Contacts of the helix formed by residues 221 - 231 (chain A) in PDB entry 2AJA
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 CYS 221 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 4.8 11.2 - - - -
194A ILE* 3.8 28.3 - - + -
217A PHE 4.5 0.4 + - - +
218A LEU 3.2 12.3 + - - +
219A LEU 3.0 2.4 - - - -
220A ASP* 1.3 78.1 - - - +
222A PRO* 1.3 62.9 - - - +
223A VAL* 3.1 35.2 - - - -
224A MSE 2.8 28.8 + - + +
225A LEU* 2.8 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP 3.5 9.4 - - - +
221A CYS* 1.3 84.4 - - + +
223A VAL* 1.3 59.2 + - + +
225A LEU* 3.8 5.2 - - + +
226A ALA* 2.8 29.9 + - - +
273A SER* 3.7 32.8 - - - +
276A LEU* 3.8 31.2 - - + -
277A GLN* 4.1 13.0 - - + +
280A TYR* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 4.2 14.8 - - - +
194A ILE* 5.5 0.7 - - + -
195A GLN* 4.1 27.1 - - + +
199A TYR* 4.7 6.7 + - + +
221A CYS* 3.1 28.0 - - - -
222A PRO* 1.3 77.8 - - + +
224A MSE 1.3 62.1 + - - +
226A ALA* 3.1 8.4 - - + +
227A TYR* 3.0 23.4 + - - +
280A TYR* 5.3 5.8 - - + +
314A THR* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 3.6 28.3 - - + +
199A TYR* 3.6 17.5 - - + -
201A ALA* 6.3 0.2 - - - -
202A PHE* 3.5 45.8 - - + -
218A LEU* 3.2 32.3 - - + +
219A LEU* 4.4 1.3 - - + +
221A CYS* 2.8 18.0 + - + +
223A VAL* 1.3 81.2 - - - +
225A LEU* 1.3 62.8 + - - +
227A TYR* 3.2 30.4 + - + -
228A ALA* 3.0 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 3.7 32.2 - - + +
221A CYS 2.8 12.8 + - - +
222A PRO* 4.0 4.3 - - + +
224A MSE 1.3 73.0 - - - +
226A ALA* 1.3 57.5 + - - +
228A ALA* 4.5 0.2 - - - -
229A GLU* 2.9 48.7 + - + +
240A VAL* 4.4 7.0 - - + -
243A PHE* 4.6 10.1 - - + -
244A ILE* 4.0 21.8 - - + -
277A GLN* 3.8 34.1 - - + +
280A TYR* 4.0 15.7 - - + +
281A MSE 3.8 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PRO 2.8 20.4 + - - +
223A VAL* 3.1 12.8 - - + +
224A MSE 3.0 0.2 - - - -
225A LEU* 1.3 77.8 - - - +
227A TYR* 1.3 62.3 + - - +
229A GLU* 3.4 5.6 - - - +
230A ILE* 3.8 5.7 + - - +
280A TYR* 3.6 31.0 - - + -
283A ARG* 2.8 26.3 + - - +
314A THR* 5.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASN* 4.6 12.0 + - - -
199A TYR* 3.7 45.3 - + + +
202A PHE* 5.2 1.3 - + - -
203A ARG* 3.8 24.8 + - + +
223A VAL 3.0 12.3 + - - +
224A MSE 3.4 25.4 - - + +
226A ALA* 1.3 77.3 - - - +
228A ALA* 1.3 60.2 + - - +
230A ILE* 2.8 30.1 - - + +
231A HIS* 2.9 46.2 + + - -
235A TYR* 4.4 16.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 3.5 38.8 - - + -
219A LEU* 4.0 9.0 - - + -
224A MSE 3.0 18.6 + - + +
225A LEU* 4.1 0.4 - - - +
227A TYR* 1.3 80.9 - - - +
229A GLU* 1.3 65.3 + - - +
231A HIS* 3.0 14.4 + - - +
235A TYR* 3.5 19.6 - - + -
240A VAL* 3.9 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 2.9 35.4 + - + +
226A ALA* 3.4 5.8 - - - +
228A ALA* 1.3 73.2 - - - +
230A ILE* 1.3 61.3 + - - +
231A HIS 3.5 0.4 + - - -
232A GLU* 3.9 11.1 + - - +
240A VAL* 3.8 23.9 - - + +
280A TYR 4.2 9.0 - - - +
283A ARG* 2.6 38.9 + - - +
284A ASN* 2.8 48.1 - - + +
287A ARG* 2.8 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA 4.1 4.9 - - - +
227A TYR* 2.8 30.9 + - + +
229A GLU* 1.3 80.8 - - - +
231A HIS* 1.3 71.3 + - + +
232A GLU* 3.0 19.1 + - - +
283A ARG* 5.0 2.0 - - - +
287A ARG* 3.4 38.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR* 2.9 68.7 - + - -
228A ALA 3.0 4.9 + - - +
230A ILE* 1.3 84.3 + - + +
232A GLU* 1.3 58.7 + - - +
233A PHE 3.2 4.1 + - - -
234A GLU* 3.3 17.6 + - - +
235A TYR* 2.8 49.8 + + + +
----------------------------------------------------------
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