Contacts of the helix formed by residues 222 - 227 (chain A) in PDB entry 2A79
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 ARG 222 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.9 5.8 - - - -
218A HIS 3.6 6.7 - - - +
219A MET 3.4 13.7 - - - +
220A PHE 4.2 0.2 - - - -
221A GLN* 1.3 79.9 + - - +
223A GLU* 1.3 69.5 + - - +
224A LYS 3.4 2.0 + - - -
225A VAL* 3.5 2.7 + - - -
226A GLU* 2.9 64.2 + - - +
310A TRP* 3.4 17.1 - - + -
313A ARG* 3.6 12.3 - - - +
352A ASP* 2.7 30.9 + - - +
355A LEU* 4.2 8.9 - - - +
357A ASN* 2.6 52.4 + - - +
358A LYS* 3.3 23.9 - - - +
359A PRO* 3.9 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLN* 3.9 7.5 + - - +
222A ARG* 1.3 74.5 - - - +
224A LYS* 1.3 54.9 + - - +
227A VAL* 2.7 71.4 + - - +
228A GLN* 2.7 28.0 + - - +
359A PRO* 4.1 19.3 - - + +
360A TYR 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 3.5 17.0 - - - +
190A TRP 3.0 25.7 + - - -
191A SER* 5.1 2.9 - - - +
192A SER 5.7 0.7 - - - +
213A GLU* 2.8 33.2 + - - -
215A ALA* 4.0 15.3 - - + +
216A GLU 5.5 3.6 - - - +
221A GLN* 5.7 0.8 + - - -
222A ARG 3.5 0.4 - - - -
223A GLU* 1.3 78.0 + - - +
225A VAL* 1.3 65.4 + - + +
228A GLN* 3.2 29.6 + - - +
229A LEU* 3.0 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ALA* 4.1 14.4 - - + -
216A GLU 3.5 25.4 - - - +
217A TYR* 3.3 36.6 - - + -
221A GLN 5.3 0.2 - - - +
222A ARG 3.5 2.0 + - - -
223A GLU 3.5 0.4 - - - -
224A LYS* 1.3 77.2 - - + +
226A GLU* 1.3 60.7 + - + +
229A LEU* 4.1 10.6 - - + +
230A PRO* 3.4 18.7 - - - +
240A ALA* 4.9 7.2 - - + -
242A THR* 4.0 11.0 - - + -
316A GLY 6.0 0.7 - - - -
317A VAL* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 2.6 32.8 + - + +
222A ARG* 2.9 59.8 + - - +
225A VAL* 1.3 80.4 - - + +
227A VAL* 1.3 60.8 + - - +
230A PRO* 3.6 12.0 - - - +
310A TRP* 3.3 1.2 - - - -
313A ARG* 3.1 17.7 + - - -
358A LYS* 5.5 1.0 - - - +
359A PRO* 4.1 15.3 - - + +
361A SER* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 2.7 40.2 + - - +
226A GLU* 1.3 79.8 - - - +
228A GLN* 1.3 65.1 + - + +
230A PRO* 3.1 14.9 - - - +
231A GLU* 4.3 6.4 + - - +
359A PRO* 3.7 26.5 - - + +
360A TYR 4.2 9.2 - - - +
361A SER* 3.9 35.3 + - - +
----------------------------------------------------------
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