Contacts of the helix formed by residues 173 - 191 (chain B) in PDB entry 3URZ
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 THR 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASP* 3.2 31.4 - - + +
166B TYR* 4.9 0.6 - - - -
171B SER* 3.7 12.6 + - - -
172B PRO* 1.3 74.0 - - - +
174B LYS* 1.3 57.4 + - - +
175B MSE 3.2 12.8 - - + +
176B GLN* 3.0 49.7 + - - +
177B TYR* 3.4 4.5 + - - +
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Residues in contact with LYS 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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178A ALA* 3.6 18.9 - - + +
181A ARG* 3.4 49.7 + - + +
182A ASP* 3.2 24.4 + - - +
185A SER* 4.0 15.4 + - - -
225A VAL 4.9 8.9 + - - -
166B TYR* 5.7 0.2 - - - -
172B PRO 3.6 3.2 + - - +
173B THR* 1.3 70.5 - - - +
175B MSE 1.3 61.3 + - - +
176B GLN 3.3 0.4 - - - -
177B TYR* 3.6 20.5 - - + +
178B ALA 3.3 15.9 + - - -
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Residues in contact with MSE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A MSE 3.3 41.0 - - + +
178A ALA* 4.3 3.1 - - - -
179A ARG* 3.6 40.2 - - + -
182A ASP* 2.8 17.8 + - + +
173B THR* 3.9 11.7 - - + -
174B LYS* 1.3 73.6 - - - +
176B GLN* 1.3 63.0 + - + +
178B ALA* 3.5 6.1 + - - +
179B ARG* 3.4 29.9 + - - +
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 4.2 11.9 - - + -
170B SER* 4.6 21.4 + - - -
172B PRO* 4.8 6.1 - - + +
173B THR* 3.0 38.2 + - - +
175B MSE 1.3 77.4 - - + +
177B TYR* 1.3 57.7 + - - +
179B ARG* 3.3 23.0 + - - +
180B TYR* 2.9 26.2 + - - +
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 3.3 38.5 - + - +
173B THR 3.4 3.0 + - - -
174B LYS* 3.6 25.4 - - + +
175B MSE 3.3 0.4 - - - -
176B GLN* 1.3 76.8 - - - +
178B ALA* 1.3 59.6 - - - +
180B TYR* 3.3 25.7 + + - +
181B ARG* 3.0 58.9 + - + +
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Residues in contact with ALA 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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174A LYS* 4.7 5.4 - - + +
175A MSE 3.8 29.2 - - + +
178A ALA* 4.0 13.7 - - + -
174B LYS 3.3 12.2 + - - +
175B MSE 3.6 10.1 - - - +
176B GLN 3.3 0.2 - - - -
177B TYR* 1.3 76.3 - - - +
179B ARG* 1.3 54.7 + - - +
181B ARG* 3.5 4.6 + - - +
182B ASP* 2.8 36.8 + - - +
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A MSE 4.3 23.3 - - + +
162B LEU* 4.8 3.3 - - - +
175B MSE 3.4 15.8 + - - +
176B GLN* 3.3 34.7 + - - +
178B ALA* 1.3 75.5 - - - +
180B TYR* 1.3 60.5 + - - +
182B ASP* 4.1 5.7 - - - +
183B GLY* 3.1 23.4 + - - -
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.8 28.0 - - + +
163B GLU* 3.5 44.0 + - + +
166B TYR* 3.9 29.8 - + + -
176B GLN 2.9 13.4 + - - +
177B TYR* 3.5 35.9 - + - +
178B ALA 3.2 0.2 - - - -
179B ARG* 1.3 76.1 - - - +
181B ARG* 1.3 71.9 + - + +
183B GLY* 3.3 3.8 + - - -
184B LEU* 3.2 48.8 + - + +
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 5.4 17.0 - - - +
177B TYR* 3.0 51.5 + - + +
178B ALA* 4.1 4.5 - - - +
180B TYR* 1.3 81.4 - - + +
182B ASP* 1.3 65.1 + - - +
184B LEU* 3.4 22.9 + - - +
185B SER* 3.2 22.3 + - - -
224B GLU 3.8 18.1 + - - -
225B VAL* 4.2 13.5 + - - +
226B ASN* 3.8 27.7 + - - +
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Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 6.1 4.2 - - - +
178B ALA 2.8 23.5 + - - +
179B ARG* 4.1 7.2 - - + +
181B ARG* 1.3 72.9 - - - +
183B GLY* 1.3 56.7 + - - +
185B SER* 3.5 6.7 + - - -
186B LYS* 3.0 39.4 + - + +
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Residues in contact with GLY 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.5 17.7 - - - +
