Contacts of the helix formed by residues 191 - 204 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ASN* 1.3 70.8 - - - +
192A GLU* 1.3 57.5 + - - +
194A ALA* 3.1 6.1 + - + +
195A LEU* 2.7 43.8 + - + +
213A GLY* 3.6 3.3 - - - -
214A PHE 2.9 23.5 + - - +
215A ASP* 4.5 0.8 + - - -
216A GLY* 3.0 9.0 + - - -
217A THR* 2.9 50.9 + - + +
220A GLY* 3.8 17.2 - - - +
229A LEU* 4.4 2.8 - - + +
232A THR* 2.7 25.3 + - - -
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PHE 3.7 15.5 - - - +
165A ASP* 5.2 0.4 - - - -
166A ARG* 3.1 62.5 + - - +
190A ASN* 3.3 14.9 + - - +
191A ASP* 1.3 78.0 - - + +
193A MET* 1.3 58.2 + - - +
195A LEU* 3.2 6.7 + - - +
196A GLY 2.8 25.5 + - - -
217A THR* 5.2 3.8 + - - +
219A ASP* 4.7 4.0 - - - +
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Residues in contact with MET 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.5 31.3 - - + +
130A GLN 3.2 26.5 - - - +
131A GLY 3.8 0.2 - - - +
162A ALA* 3.4 18.8 - - + -
164A PHE* 3.2 32.3 - - + -
165A ASP 3.4 26.9 - - - +
169A GLY* 4.2 2.5 - - - -
188A ALA* 3.9 8.7 - - + -
189A GLN* 3.5 14.6 - - + +
190A ASN* 2.7 26.8 + - - +
192A GLU* 1.3 71.9 - - - +
194A ALA* 1.3 52.7 + - - +
196A GLY* 3.2 1.2 + - - -
197A ALA* 2.7 36.0 + - - +
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA* 3.3 13.3 - - + +
190A ASN 3.0 15.1 + - - +
191A ASP* 3.1 8.7 + - - +
193A MET* 1.3 75.7 - - - +
195A LEU* 1.3 57.4 + - - +
197A ALA* 3.2 4.4 + - - +
198A LEU* 2.8 32.6 + - - +
211A VAL* 3.8 16.1 - - + +
213A GLY* 3.7 24.7 - - - -
229A LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 3.9 32.1 - - - +
191A ASP* 2.7 30.1 + - + +
192A GLU* 3.7 5.6 - - - +
194A ALA* 1.3 68.8 - - + +
196A GLY* 1.3 66.8 + - - +
198A LEU* 3.0 17.9 + - + +
199A ARG* 2.9 23.3 + - - +
219A ASP* 3.8 35.7 - - + +
220A GLY* 4.2 4.7 - - - +
223A ALA* 3.6 31.0 - - + -
228A LYS* 5.6 2.9 - - - +
229A LEU* 4.8 3.8 - - + -
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Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 3.4 34.1 - - - +
170A LEU* 3.4 18.5 - - - -
192A GLU 2.8 11.5 + - - -
193A MET 3.6 3.1 - - - -
195A LEU* 1.3 77.2 - - - +
197A ALA* 1.3 60.8 + - - +
199A ARG* 3.2 6.8 + - - +
200A ALA 3.0 18.0 + - - -
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.7 20.6 - - + -
169A GLY 3.9 1.8 + - - -
173A MET* 3.7 25.6 - - + +
186A VAL* 4.6 9.4 - - + -
193A MET 2.7 20.2 + - - +
194A ALA* 3.5 8.1 - - - +
196A GLY* 1.3 72.1 - - - +
198A LEU* 1.3 57.0 + - - +
200A ALA* 3.4 2.4 + - - +
201A LEU* 3.0 35.8 + - + +
211A VAL* 4.7 4.0 - - + -
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA 2.8 16.6 + - - +
195A LEU* 3.0 25.1 + - + +
197A ALA* 1.3 69.3 - - - +
199A ARG* 1.3 61.4 + - - +
201A LEU* 3.3 7.7 + - + +
202A GLN* 2.9 31.5 + - - +
207A SER* 6.3 3.8 - - - -
209A VAL 5.5 2.0 - - - +
211A VAL* 3.8 25.5 - - + +
223A ALA* 4.6 0.2 - - + -
228A LYS* 3.6 33.0 - - + +
229A LEU* 3.8 35.4 - - + +
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 6.3 1.1 - - - -
170A LEU* 4.0 23.3 - - + -
195A LEU 2.9 11.7 + - - +
196A GLY* 3.4 11.7 - - - +
198A LEU* 1.3 75.4 - - - +
200A ALA* 1.3 62.5 + - - +
202A GLN* 3.3 28.0 + - - +
203A THR* 3.1 38.9 + - - -
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 3.4 37.4 - - + +
173A MET* 3.8 16.2 - - + -
174A GLN* 3.9 19.6 + - - +
177A LEU* 4.1 3.5 - - + +
196A GLY 3.0 7.9 + - - +
197A ALA 3.5 8.7 - - - +
198A LEU 3.3 0.2 - - - -
199A ARG* 1.3 76.5 - - - +
201A LEU* 1.3 61.4 + - - +
203A THR* 3.4 4.2 + - - -
204A ALA* 3.2 21.5 + - - +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A MET* 4.4 12.8 - - + -
177A LEU* 3.8 30.7 - - + -
183A VAL* 5.3 0.2 - - + -
186A VAL* 4.5 4.7 - - + -
197A ALA 3.0 24.3 + - - +
198A LEU* 3.3 7.2 + - + +
200A ALA* 1.3 73.0 - - - +
202A GLN* 1.3 63.8 + - - +
204A ALA* 3.2 2.1 + - - -
205A GLY 3.1 4.5 + - - -
206A LYS* 2.8 55.1 + - + +
207A SER* 5.1 1.3 - - - -
209A VAL* 3.7 31.9 - - + +
211A VAL* 3.5 30.1 - - + -
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Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU 2.9 18.6 + - - +
199A ARG* 3.3 32.5 + - - +
201A LEU* 1.3 75.0 - - - +
203A THR* 1.3 62.8 + - - +
205A GLY* 3.1 14.2 + - - -
207A SER* 4.8 20.1 + - - +
228A LYS* 5.9 2.8 - - - +
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 5.6 0.3 - - - +
174A GLN* 4.0 19.6 + - - +
199A ARG* 3.1 26.6 + - - -
200A ALA 3.5 9.2 - - - -
201A LEU 3.3 0.2 - - - -
202A GLN* 1.3 77.9 - - - +
204A ALA* 1.3 59.1 + - + +
205A GLY 3.6 0.3 + - - -
171D ASN* 3.6 35.7 + - + +
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 6.5 0.7 - - + -
177A LEU* 3.8 30.1 - - + -
200A ALA 3.2 8.3 + - - +
201A LEU 3.2 2.2 + - - +
203A THR* 1.3 75.3 - - + +
205A GLY* 1.3 61.4 + - - +
206A LYS* 4.3 9.1 - - + +
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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