Contacts of the helix formed by residues 176 - 191 (chain B) in PDB entry 4CRU
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 GLU 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B SER* 1.3 73.0 - - - +
177B LEU* 1.3 60.6 + - + +
179B LYS* 3.4 12.1 + - - +
180B THR* 3.0 36.1 + - - +
225B SER* 2.3 42.0 + - - +
227B ARG* 2.9 41.2 + - - -
228B LEU* 5.0 5.2 - - + -
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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
----------------------------------------------------------
137B LEU* 4.0 30.1 - - + -
175B SER* 3.2 7.9 + - - +
176B GLU* 1.3 84.0 - - + +
178B SER* 1.3 61.7 + - - +
180B THR* 3.2 6.7 + - - -
181B VAL* 3.1 27.0 + - + +
227B ARG* 3.0 39.5 - - - +
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 4.2 5.2 + - - +
136B ARG* 4.5 5.5 + - - +
137B LEU* 3.7 32.1 + - - +
140B LEU* 3.7 11.9 - - - +
170B ILE* 3.7 19.1 - - - -
174B GLY* 4.8 0.7 - - - -
175B SER* 3.1 23.6 + - - -
177B LEU* 1.3 74.6 - - - +
179B LYS* 1.3 67.6 + - - +
181B VAL 3.3 0.7 + - - -
182B ALA* 2.9 25.6 + - - +
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 3.4 21.0 - - - +
171B MET* 3.4 26.5 - - - +
172B GLU 4.0 5.8 - - - -
173B SER* 4.4 0.9 - - - +
174B GLY 3.3 27.0 + - - +
175B SER 2.8 22.8 + - - +
176B GLU* 3.6 7.9 - - - +
178B SER* 1.3 71.7 - - - +
180B THR* 1.3 56.9 + - - +
182B ALA* 3.9 0.7 - - - +
183B THR* 2.7 38.3 + - - -
216B MET* 4.7 1.6 - - + -
219B GLN* 3.3 30.5 + - - +
228B LEU* 3.9 25.3 - - + +
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Residues in contact with THR 180 (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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176B GLU* 3.0 32.7 + - - -
177B LEU* 3.6 7.9 - - - -
178B SER 3.2 0.6 - - - -
179B LYS* 1.3 77.3 - - - +
181B VAL* 1.3 65.5 + - + +
183B THR* 3.4 1.7 + - - -
184B PHE* 3.0 22.8 + - + +
227B ARG* 3.8 27.2 - - + +
228B LEU* 3.7 19.0 - - - +
231B HIS* 3.7 24.5 - - + +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 4.0 16.6 - - + +
140B LEU* 3.7 40.2 - - + +
141B GLY* 4.3 6.1 - - - +
144B GLY* 4.9 5.6 - - - -
177B LEU* 3.1 17.8 + - + +
178B SER 4.0 2.7 - - - +
180B THR* 1.3 77.6 - - + +
182B ALA* 1.3 63.4 + - - +
184B PHE* 3.2 11.0 + - + +
185B ILE* 3.0 27.3 + - + +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.4 8.2 - - + +
167B CYS* 3.8 32.4 - - + +
170B ILE* 3.9 13.5 - - + -
171B MET* 3.8 10.4 - - + +
178B SER 2.9 18.5 + - - +
179B LYS 3.9 0.4 - - - +
181B VAL* 1.3 77.3 - - - +
183B THR* 1.3 63.2 + - - +
185B ILE* 3.3 13.6 + - - +
186B LEU* 3.0 21.5 + - - +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B MET* 3.4 21.6 - - + +
179B LYS 2.7 22.0 + - - -
180B THR 3.8 3.1 - - - -
182B ALA* 1.3 76.9 - - - +
184B PHE* 1.3 57.5 + - - +
186B LEU* 3.2 1.9 + - - +
187B GLN* 2.8 28.1 + - - +
213B LEU* 5.0 0.4 - - + -
216B MET* 3.3 20.6 - - - +
228B LEU* 3.5 6.1 - - - +
231B HIS* 3.5 33.9 - - + +
232B VAL* 4.1 12.6 - - + +
235B CYS* 4.1 9.0 - - - -
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Residues in contact with PHE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY* 3.9 16.4 - - - -
147B VAL* 3.9 10.5 - - + -
148B LYS* 3.5 40.6 - - + -
180B THR* 3.0 14.1 + - + +
181B VAL* 3.2 15.2 + - + +
183B THR* 1.3 77.2 - - - +
