Contacts of the helix formed by residues 209 - 219 (chain A) in PDB entry 2O2C
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 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASN* 4.5 4.6 + - - +
204A GLY 3.3 18.5 - - - +
205A ILE* 3.8 8.2 - - - +
206A GLY 3.0 7.2 + - - +
207A GLY 3.3 2.0 + - - -
208A SER* 1.3 78.0 - - - +
210A LEU* 1.3 76.5 + - - +
211A GLY 3.3 1.7 + - - -
212A PRO* 3.3 6.5 - - - +
213A VAL* 3.0 48.9 + - - +
231A PHE* 3.9 14.2 - - - +
232A VAL 5.0 0.5 - - - +
233A SER* 3.7 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY* 2.9 23.6 + - - +
207A GLY* 5.6 0.4 - - - -
209A ASP* 1.3 85.7 - - - +
211A GLY* 1.3 56.1 + - - +
213A VAL* 3.8 7.7 - - + +
214A MET* 2.9 32.2 + - - +
400A ARG* 4.6 12.4 - - + +
403A ALA* 3.7 39.9 - - + +
404A TYR* 3.7 16.4 - - + +
407A GLN* 3.2 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY 4.7 0.6 + - - -
207A GLY* 4.8 5.1 + - - -
209A ASP 4.7 0.2 - - - +
210A LEU* 1.3 76.2 - - - +
212A PRO* 1.4 65.5 - - - +
214A MET* 3.3 2.1 + - - +
215A ALA* 2.9 34.1 + - - +
329A MET* 4.1 13.0 - - - -
337A ILE* 4.5 5.4 - - - -
404A TYR* 3.4 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASN* 4.6 4.3 - - - +
207A GLY 4.6 1.3 - - - +
208A SER 4.6 7.2 - - - +
209A ASP 3.3 17.3 - - - +
211A GLY* 1.4 86.9 - - - +
213A VAL* 1.3 53.8 + - - +
216A THR* 2.7 39.4 + - - +
231A PHE* 3.7 18.4 - - + -
329A MET* 4.9 3.1 - - + -
333A ILE* 3.6 40.6 - - + +
336A PRO* 3.9 15.3 - - + -
337A ILE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 3.0 41.9 + - - +
210A LEU* 3.8 9.2 - - + +
212A PRO* 1.3 75.3 - - - +
214A MET* 1.3 65.3 + - - +
216A THR* 3.2 6.5 + - - -
217A GLU* 3.1 33.2 + - + +
231A PHE* 3.6 29.6 - - + -
399A TRP* 5.9 0.4 - - + -
400A ARG* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU 2.9 21.7 + - - +
211A GLY 4.1 2.7 - - - +
213A VAL* 1.3 74.6 - - - +
215A ALA* 1.3 64.0 + - + +
217A GLU* 3.5 2.3 + - - +
218A ALA* 2.9 32.1 + - - +
329A MET* 3.8 28.9 - - + -
397A TYR 4.5 1.0 - - - +
398A LEU* 4.9 2.6 - - + -
400A ARG* 3.8 33.8 - - + +
401A LEU* 3.9 22.7 - - + +
404A TYR* 4.0 16.6 - - + -
539A LEU* 3.9 24.2 - - + -
543A ILE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLY 2.9 21.0 + - - +
214A MET* 1.3 78.6 - - + +
216A THR* 1.3 58.7 + - - +
219A LEU* 3.0 35.8 + - + +
329A MET* 4.1 11.9 - - + -
337A ILE* 3.7 30.9 - - + +
349A LEU* 5.0 0.2 - - + -
539A LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PRO 2.7 23.4 + - - +
213A VAL 3.2 6.6 + - - -
215A ALA* 1.3 75.1 - - - +
217A GLU* 1.3 65.7 + - - +
219A LEU* 3.9 2.2 - - - -
220A LYS* 3.4 25.5 + - - +
223A SER* 5.6 0.3 - - - -
229A LEU* 4.4 8.0 - - + +
231A PHE* 3.4 25.0 - - + -
336A PRO 4.0 9.6 - - - +
337A ILE* 3.9 29.2 - - + +
340A SER* 4.1 20.0 + - - -
341A ILE* 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 3.1 27.2 + - + +
214A MET* 3.7 5.2 - - - +
216A THR* 1.3 81.1 + - - +
218A ALA* 1.3 61.9 + - - +
219A LEU 3.4 0.5 + - - -
220A LYS* 3.5 35.6 + - - +
231A PHE* 5.5 4.8 - - + -
397A TYR* 3.3 35.9 - - - +
399A TRP* 2.8 41.1 + - + +
400A ARG* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 2.9 20.2 + - - +
215A ALA 3.4 4.0 + - - +
217A GLU* 1.3 77.0 - - - +
219A LEU* 1.3 63.3 + - + +
220A LYS 3.8 1.0 + - - -
221A PRO* 4.3 3.5 - - - +
397A TYR* 3.2 26.8 + - - +
398A LEU* 3.8 27.6 - - + -
534A LEU* 3.8 13.0 - - + +
539A LEU* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ALA* 3.0 18.4 + - + +
216A THR 3.9 3.6 - - - -
217A GLU 3.3 0.2 - - - -
218A ALA* 1.3 84.1 - - + +
220A LYS* 1.3 62.7 + - - +
221A PRO* 3.3 6.3 - - - -
222A PHE* 3.0 23.4 + - + +
223A SER 3.6 5.9 + - - -
341A ILE* 3.6 39.6 - - + +
349A LEU* 4.4 10.3 - - + -
534A LEU* 4.3 6.7 - - + +
535A THR 3.8 8.3 - - - +
536A PRO* 3.7 40.2 - - + -
539A LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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