Contacts of the helix formed by residues 166 - 179 (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 ARG 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ASP* 1.3 72.8 + - - +
167A ILE* 1.3 68.0 + - + +
170A LEU* 2.9 29.3 + - + +
192A GLU* 3.1 64.0 + - - +
195A LEU* 3.9 25.0 - - - +
196A GLY* 3.4 18.3 - - - +
199A ARG* 6.3 1.1 - - - -
219A ASP* 3.3 24.4 + - - -
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Residues in contact with ILE 167 (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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165A ASP* 2.9 12.0 + - - +
166A ARG* 1.3 83.8 - - + +
168A LYS* 1.3 63.4 + - + +
170A LEU* 3.2 20.0 + - + +
171A ASN* 3.0 38.3 + - - +
178D THR* 4.3 13.2 - - + -
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Residues in contact with LYS 168 (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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162A ALA* 3.4 22.2 - - - +
163A ASP* 2.8 37.6 + - + +
165A ASP* 2.7 26.0 + - + +
167A ILE* 1.3 72.6 - - + +
169A GLY* 1.3 55.5 + - - +
171A ASN* 4.5 5.8 - - - +
172A VAL* 2.8 43.1 + - + +
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Residues in contact with GLY 169 (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* 3.9 7.6 - - - +
162A ALA* 3.6 15.8 - - - +
165A ASP 2.9 19.5 + - - -
166A ARG 3.6 1.6 - - - -
168A LYS* 1.3 77.4 - - - +
170A LEU* 1.3 59.8 + - - +
173A MET* 3.1 27.0 + - - +
193A MET* 4.2 13.7 - - - -
196A GLY 4.0 6.3 - - - -
197A ALA 3.9 1.2 + - - -
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Residues in contact with LEU 170 (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* 2.9 12.8 + - + +
167A ILE* 3.3 24.9 - - + +
169A GLY* 1.3 76.6 - - - +
171A ASN* 1.3 68.2 + - - +
174A GLN* 2.9 43.3 + - - +
196A GLY* 3.4 15.6 - - - +
199A ARG* 4.0 20.9 - - + -
200A ALA* 3.4 35.7 - - + +
203A THR* 5.6 0.4 - - - +
174D GLN* 6.4 2.0 - - + -
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Residues in contact with ASN 171 (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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167A ILE* 3.0 26.1 + - - +
168A LYS* 4.0 5.7 - - - +
170A LEU* 1.3 81.9 - - - +
172A VAL* 1.3 64.7 + - + +
174A GLN* 3.2 18.9 + - - +
175A ASN* 3.0 31.8 + - - +
174D GLN 4.8 0.5 - - - -
175D ASN* 3.9 21.3 + - - +
178D THR* 2.5 44.5 + - - +
179D ALA* 6.5 0.2 - - + -
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Residues in contact with VAL 172 (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* 3.8 10.5 - - + -
160A GLN* 4.1 19.3 - - + +
161A PRO 3.6 20.4 - - - +
162A ALA* 4.1 9.9 - - + -
168A LYS* 2.8 29.6 + - + +
169A GLY 4.3 0.7 - - - +
171A ASN* 1.3 72.7 - - + +
173A MET* 1.3 57.7 + - - +
175A ASN* 3.2 11.3 + - + +
176A LEU* 2.9 50.3 + - + +
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Residues in contact with MET 173 (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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127A ILE* 4.0 31.2 - - + -
129A LEU* 4.4 7.4 - - + +
169A GLY 3.1 20.6 + - - +
170A LEU 3.8 2.7 - - - +
172A VAL* 1.3 76.6 - - - +
174A GLN* 1.3 53.7 + - - +
176A LEU* 4.5 2.0 - - + +
177A LEU* 2.7 57.1 + - + +
183A VAL* 4.6 4.0 - - + -
186A VAL* 3.8 36.1 - - + -
197A ALA* 3.7 36.8 - - + +
200A ALA* 3.8 6.3 - - + -
201A LEU* 4.4 11.2 - - + -
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Residues in contact with GLN 174 (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* 2.9 31.8 + - - +
171A ASN* 3.3 26.6 - - - +
173A MET* 1.3 78.2 - - - +
175A ASN* 1.3 62.3 + - - +
177A LEU* 3.5 7.1 + - + +
178A THR* 3.2 30.5 + - + +
200A ALA* 3.9 14.4 + - + +
203A THR* 4.0 25.1 + - - +
171D ASN* 5.0 8.9 - - - +
175D ASN* 4.2 27.4 + - - +
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Residues in contact with ASN 175 (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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160A GLN* 6.1 0.2 - - - +
171A ASN* 3.0 23.8 + - - +
172A VAL* 3.2 10.7 + - - +
174A GLN* 1.3 75.1 - - - +
176A LEU* 1.3 65.5 - - + +
178A THR* 3.2 20.8 + - - -
179A ALA* 3.2 11.3 + - - +
153B LYS* 3.2 31.8 + - - +
175D ASN* 3.7 20.7 + - - +
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Residues in contact with LEU 176 (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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127A ILE* 3.8 38.4 - - + -
129A LEU* 4.0 8.7 - - + -
158A ALA* 3.7 23.6 - - + -
160A GLN* 3.3 34.3 - - + +
172A VAL* 2.9 36.5 + - + +
173A MET* 3.9 4.3 - - + +
175A ASN* 1.3 75.9 - - + +
177A LEU* 1.3 55.7 + - - +
179A ALA* 3.6 5.4 - - + +
180A HIS* 2.7 43.3 + - + +
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Residues in contact with LEU 177 (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* 2.7 36.5 + - + +
174A GLN* 3.6 8.5 - - + +
176A LEU* 1.3 74.6 - - - +
178A THR* 1.3 64.0 + - + +
180A HIS 3.2 3.7 - - - +
181A PRO* 3.2 29.7 - - + +
183A VAL* 4.2 16.6 - - + -
200A ALA* 4.1 5.8 - - + +
201A LEU* 3.8 38.6 - - + +
204A ALA* 3.8 27.8 - - + -
206A LYS* 4.4 18.8 - - + -
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Residues in contact with THR 178 (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* 3.2 19.9 + - + +
175A ASN* 3.2 10.5 + - - -
177A LEU* 1.3 79.1 - - + +
179A ALA* 1.3 63.8 + - - +
180A HIS 3.6 0.2 + - - -
181A PRO* 3.8 10.7 - - - +
153B LYS* 4.6 13.0 + - - +
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Residues in contact with ALA 179 (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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175A ASN 3.2 14.3 + - - +
176A LEU* 3.8 7.0 - - + +
178A THR* 1.3 82.1 + - - +
180A HIS* 1.3 79.0 + - + +
181A PRO* 3.6 5.3 - - - +
122B GLU* 5.9 2.7 - - - +
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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