Contacts of the helix formed by residues 215 - 234 (chain F) in PDB entry 2B05
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 SER 215 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168F THR 4.7 1.0 + - - -
169F HIS* 5.5 0.3 - - - -
170F PRO* 3.9 24.4 - - - +
211F LEU* 4.4 3.5 - - - +
212F ASN* 2.8 28.5 + - - +
214F ASP* 1.3 75.0 - - - +
216F TYR* 1.3 66.4 + - - +
217F LYS 3.0 4.8 + - - -
218F ASP* 3.1 8.9 + - - +
219F SER* 3.0 31.2 + - - -
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Residues in contact with TYR 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F LEU* 3.9 33.7 - - + -
212F ASN 2.9 11.0 + - - +
213F GLU* 3.5 36.1 - - + -
214F ASP 5.3 0.2 - - - -
215F SER* 1.3 77.9 + - - +
217F LYS* 1.3 82.7 + - + +
219F SER* 3.7 0.2 - - - -
220F THR* 2.8 49.2 + - + +
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Residues in contact with LYS 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F ASP 5.4 1.8 - - - +
215F SER* 3.0 1.4 + - - -
216F TYR* 1.3 106.9 - - + +
218F ASP* 1.3 69.8 + - - +
220F THR* 3.2 16.1 + - - +
221F LEU* 3.2 15.1 + - - +
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Residues in contact with ASP 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F PRO* 3.9 22.7 - - + +
214F ASP 5.3 3.5 - - - +
215F SER* 3.1 8.5 + - - +
217F LYS* 1.3 82.0 - - - +
219F SER* 1.3 62.4 + - - +
221F LEU* 3.5 5.1 + - - +
222F ILE* 3.2 33.1 + - + +
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Residues in contact with SER 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F THR 2.8 26.9 + - - -
170F PRO* 3.2 17.8 - - - +
173F LEU* 3.7 14.7 - - - +
211F LEU* 3.6 18.2 - - - -
215F SER* 3.0 20.4 + - - -
216F TYR 3.7 0.2 - - - -
218F ASP* 1.3 74.5 - - - +
220F THR* 1.3 64.3 + - - +
222F ILE* 3.3 2.8 + - - +
223F MET* 3.2 28.1 + - - +
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Residues in contact with THR 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F LEU* 5.7 1.6 - - + -
211F LEU* 4.1 20.4 - - + -
216F TYR* 2.8 39.2 + - + +
217F LYS* 3.2 11.1 + - - +
219F SER* 1.3 70.5 - - - +
221F LEU* 1.3 67.0 + - - +
223F MET* 3.3 17.1 + - + +
224F GLN* 3.2 26.3 + - - +
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Residues in contact with LEU 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F LYS 3.2 15.1 + - - +
218F ASP* 3.7 7.2 - - - +
220F THR* 1.3 81.7 + - - +
222F ILE* 1.3 61.8 + - + +
224F GLN* 3.5 20.5 - - - +
225F LEU* 3.4 27.0 + - + +
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Residues in contact with ILE 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F PRO* 3.3 36.6 - - + +
173F LEU* 3.6 33.0 - - + +
174F GLY* 3.8 7.0 - - - +
177F LEU* 4.2 15.3 - - + -
218F ASP* 3.2 20.3 + - + +
219F SER* 3.8 5.6 - - - +
220F THR 3.3 0.6 - - - -
221F LEU* 1.3 74.9 - - + +
223F MET* 1.3 60.2 + - - +
225F LEU* 3.1 10.1 + - + +
226F LEU* 2.9 29.9 + - + +
506L LEU* 3.8 24.9 - - + -
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Residues in contact with MET 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F THR* 5.8 0.2 - - - -
173F LEU* 4.3 15.9 - - + -
201F PHE* 3.2 33.0 - - + -
204F ALA* 4.2 17.9 - - + -
205F ILE* 3.7 32.1 - - + -
208F LEU* 3.9 31.6 - - + -
211F LEU* 5.7 0.4 - - - -
219F SER* 3.2 20.5 + - - +
220F THR* 3.3 20.4 + - + +
222F ILE* 1.3 72.4 - - - +
224F GLN* 1.3 63.2 + - - +
226F LEU* 3.5 8.4 + - + -
227F ARG* 3.2 16.3 + - - +
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Residues in contact with GLN 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F PHE* 5.4 0.4 - - - -
220F THR 3.2 10.9 + - - +
221F LEU* 3.5 24.0 + - - +
223F MET* 1.3 78.1 - - - +
225F LEU* 1.3 53.9 + - + +
227F ARG* 3.1 7.3 + - - +
228F ASP* 2.7 47.4 + - - +
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Residues in contact with LEU 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F LEU* 3.7 24.5 - - + -