179B ARG 3.1 16.2 + - - -
180B TYR 3.3 4.9 + - - -
182B ASP* 1.3 75.0 - - - +
184B LEU* 1.3 57.6 + - - +
186B LYS* 3.7 5.4 + - - +
187B LEU* 3.0 31.0 + - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LYS* 3.8 35.9 - - + +
162B LEU* 3.4 20.2 - - + +
163B GLU* 4.7 3.4 - - - +
180B TYR* 3.2 41.8 + - + +
181B ARG* 3.7 28.5 - - - +
182B ASP 3.4 0.4 - - - -
183B GLY* 1.3 72.6 - - - +
185B SER* 1.3 60.6 + - - +
187B LEU* 3.6 9.3 + - + +
188B PHE* 3.0 28.1 + - - +
192B TYR* 5.5 0.3 - - - -
225B VAL* 3.5 27.1 - - + +
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 6.1 3.1 - - - -
181B ARG 3.2 16.0 + - - -
182B ASP* 3.7 8.7 - - - -
183B GLY 3.3 0.2 - - - -
184B LEU* 1.3 74.5 - - - +
186B LYS* 1.3 65.5 + - - +
188B PHE* 3.1 13.5 + - - +
189B THR* 3.1 21.8 + - - +
225B VAL* 3.5 17.2 - - - +
226B ASN 5.4 3.6 + - - -
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASP* 3.0 24.8 + - + +
183B GLY* 4.1 5.2 - - - +
185B SER* 1.3 76.3 - - - +
187B LEU* 1.3 56.7 + - - +
189B THR* 3.4 7.7 + - - -
190B THR* 2.7 39.9 + - - +
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Residues in contact with LEU 187 (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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155B ALA* 3.4 16.4 - - + +
158B GLU* 3.2 40.8 - - + +
159B LYS* 4.7 10.1 - - + +
162B LEU* 5.3 4.0 - - + -
183B GLY 3.0 21.5 + - - +
184B LEU* 3.9 7.9 - - + +
185B SER 3.3 0.2 - - - -
186B LYS* 1.3 76.5 - - - +
188B PHE* 1.3 57.8 + - - +
190B THR* 4.4 3.8 - - + -
191B ARG* 3.0 41.3 + - + -
192B TYR* 3.4 34.3 + - + -
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Residues in contact with PHE 188 (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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184B LEU 3.0 18.6 + - - +
185B SER* 3.1 8.5 + - - +
187B LEU* 1.3 77.1 - - - +
189B THR* 1.3 66.0 + - + +
192B TYR* 3.1 37.4 + + + -
193B GLU* 2.8 37.2 + - + -
196B ARG* 3.4 31.2 - - - -
218B ILE* 3.6 20.0 - - + -
221B ILE* 4.1 10.8 - - + -
222B GLU* 3.5 42.6 - - + -
225B VAL* 4.8 7.2 - - + -
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Residues in contact with THR 189 (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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185B SER* 3.1 16.0 + - - +
186B LYS* 3.4 12.8 + - - -
188B PHE* 1.3 84.2 - - + +
190B THR* 1.3 63.0 + - - +
193B GLU* 3.7 19.2 - - + +
194B LYS* 5.0 4.0 + - - +
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Residues in contact with THR 190 (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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151B TYR* 5.1 0.2 - - - -
186B LYS* 2.7 26.3 + - - +
187B LEU* 4.1 5.2 - - + -
189B THR* 1.3 79.7 + - - +
191B ARG* 1.3 75.1 + - + +
194B LYS* 3.2 38.9 - - - +
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Residues in contact with ARG 191 (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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150B TYR* 3.9 18.2 + - - -
151B TYR* 3.5 30.0 - - + +
154B THR* 3.0 39.6 + - - +
155B ALA* 3.6 24.0 - - + +
158B GLU* 3.8 22.8 + - - +
187B LEU* 3.0 20.3 + - + +
190B THR* 1.3 95.4 - - + +
192B TYR* 1.3 64.8 + - - +
193B GLU 3.3 1.6 - - - -
194B LYS 3.4 1.3 + - - -
195B ALA* 3.0 23.9 + - - +
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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
------------------------------------------------------------
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