185B ILE* 1.3 62.8 + - + +
187B GLN* 3.3 14.6 + - - +
188B LYS* 3.0 64.0 + - + +
231B HIS* 3.8 32.6 - + - +
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.8 37.9 - - + +
143B ILE* 3.7 35.4 - - + -
144B GLY* 4.1 14.8 - - - +
147B VAL* 4.4 10.3 - - + +
158B LEU* 4.6 5.6 - - + -
163B ILE* 4.8 2.0 - - + -
167B CYS* 3.9 18.6 - - - -
181B VAL* 3.0 20.1 + - + +
182B ALA* 3.6 7.2 - - - +
183B THR 3.3 0.2 - - - -
184B PHE* 1.3 78.9 - - + +
186B LEU* 1.3 63.2 + - - +
188B LYS* 3.1 4.2 + - - +
189B ILE* 3.0 37.2 + - + +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 4.4 26.2 - - + -
167B CYS* 5.1 6.0 - - + -
168B LEU* 4.2 7.6 - - + -
171B MET* 3.7 32.1 - - + -
182B ALA 3.0 13.6 + - - +
183B THR 3.6 7.4 - - - +
185B ILE* 1.3 75.9 - - - +
187B GLN* 1.3 56.3 + - - +
189B ILE* 3.2 9.0 + - + +
190B LEU* 2.8 35.2 + - + +
199B ILE* 4.0 22.9 - - + -
209B VAL* 4.1 24.9 - - + -
213B LEU* 4.9 1.3 - - + -
235B CYS* 4.3 13.7 - - - -
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B THR 2.8 17.3 + - - +
184B PHE* 3.3 19.6 - - - +
186B LEU* 1.3 72.8 - - - +
188B LYS* 1.3 60.7 + - - +
190B LEU* 3.2 4.9 + - - +
191B LEU* 2.9 48.9 + - + +
230B LYS 5.0 0.2 - - - -
231B HIS* 2.7 47.2 + - - -
234B ARG* 3.6 32.7 - - + +
235B CYS* 3.8 16.5 - - - +
275B TRP* 5.2 6.3 - - - -
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Residues in contact with LYS 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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147B VAL* 3.8 33.2 - - + +
148B LYS* 3.5 12.0 + - - +
150B ASP* 2.5 43.2 + - - +
155B ILE* 4.0 10.7 - - + +
184B PHE* 3.0 52.8 + - + +
185B ILE 3.6 7.0 - - - +
187B GLN* 1.3 80.1 - - - +
189B ILE* 1.3 63.1 + - - +
191B LEU* 3.4 25.2 + - + +
192B ASP* 3.5 9.0 + - - +
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Residues in contact with ILE 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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155B ILE* 4.0 24.0 - - + -
158B LEU* 4.3 18.4 - - + -
159B LEU* 3.7 26.5 - - + -
163B ILE* 4.3 10.3 - - + -
164B ILE* 4.1 21.1 - - + -
167B CYS* 5.7 1.3 - - - -
185B ILE* 3.0 35.1 + - + +
186B LEU* 3.6 10.1 - - + +
188B LYS* 1.3 76.4 - - + +
190B LEU* 1.3 62.5 + - - +
192B ASP* 3.2 10.6 + - - +
195B GLY* 3.2 27.5 - - - -
199B ILE* 4.1 14.4 - - + -
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Residues in contact with LEU 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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186B LEU* 2.8 29.1 + - + +
187B GLN* 3.2 4.7 + - - +
189B ILE* 1.3 79.4 - - - +
191B LEU* 1.3 59.4 + - - +
192B ASP 3.2 7.4 - - - +
195B GLY 4.5 0.2 - - - -
196B LEU* 3.4 21.4 - - + +
199B ILE* 3.4 32.5 - - + -
209B VAL* 5.3 1.3 - - + -
235B CYS* 3.8 44.0 - - + +
238B ARG* 2.8 30.7 + - + +
239B LEU* 3.7 29.2 - - + -
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Residues in contact with LEU 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 ASP* 5.4 3.1 - - - +
187B GLN* 2.9 44.6 + - + +
188B LYS* 3.8 20.6 - - + +
189B ILE 3.3 0.4 - - - -
190B LEU* 1.3 76.4 - - - +
192B ASP* 1.3 57.3 + - - +
193B ASP* 3.6 1.7 + - - +
234B ARG* 3.3 43.7 - - + +
238B ARG* 3.1 31.6 + - + +
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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