221F LEU* 3.4 17.7 + - + +
222F ILE* 3.1 11.9 + - + +
224F GLN* 1.3 77.9 - - + +
226F LEU* 1.3 60.7 + - - +
228F ASP* 3.6 14.7 - - - +
229F ASN* 3.0 34.7 + - - -
504L ILE* 4.0 30.0 - - + +
505L SEP 4.5 4.3 - - - +
506L LEU* 5.3 1.1 - - + -
507L PRO* 3.7 34.3 - - + -
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Residues in contact with LEU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F LEU* 4.1 27.8 - - + +
176F ALA* 4.2 4.3 - - + -
177F LEU* 3.6 37.7 - - + +
180F SER* 4.7 0.7 - - - +
197F ALA* 4.0 32.2 - - + +
200F ALA* 4.4 3.4 - - + -
201F PHE* 4.3 24.2 - - + +
222F ILE* 2.9 23.2 + - + +
223F MET* 3.6 13.5 - - + +
225F LEU* 1.3 77.8 - - - +
227F ARG* 1.3 57.5 + - - +
229F ASN* 3.5 4.6 + - - +
230F LEU* 3.0 33.0 + - - +
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Residues in contact with ARG 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F PHE* 4.1 17.4 - - + -
223F MET 3.2 10.4 + - - +
224F GLN* 3.1 11.3 + - - +
226F LEU* 1.3 78.8 - - - +
228F ASP* 1.3 60.3 - - - +
230F LEU* 3.2 12.2 + - + +
231F THR* 2.9 36.5 + - - +
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Residues in contact with ASP 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F GLN* 2.7 32.8 + - - +
225F LEU* 3.6 19.0 - - - +
227F ARG* 1.3 73.8 - - - +
229F ASN* 1.3 63.1 + - - +
231F THR* 3.4 7.2 + - - -
232F LEU* 3.1 22.3 + - - +
504L ILE* 4.9 8.5 - - + -
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Residues in contact with ASN 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F LEU* 3.4 21.0 - - - +
180F SER* 5.1 0.4 + - - -
181F VAL* 4.0 10.5 - - - +
225F LEU 3.0 12.4 + - - +
226F LEU* 3.7 4.9 - - - +
228F ASP* 1.3 75.5 - - - +
230F LEU* 1.3 57.0 + - - +
232F LEU* 3.3 6.1 + - - +
233F TRP* 2.9 64.5 + - + +
502L ARG 4.8 0.7 - - - +
503L ALA* 3.5 5.0 - - - -
504L ILE* 2.9 51.9 + - - +
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Residues in contact with LEU 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F CYS* 3.9 34.5 - - + +
197F ALA* 3.8 14.4 - - + +
198F LYS* 3.8 37.5 - - + +
201F PHE* 4.9 7.4 - - + -
226F LEU 3.0 24.8 + - - +
227F ARG* 3.2 10.1 + - - +
229F ASN* 1.3 74.7 - - - +
231F THR* 1.3 61.9 + - - +
233F TRP* 3.4 5.8 + - + -
234F THR* 2.9 38.7 + - + +
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Residues in contact with THR 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F ARG* 2.9 20.1 + - - +
228F ASP* 3.5 9.2 + - - -
229F ASN 3.3 0.2 - - - -
230F LEU* 1.3 74.4 - - - +
232F LEU* 1.3 62.5 + - - +
234F THR* 3.2 25.1 + - - -
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Residues in contact with LEU 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F TYR* 5.1 1.9 + - + +
228F ASP 3.1 10.7 + - - +
229F ASN* 3.3 9.8 + - - +
231F THR* 1.3 82.2 - - - +
233F TRP* 1.3 70.4 + - + +
234F THR 3.3 4.7 + - - -
502L ARG* 3.5 46.4 - - + +
503L ALA* 4.0 6.1 - - - +
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Residues in contact with TRP 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F SER* 3.7 32.1 - - - -
181F VAL* 4.0 4.3 - - - -
184F TYR* 3.3 63.5 + + + -
190F PRO* 5.9 1.6 - - + +
193F ALA* 4.0 26.0 - - + -
194F CYS* 3.9 32.4 - - - -
197F ALA* 4.2 7.2 - - + -
229F ASN* 2.9 47.4 + - + +
230F LEU* 4.1 4.0 - - - +
231F THR 3.4 0.4 - - - -
232F LEU* 1.3 86.9 - - + +
234F THR* 1.3 60.2 + - - +
503L ALA* 3.6 31.0 - - + +
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Residues in contact with THR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F CYS* 4.4 15.7 - - - -
230F LEU* 2.9 27.0 + - + +
231F THR* 3.2 19.0 + - - -
232F LEU 3.2 4.2 - - - -
233F TRP* 1.3 82.7 - - - +
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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