Contacts of the helix formed by residues 219 - 232 (chain A) in PDB entry 2ADS
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 HIS 219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLY 3.5 15.0 + - - +
190A ILE* 3.6 33.2 - - + +
191A ASP 5.4 1.5 + - - -
218A THR* 1.3 87.9 + - - +
220A LYS* 1.3 67.0 + - - +
221A SER* 3.6 17.3 - - - +
222A SER* 2.6 26.5 + - - +
223A LYS* 2.9 8.7 + - - +
5M G 3.9 3.3 + - - -
6M G 3.3 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR 3.5 3.1 + - - -
219A HIS* 1.3 72.7 + - - +
221A SER* 1.3 55.6 + - - +
223A LYS* 3.6 11.1 - - + +
224A LYS* 2.9 65.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 5.7 0.9 - - - -
189A GLY* 3.6 24.5 + - - -
190A ILE* 3.3 28.8 - - - +
219A HIS* 3.6 1.7 - - - +
220A LYS* 1.3 79.0 - - - +
222A SER* 1.3 61.9 + - - -
224A LYS* 3.3 8.1 + - - +
225A ALA* 2.8 26.7 + - - +
254A ILE* 3.7 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ILE* 4.3 3.8 - - - -
217A SER* 3.5 12.4 - - - -
218A THR 4.1 0.2 + - - -
219A HIS* 2.6 35.0 + - - +
221A SER* 1.3 75.4 + - - +
223A LYS* 1.3 64.1 + - - +
225A ALA* 3.0 12.7 + - - +
226A TRP* 3.0 21.9 + - - -
250A TYR* 3.2 37.8 + - - -
254A ILE* 3.7 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MSE 3.5 29.0 - - + +
215A GLU* 5.1 2.0 - - - +
217A SER* 3.0 33.0 + - - +
218A THR* 2.8 29.0 + - - +
219A HIS 2.9 15.0 + - - +
220A LYS* 3.6 9.9 - - + +
222A SER* 1.3 77.4 + - - +
224A LYS* 1.3 57.1 + - + +
226A TRP* 3.3 4.6 + - - +
227A GLU* 3.0 25.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
220A LYS* 2.9 54.1 + - + +
221A SER* 3.6 5.6 - - - +
223A LYS* 1.3 73.3 - - + +
225A ALA* 1.3 66.4 + - - +
227A GLU* 3.0 20.2 + - + +
228A GLU* 2.9 31.8 + - + +
254A ILE* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A SER 2.8 14.5 + - - +
222A SER 3.2 11.0 - - - +
224A LYS* 1.3 78.0 - - - +
226A TRP* 1.3 62.0 + - - +
228A GLU* 3.5 12.3 + - - +
229A LEU* 3.5 15.1 - - - +
251A PRO* 3.8 23.2 - - + +
253A THR* 3.4 23.6 + - - +
254A ILE* 3.9 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 3.9 27.8 - + - -
210A PHE* 3.8 38.4 - + - +
213A CYS* 3.4 35.0 + - + -
214A MSE 3.9 7.4 - - + -
217A SER* 3.5 24.8 - - - -
222A SER* 3.0 29.6 + - - -
223A LYS 3.6 4.5 - - - +
225A ALA* 1.3 73.0 - - - +
227A GLU* 1.3 66.3 + - - +
229A LEU* 2.9 16.6 + - + +
230A LEU* 3.0 12.9 + - - +
241A LEU* 3.7 25.8 - - + -
249A THR* 3.4 33.7 - - + -
250A TYR* 4.7 1.4 - - - -
251A PRO* 3.8 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MSE 3.6 23.9 - - + +
223A LYS 3.0 14.6 + - - +
224A LYS* 3.3 24.8 - - - +
226A TRP* 1.3 75.9 - - - +
228A GLU* 1.3 68.2 + - - +
230A LEU* 3.2 5.6 + - + +
231A LYS* 2.9 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LYS* 2.9 21.5 + - + +
225A ALA* 3.6 11.9 - - - +
226A TRP 3.2 0.4 - - - -
227A GLU* 1.3 82.4 - - - +
229A LEU* 1.3 60.6 + - + +
231A LYS* 4.9 5.2 - - - +
232A ASN* 2.8 43.4 + - - +
235A LEU* 4.0 25.5 - - + +
253A THR* 5.1 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ALA* 4.3 3.1 - - + -
210A PHE* 3.6 41.7 - - + -
225A ALA 3.5 13.0 - - - +
226A TRP* 2.9 8.2 + - + +
228A GLU* 1.3 78.6 - - + +
230A LEU* 1.3 68.0 + - - +
231A LYS 3.2 0.7 + - - -
232A ASN 3.4 8.5 - - - +
235A LEU* 4.2 9.6 - - + -
236A ARG* 2.9 31.3 + - + -
239A ALA* 3.3 28.5 - - + -
241A LEU* 3.7 13.5 - - + -
251A PRO* 3.7 29.4 - - + -
253A THR* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.7 45.3 - - + +
210A PHE* 3.6 10.4 - - + -
211A ARG* 5.0 15.3 - - + -
214A MSE 4.1 20.4 - - + -
226A TRP 3.0 11.5 + - - +
227A GLU* 3.4 11.9 - - + +
229A LEU* 1.3 76.5 - - - +
231A LYS* 1.3 66.8 + - + +
233A ARG* 5.0 0.2 - - - +
236A ARG* 2.8 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 2.9 56.2 + - + +
228A GLU* 4.2 5.4 - - - +
230A LEU* 1.3 86.5 - - + +
232A ASN* 1.3 62.2 + - + +
233A ARG* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLU* 2.8 30.8 + - - +
229A LEU 3.4 1.5 - - - +
231A LYS* 1.3 72.2 - - + +
233A ARG* 1.3 58.1 + - - +
234A GLU* 3.0 25.6 + - - +
235A LEU* 3.1 29.2 + - + +
236A ARG* 3.0 23.9 + - - +
----------------------------------------------------------
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