Contacts of the helix formed by residues 211 - 221 (chain A) in PDB entry 5Z66
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 PHE 211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 3.1 5.0 + - + -
160A TRP* 3.8 24.5 - + + -
163A TYR* 3.5 46.0 - + + -
164A PHE* 3.7 19.5 - + - -
209A PRO* 3.0 27.1 + - + +
210A PRO* 1.3 72.8 - - - +
212A PHE* 1.3 58.7 + - - +
213A SER 3.3 2.5 - - - -
214A MET* 2.9 35.6 + - - -
215A MET* 2.8 33.8 + - + +
340A LEU* 3.7 28.0 - - + -
407A PHE* 4.4 12.1 - + - -
410A TYR* 4.1 10.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 2.9 18.3 + - - +
182A VAL* 4.0 16.4 - - + -
185A PHE* 3.7 32.3 - - + -
186A ALA* 4.0 10.3 - - + -
189A ILE* 3.7 22.4 - - + -
195A ILE* 3.6 10.5 - - + -
210A PRO 3.4 1.2 - - - -
211A PHE* 1.3 76.2 - - - +
213A SER* 1.3 64.8 + - - +
215A MET* 3.0 18.1 + - + +
216A VAL* 2.9 40.1 + - + +
230A TYR* 4.4 6.3 - - + -
233A GLN* 4.0 10.3 - - + -
234A MET* 3.8 35.9 - - + -
237A GLU* 3.5 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PRO 5.0 2.4 + - - -
211A PHE 3.3 0.6 - - - -
212A PHE* 1.3 77.6 - - - +
214A MET* 1.3 59.5 + - - +
216A VAL* 3.2 4.4 + - - +
217A GLU 2.9 21.8 + - - -
227A LEU* 4.6 2.4 - - - +
234A MET* 3.5 38.4 - - - +
237A GLU* 4.7 3.2 + - - -
344A MET* 3.5 32.8 - - - +
347A LEU* 3.4 26.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
163A TYR* 3.5 30.6 + - + +
210A PRO 5.4 1.6 - - - +
211A PHE* 2.9 34.1 + - + +
213A SER* 1.3 75.6 - - - +
215A MET* 1.3 60.3 + - - +
217A GLU* 3.6 8.6 - - - +
218A LEU* 3.0 22.9 + - - +
340A LEU* 4.0 15.9 - - - -
343A LYS* 3.8 40.8 - - + -
347A LEU* 3.9 7.0 - - + -
410A TYR* 3.5 34.8 - - + +
411A VAL* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 3.3 42.6 - - + +
162A SER* 3.9 0.9 - - - -
163A TYR* 3.6 32.9 - - + +
166A MET* 3.6 23.9 - - - +
178A ILE* 5.3 0.3 - - - +
182A VAL* 4.4 11.4 - - + +
185A PHE* 3.5 37.9 - - + -
211A PHE* 2.8 14.0 + - + +
212A PHE* 3.0 22.2 + - + +
214A MET* 1.3 77.5 - - - +
216A VAL* 1.3 57.1 + - - +
218A LEU* 3.2 6.0 + - - +
219A LEU* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.3 8.5 - - + -
212A PHE* 2.9 49.8 + - + +
213A SER 3.2 6.9 + - - +
215A MET* 1.3 72.7 - - - +
217A GLU* 1.3 60.8 + - - +
219A LEU* 3.2 7.9 + - - +
220A ALA* 2.8 27.2 + - - +
226A ALA* 3.3 28.6 - - + +
227A LEU* 3.7 19.7 - - + -
230A TYR* 3.9 17.0 - - + -
234A MET* 4.1 8.1 - - - -
----------------------------------------------------------
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 SER 2.9 16.0 + - - +
214A MET* 3.6 12.6 - - - +
216A VAL* 1.3 76.5 - - - +
218A LEU* 1.3 62.7 + - - +
220A ALA* 3.2 16.4 + - - +
221A THR* 3.4 15.7 + - + +
227A LEU* 4.2 9.3 - - + +
343A LYS* 3.7 5.7 - - - -
347A LEU* 3.5 30.8 - - + +
350A ARG* 3.0 23.3 + - - +
603A SO4 2.6 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 4.5 11.4 - - + +
166A MET* 3.7 46.4 - - + +
167A LEU* 4.1 20.0 - - + +
170A ALA* 4.2 9.2 - - + -
175A TRP* 3.7 21.3 - - + -
178A ILE* 4.8 4.5 - - + -
214A MET 3.0 15.0 + - - +
215A MET* 3.2 7.6 + - - +
217A GLU* 1.3 77.7 - - - +
219A LEU* 1.3 59.6 + - - +
221A THR* 2.7 36.0 + - + +
527A LYS* 6.2 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
175A TRP* 4.1 24.5 - - + +
178A ILE* 4.1 12.3 - - + +
179A SER* 4.2 21.3 - - - +
182A VAL* 4.1 22.9 - - + -
215A MET 2.9 13.3 + - - +
216A VAL* 3.2 9.4 + - - +
218A LEU* 1.3 76.9 - - - +
220A ALA* 1.3 50.7 + - - +
222A HIS* 2.9 6.6 + - - +
223A ASP* 2.8 53.1 + - - +
226A ALA* 3.9 17.5 - - + -
230A TYR* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL 2.8 12.8 + - - +
217A GLU* 3.4 14.1 - - + +
218A LEU 3.2 0.8 - - - -
219A LEU* 1.3 72.5 - - - +
221A THR* 1.3 64.6 + - - +
222A HIS 3.0 2.1 + - - -
223A ASP 3.2 13.2 - - - +
224A SER* 3.4 26.0 - - - +
226A ALA* 3.8 8.5 - - + +
227A LEU* 4.2 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TRP* 3.6 13.0 - - - -
217A GLU* 3.5 17.5 - - + +
218A LEU* 2.7 26.8 + - + +
220A ALA* 1.3 76.6 - - - +
222A HIS* 1.3 56.6 + - - +
----------------------------------------------------------
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