Contacts of the helix formed by residues 166 - 179 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C ASP* 1.3 71.7 + - - +
167C ILE* 1.3 69.6 + - + +
170C LEU* 2.9 25.9 + - + +
192C GLU* 3.1 64.9 + - - +
195C LEU* 3.9 25.4 - - - +
196C GLY* 3.4 20.5 - - - +
199C ARG* 6.3 1.1 - - - -
219C ASP* 3.3 23.8 + - - -
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Residues in contact with ILE 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ASP* 2.9 10.7 + - - +
166C ARG* 1.3 82.5 - - + +
168C LYS* 1.3 59.9 + - + +
170C LEU* 3.2 17.9 + - + +
171C ASN* 3.0 43.0 + - - +
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ALA* 3.4 22.7 - - - +
163C ASP* 2.8 36.8 + - + +
165C ASP* 2.7 26.2 + - - +
167C ILE* 1.3 73.7 - - + +
169C GLY* 1.3 57.3 + - - +
171C ASN* 4.5 6.3 - - - +
172C VAL* 2.8 40.6 + - + +
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Residues in contact with GLY 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU* 3.9 6.2 - - - +
162C ALA* 3.6 16.1 - - - +
165C ASP 2.9 20.1 + - - -
166C ARG 3.6 1.8 - - - -
167C ILE 3.2 0.2 - - - -
168C LYS* 1.3 75.5 - - - +
170C LEU* 1.3 61.6 + - - +
173C MET* 3.0 28.4 + - - +
193C MET* 4.2 14.6 - - - -
196C GLY 4.0 6.7 - - - -
197C ALA 4.1 0.4 - - - -
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ARG* 2.9 13.6 + - + +
167C ILE* 3.3 25.1 - - + +
169C GLY* 1.3 77.8 - - - +
171C ASN* 1.3 68.4 + - - +
174C GLN* 2.9 43.8 + - - +
196C GLY* 3.4 14.9 - - - +
199C ARG* 4.1 20.6 - - + -
200C ALA* 3.4 36.9 - - + +
203C THR* 5.7 0.4 - - - +
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Residues in contact with ASN 171 (chain C).
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* 4.9 11.0 - - - +
203B THR* 3.7 29.6 + - + +
167C ILE* 3.0 39.2 + - - +
168C LYS* 4.0 5.4 - - - +
170C LEU* 1.3 80.6 - - - +
172C VAL* 1.3 62.9 + - + +
174C GLN* 3.3 20.0 + - - +
175C ASN* 3.0 22.9 + - - +
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU* 3.8 12.1 - - + -
160C GLN* 4.1 19.5 - - + +
161C PRO 3.7 19.3 - - - +
162C ALA* 4.1 7.2 - - + -
168C LYS* 2.8 31.4 + - + +
169C GLY 4.3 1.3 - - - +
171C ASN* 1.3 72.2 - - + +
173C MET* 1.3 56.3 + - - +
175C ASN* 3.2 8.7 + - + +
176C LEU* 2.9 50.3 + - + +
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Residues in contact with MET 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 4.0 31.6 - - + -
129C LEU* 4.4 6.9 - - + +
169C GLY 3.0 20.6 + - - +
170C LEU 3.8 2.0 - - - +
172C VAL* 1.3 76.6 - - - +
174C GLN* 1.3 54.0 + - - +
176C LEU* 4.4 2.7 - - + +
177C LEU* 2.7 56.3 + - + +
183C VAL* 4.6 3.8 - - + -
186C VAL* 3.7 36.6 - - + -
197C ALA* 3.8 37.0 - - + +
200C ALA* 3.8 6.5 - - + -
201C LEU* 4.5 12.1 - - + -
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Residues in contact with GLN 174 (chain C).
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* 6.3 3.1 - - + -
171B ASN* 4.8 2.0 - - - +
170C LEU* 2.9 33.0 + - - +
171C ASN* 3.3 26.2 - - - +
173C MET* 1.3 78.0 - - - +
175C ASN* 1.3 62.0 + - - +
177C LEU* 3.5 7.0 - - + +
178C THR* 3.2 31.2 + - + +
200C ALA* 3.9 15.4 + - + +
203C THR* 4.0 24.9 - - - +
204C ALA* 6.5 0.7 - - + -
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Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ASN* 3.8 23.3 + - - +
174B GLN* 4.2 26.5 + - - +
175B ASN* 3.8 23.2 + - - +
160C GLN* 4.8 10.9 + - - -
171C ASN 3.0 12.6 + - - +
172C VAL* 3.4 13.1 + - - +
174C GLN* 1.3 77.8 - - - +
176C LEU* 1.3 63.9 + - - +
178C THR* 3.3 15.1 + - - -
179C ALA* 3.3 12.0 + - - +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 3.8 37.4 - - + +
129C LEU* 4.0 9.4 - - + -
158C ALA* 3.7 23.6 - - + -
160C GLN* 3.3 33.0 - - + +
172C VAL* 2.9 37.2 + - + +
173C MET* 3.9 4.7 - - - +
175C ASN* 1.3 79.8 - - + +
177C LEU* 1.3 55.1 + - - +
179C ALA* 3.6 4.7 - - + -
180C HIS* 2.7 43.8 + - + +
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C MET* 2.7 36.0 + - + +
174C GLN* 3.5 10.1 - - + +
176C LEU* 1.3 73.4 - - - +
178C THR* 1.3 64.5 + - + +
180C HIS 3.2 3.3 - - - +
181C PRO* 3.2 30.3 - - + +
183C VAL* 4.2 16.4 - - + -
200C ALA 4.1 5.6 - - - +
201C LEU* 3.8 38.4 - - + +
204C ALA* 3.8 27.6 - - + -
206C LYS* 4.3 19.1 - - + -
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Residues in contact with THR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 4.2 14.1 - - + -
171B ASN* 2.6 36.6 + - - +
174C GLN* 3.2 19.2 + - + +
175C ASN 3.3 6.9 + - - -
176C LEU 3.4 0.2 - - - -
177C LEU* 1.3 77.3 - - + +
179C ALA* 1.3 64.1 + - - +
180C HIS 3.6 0.2 + - - -
181C PRO* 3.8 10.4 - - - +
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Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ASN* 3.3 17.4 + - - +
176C LEU* 3.8 6.7 - - + +
177C LEU 3.3 0.2 - - - -
178C THR* 1.3 82.9 + - - +
180C HIS* 1.3 78.7 + - + +
181C PRO* 3.6 5.3 - - - +
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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