Contacts of the helix formed by residues 180 - 194 (chain B) in PDB entry 4CQ8
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 ASP 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B TYR 4.3 0.6 + - - -
179B ILE* 1.4 74.8 - - - +
181B GLY* 1.3 66.8 + - - +
182B GLU* 3.2 12.7 + - - +
183B ILE* 3.1 47.2 + - + +
184B CYS* 3.1 19.2 + - - -
261B PRO* 3.9 23.2 - - - +
263B ILE 4.6 5.5 + - - +
264B PHE* 5.7 0.7 - - - -
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE 3.5 2.0 + - - -
180B ASP* 1.3 74.1 + - - +
182B GLU* 1.3 56.8 + - - +
184B CYS* 3.3 6.4 + - - +
185B HIS* 3.1 24.3 + - - +
263B ILE* 4.3 18.9 + - - -
264B PHE* 5.9 0.2 - - - -
265B ARG* 3.6 28.6 - - - +
4000B JBW 3.6 12.5 - - - +
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Residues in contact with GLU 182 (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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180B ASP* 3.2 11.0 + - - +
181B GLY* 1.3 70.3 - - - +
183B ILE* 1.4 60.8 + - + +
185B HIS* 3.4 6.1 + - + +
186B ASP* 3.0 43.4 + - - +
260B LYS* 3.8 20.4 + - + +
262B ARG* 2.8 56.1 + - - +
263B ILE* 3.7 33.5 + - + +
276B CYS* 5.2 0.7 - - - -
279B ASN* 3.8 10.0 + - - -
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.6 18.8 - - + -
180B ASP* 3.1 34.8 + - + +
182B GLU* 1.4 71.9 - - - +
184B CYS* 1.4 52.9 + - - +
186B ASP* 3.3 7.6 + - - +
187B LEU* 2.9 39.1 + - + +
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Residues in contact with CYS 184 (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 CYS* 3.5 37.2 - - - -
179B ILE* 3.7 12.6 - - - -
180B ASP 3.1 15.8 + - - -
181B GLY 3.4 8.5 - - - +
183B ILE* 1.4 73.5 - - - +
185B HIS* 1.3 59.0 + - - +
187B LEU* 3.2 9.1 + - - +
188B PHE* 2.9 25.1 + - - +
265B ARG* 3.1 27.1 - - - +
4000B JBW 3.5 25.9 - - + +
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Residues in contact with HIS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY 3.1 7.0 + - - +
182B GLU* 3.6 13.9 - - + +
183B ILE 3.3 0.2 - - - -
184B CYS* 1.3 78.4 - - - +
186B ASP* 1.4 60.5 + - - +
188B PHE* 3.2 5.4 + + - +
189B LEU* 3.0 46.8 + - + +
226B GLY 4.3 2.0 + - - -
227B PHE* 2.7 56.4 + + - -
263B ILE* 5.4 3.8 - - + -
528B TYR* 3.5 21.2 + - - -
4000B JBW 2.9 43.9 + + + +
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Residues in contact with ASP 186 (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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182B GLU* 3.0 36.9 + - - +
183B ILE* 3.9 6.4 - - - +
185B HIS* 1.4 75.2 - - - +
187B LEU* 1.3 58.9 + - - +
189B LEU* 3.5 21.3 + - - +
190B LEU* 3.0 27.9 + - - +
260B LYS* 4.9 7.3 + - - -
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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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175B CYS* 4.6 9.9 - - - -
179B ILE* 5.9 3.4 - - + -
183B ILE* 2.9 20.5 + - + +
184B CYS* 3.4 10.1 - - - +
186B ASP* 1.3 72.7 - - - +
188B PHE* 1.4 64.8 + - - +
190B LEU* 3.2 19.0 + - + +
191B LEU* 3.0 35.4 + - + +
4000B JBW 3.8 27.4 - - + -
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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 CYS 2.9 9.5 + - - +
185B HIS 3.2 8.9 + - - +
187B LEU* 1.4 74.9 - - - +
189B LEU* 1.4 64.2 + - + +
191B LEU* 3.2 12.9 + - - +
192B GLY* 3.0 24.9 + - - -
197B LEU* 3.7 21.3 - - + +
227B PHE* 3.6 33.2 - + - -
233B CYS* 5.4 0.4 - - - -
237B ILE* 4.1 18.2 - - + -
240B LEU* 3.9 16.8 - - + -
531B LEU* 5.0 3.4 - - + -
536B MET* 3.6 32.8 - - + -
4000B JBW 3.4 51.7 - + + +
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Residues in contact with LEU 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 HIS* 3.0 36.5 + - + +
186B ASP* 3.8 20.9 - - - +
187B LEU 3.3 0.2 - - - -
188B PHE* 1.4 81.9 - - + +
190B LEU* 1.3 52.3 + - - +
192B GLY* 3.3 1.2 + - - -
193B LYS* 2.8 34.6 + - - +
227B PHE* 3.8 20.0 - - + +
228B ASP* 4.3 12.1 - - - +
229B LYS 5.7 0.9 - - - +
232B VAL* 4.6 16.5 - - + +
233B CYS* 3.8 25.7 - - - -
237B ILE* 4.4 9.6 - - + -
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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 ASP 3.0 14.3 + - - +
187B LEU* 3.2 22.6 + - + +
189B LEU* 1.3 72.9 - - - +
191B LEU* 1.4 64.1 + - + +
193B LYS* 3.2 19.2 + - + +
194B TYR* 3.1 58.5 + - + +
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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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187B LEU* 3.0 27.4 + - + +
188B PHE* 3.2 14.1 + - - +
190B LEU* 1.4 76.1 - - + +
192B GLY* 1.3 60.3 + - - +
194B TYR 3.5 1.4 + - - -
195B ASN 3.3 3.8 + - - -
196B ILE* 3.0 55.5 + - + +
197B LEU* 3.7 20.6 - - + -
536B MET* 4.7 7.4 - - + -
4000B JBW 4.6 20.2 - - + -
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Residues in contact with GLY 192 (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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188B PHE 3.0 11.3 + - - -
189B LEU 3.3 4.2 + - - -
190B LEU 3.2 0.2 - - - -
191B LEU* 1.3 74.5 - - - +
193B LYS* 1.3 62.2 + - - +
195B ASN* 3.0 8.3 + - - -
197B LEU* 3.8 12.9 - - - +
233B CYS* 3.4 15.2 - - - +
236B SER* 2.7 37.8 + - - -
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Residues in contact with LYS 193 (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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189B LEU 2.8 20.1 + - - +
190B LEU* 3.2 19.3 + - + +
192B GLY* 1.3 72.7 - - - +
194B TYR* 1.3 90.8 + - + +
195B ASN* 3.4 12.5 + - - +
232B VAL* 4.3 24.9 - - + +
233B CYS* 3.6 8.0 - - - +
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Residues in contact with TYR 194 (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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190B LEU* 3.1 45.6 + - + +
191B LEU 3.5 0.2 + - - -
193B LYS* 1.3 105.0 + - + +
195B ASN* 1.4 68.7 + - - +
196B ILE* 3.4 30.5 - - + +
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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