.4 + - - +
191B ASP* 3.1 8.9 + - - +
193B MET* 1.3 74.4 - - - +
195B LEU* 1.3 57.9 + - - +
197B ALA* 3.3 3.9 + - - +
198B LEU* 2.8 33.1 + - - +
211B VAL* 3.8 17.1 - - + +
213B GLY* 3.7 24.5 - - - -
229B LEU* 4.1 10.8 - - + -
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Residues in contact with LEU 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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166B ARG* 3.9 31.4 - - - +
191B ASP* 2.7 32.4 + - + +
192B GLU* 3.7 4.9 - - - +
194B ALA* 1.3 69.2 - - + +
196B GLY* 1.3 67.2 + - - +
198B LEU* 3.0 18.2 + - + +
199B ARG* 2.9 23.0 + - - +
219B ASP* 3.8 35.4 - - + +
220B GLY* 4.2 3.8 - - - +
223B ALA* 3.6 31.2 - - + -
228B LYS* 5.6 2.9 - - - +
229B LEU* 4.8 3.6 - - + -
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Residues in contact with GLY 196 (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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166B ARG* 3.4 34.1 - - - +
170B LEU* 3.4 18.3 - - - -
192B GLU 2.8 15.3 + - - -
193B MET 3.6 3.1 - - - -
195B LEU* 1.3 73.8 - - - +
197B ALA* 1.3 60.1 + - - +
199B ARG* 3.2 7.3 + - - +
200B ALA 3.0 18.4 + - - -
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Residues in contact with ALA 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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129B LEU* 3.7 20.4 - - + -
169B GLY 3.9 2.0 + - - -
173B MET* 3.7 26.1 - - + +
186B VAL* 4.6 9.4 - - + -
193B MET 2.7 19.8 + - - +
194B ALA* 3.5 7.9 - - - +
196B GLY* 1.3 72.0 - - - +
198B LEU* 1.3 57.6 + - - +
200B ALA* 3.4 2.4 + - - +
201B LEU* 3.0 37.0 + - + +
211B VAL* 4.7 4.0 - - + -
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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 ALA 2.8 16.2 + - - +
195B LEU* 3.2 25.8 - - + +
197B ALA* 1.3 69.7 - - - +
199B ARG* 1.3 61.3 + - - +
201B LEU* 3.2 8.2 + - + +
202B GLN* 2.8 31.5 + - - +
207B SER* 6.3 4.0 - - - -
209B VAL 5.5 2.5 - - - +
211B VAL* 3.8 24.7 - - + +
228B LYS* 3.6 32.8 - - + +
229B LEU* 3.8 35.0 - - + +
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Residues in contact with ARG 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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166B ARG* 6.3 1.1 - - - -
170B LEU* 4.0 22.9 - - + -
195B LEU 2.9 11.0 + - - +
196B GLY* 3.4 11.7 - - - +
198B LEU* 1.3 76.0 - - - +
200B ALA* 1.3 61.9 + - - +
202B GLN* 3.2 28.0 + - - +
203B THR* 3.0 39.3 + - - -
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Residues in contact with ALA 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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170B LEU* 3.4 37.6 - - + +
173B MET* 3.8 14.4 - - + -
174B GLN* 3.9 20.1 + - - +
177B LEU* 4.1 3.5 - - + +
196B GLY 3.0 9.3 + - - +
197B ALA 3.5 8.5 - - - +
199B ARG* 1.3 76.7 - - - +
201B LEU* 1.3 61.6 + - - +
203B THR* 3.3 4.3 + - - -
204B ALA* 3.2 21.3 + - - +
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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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173B MET* 4.4 12.8 - - + -
177B LEU* 3.8 27.6 - - + -
183B VAL* 5.3 0.2 - - + -
186B VAL* 4.5 8.5 - - + -
197B ALA 3.0 25.2 + - - +
198B LEU* 3.8 6.5 - - + +
200B ALA* 1.3 73.4 - - - +
202B GLN* 1.3 63.9 + - - +
204B ALA* 3.2 2.1 + - - -
205B GLY 3.1 4.7 + - - -
206B LYS* 2.8 59.0 + - + +
207B SER* 5.1 1.6 - - - -
209B VAL* 3.8 27.6 - - + +
211B VAL* 3.5 29.8 - - + -
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Residues in contact with GLN 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 17.2 + - - +
199B ARG* 3.6 31.6 + - - +
201B LEU* 1.3 74.7 - - - +
203B THR* 1.3 63.6 + - - +
205B GLY* 3.1 14.6 + - - -
206B LYS 4.9 0.2 - - - +
207B SER* 4.8 19.9 + - - +
228B LYS* 5.9 3.1 - - - +
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Residues in contact with THR 203 (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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170B LEU* 5.6 0.3 - - - +
174B GLN* 4.0 20.6 + - - +
199B ARG* 3.0 26.1 + - - -
200B ALA 3.5 9.6 - - - -
201B LEU 3.3 0.2 - - - -
202B GLN* 1.3 78.9 - - - +
204B ALA* 1.3 58.7 + - + +
205B GLY 3.6 0.3 + - - -
171C ASN* 3.7 31.6 + - + +
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Residues in contact with ALA 204 (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 GLN* 6.5 0.7 - - + -
177B LEU* 3.8 29.2 - - + -
200B ALA 3.2 5.9 + - - +
201B LEU 3.2 4.4 + - - +
203B THR* 1.3 75.1 - - + +
205B GLY* 1.3 61.4 + - - +
206B LYS* 4.3 9.5 - - + +
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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