Contacts of the helix formed by residues 166 - 179 (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 ARG 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B ASP* 1.3 72.8 + - - +
167B ILE* 1.3 67.9 + - + +
169B GLY 3.3 0.2 + - - -
170B LEU* 2.9 26.4 + - + +
192B GLU* 3.2 65.7 + - - +
195B LEU* 3.9 25.2 - - - +
196B GLY* 3.4 20.4 - - - +
199B ARG* 6.3 1.6 - - - -
219B ASP* 3.3 23.8 + - - -
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Residues in contact with ILE 167 (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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165B ASP* 2.9 11.7 + - - +
166B ARG* 1.3 84.0 - - + +
168B LYS* 1.3 59.4 + - + +
170B LEU* 3.2 19.7 + - + +
171B ASN* 3.0 44.1 + - - +
178C THR* 4.2 13.0 - - + -
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Residues in contact with LYS 168 (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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162B ALA* 3.4 22.2 - - - +
163B ASP* 2.8 36.8 + - + +
165B ASP* 2.7 26.3 + - + +
167B ILE* 1.3 71.2 - - + +
169B GLY* 1.3 57.3 + - - +
171B ASN* 4.4 6.5 - - - +
172B VAL* 2.7 43.8 + - + +
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Residues in contact with GLY 169 (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* 3.9 9.0 - - - +
162B ALA* 3.6 14.5 - - - +
165B ASP 2.9 18.6 + - - -
166B ARG 3.6 1.6 - - - -
168B LYS* 1.3 78.8 - - - +
170B LEU* 1.3 60.8 + - - +
173B MET* 3.1 27.0 + - - +
193B MET* 4.2 12.8 - - - -
196B GLY 4.0 6.3 - - - -
197B ALA 3.9 1.2 + - - -
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Residues in contact with LEU 170 (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* 2.9 13.9 + - + +
167B ILE* 3.3 24.5 - - + +
169B GLY* 1.3 77.5 - - - +
171B ASN* 1.3 67.9 + - - +
174B GLN* 2.9 43.6 + - - +
196B GLY* 3.4 14.7 - - - +
199B ARG* 4.0 20.2 - - + -
200B ALA* 3.4 39.9 - - + +
203B THR* 5.6 0.4 - - - +
174C GLN* 6.3 3.1 - - + -
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Residues in contact with ASN 171 (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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167B ILE* 3.0 24.1 + - - +
168B LYS* 4.0 5.5 - - - +
170B LEU* 1.3 83.1 - - - +
172B VAL* 1.3 64.3 + - + +
174B GLN* 3.2 19.9 + - - +
175B ASN* 3.0 30.5 + - - +
174C GLN* 4.6 0.9 - - - +
175C ASN* 3.8 23.1 + - - +
178C THR* 2.6 45.1 + - - +
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Residues in contact with VAL 172 (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* 3.9 10.5 - - + -
160B GLN* 4.1 19.3 - - + +
161B PRO 3.7 20.2 - - - +
162B ALA* 4.1 9.6 - - + -
168B LYS* 2.7 30.0 + - + +
169B GLY 4.4 0.9 - - - +
171B ASN* 1.3 72.3 - - + +
173B MET* 1.3 57.2 + - - +
175B ASN* 3.2 13.0 + - - +
176B LEU* 2.9 50.5 + - + +
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Residues in contact with MET 173 (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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127B ILE* 3.9 31.6 - - + -
129B LEU* 4.4 7.5 - - + +
169B GLY 3.1 20.3 + - - +
170B LEU 3.8 2.7 - - - +
172B VAL* 1.3 76.8 - - - +
174B GLN* 1.3 54.3 + - - +
176B LEU* 3.2 2.9 + - + +
177B LEU* 2.7 56.5 + - + +
183B VAL* 4.6 4.3 - - + -
186B VAL* 3.7 37.0 - - + -
197B ALA* 3.7 31.9 - - + +
200B ALA* 3.8 9.2 - - + -
201B LEU* 4.4 11.4 - - + -
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Residues in contact with GLN 174 (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* 2.9 35.8 + - - +
171B ASN* 3.3 23.3 - - - +
173B MET* 1.3 77.3 - - - +
175B ASN* 1.3 61.8 + - - +
177B LEU* 3.5 6.7 + - + +
178B THR* 3.2 29.6 + - + +
200B ALA* 3.9 14.4 + - + +
203B THR* 4.0 25.5 + - - +
171C ASN* 4.9 11.2 - - - +
175C ASN* 4.2 23.0 + - - +
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Residues in contact with ASN 175 (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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171B ASN* 3.0 22.7 + - - +
172B VAL* 3.6 15.4 - - - +
174B GLN* 1.3 76.2 - - - +
176B LEU* 1.3 68.5 + - + +
178B THR* 3.2 9.5 + - - -
179B ALA* 3.1 22.8 + - - +
175C ASN* 3.8 22.5 + - - +
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Residues in contact with LEU 176 (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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127B ILE* 3.8 38.1 - - + -
129B LEU* 4.0 8.3 - - + -
158B ALA* 3.7 23.8 - - + -
160B GLN* 3.3 34.1 - - + +
172B VAL* 2.9 36.3 + - + +
173B MET* 3.9 4.3 - - + +
175B ASN* 1.3 81.3 - - + +
177B LEU* 1.3 53.0 + - - +
179B ALA* 3.3 5.4 + - + +
180B HIS* 2.7 44.3 + - + +
153D LYS* 5.6 4.9 - - + -
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Residues in contact with LEU 177 (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* 2.7 36.1 + - + +
174B GLN* 3.5 8.5 - - + +
176B LEU* 1.3 74.0 - - - +
178B THR* 1.3 63.4 + - + +
180B HIS 3.3 3.4 - - - +
181B PRO* 3.2 29.2 - - + +
183B VAL* 4.2 17.0 - - + -
200B ALA* 4.1 6.3 - - + +
201B LEU* 3.8 39.5 - - + +
204B ALA* 3.8 28.0 - - + -
206B LYS* 4.4 18.6 - - + -
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Residues in contact with THR 178 (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* 3.2 19.9 + - + +
175B ASN* 3.2 10.0 + - - -
177B LEU* 1.3 78.5 - - + +
179B ALA* 1.3 64.3 + - - +
180B HIS 3.6 0.2 + - - -
181B PRO* 3.8 10.0 - - - +
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Residues in contact with ALA 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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175B ASN 3.1 14.1 + - - +
176B LEU* 3.8 6.5 - - + +
178B THR* 1.3 83.2 + - - +
180B HIS* 1.3 79.9 + - + +
181B PRO* 3.7 5.4 - - - +
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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