Contacts of the helix formed by residues 221 - 238 (chain A) in PDB entry 2HE7
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 SER 221 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A CYS* 1.3 79.4 - - - +
222A PHE* 1.3 65.0 - - - +
223A VAL* 3.7 8.9 + - - +
224A THR* 3.2 25.0 + - - -
225A LEU* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A CYS 3.8 0.4 + - - -
221A SER* 1.3 72.6 - - - +
223A VAL* 1.3 72.0 + - + +
225A LEU* 3.4 13.8 + - + +
226A ALA* 3.0 22.0 + - - +
260A THR* 4.6 1.6 - - - -
262A GLU* 3.5 46.4 - - + -
263A LEU* 3.6 37.3 - - + +
266A LYS* 4.1 27.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
221A SER* 3.2 8.0 + - - +
222A PHE* 1.3 89.2 - - + +
224A THR* 1.3 63.4 + - - +
226A ALA* 3.3 7.1 + - - +
227A LEU* 3.1 30.8 + - + +
266A LYS* 5.0 12.5 + - - +
270A LEU* 5.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A CYS* 3.7 19.1 - - - -
221A SER* 3.2 20.4 + - - -
223A VAL* 1.3 80.2 - - - +
225A LEU* 1.3 56.2 + - - +
227A LEU* 3.7 7.6 - - + +
228A LEU* 2.8 48.9 + - + +
289A ASN* 5.4 9.7 + - + +
293A LEU* 3.8 20.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
213A ILE* 3.5 19.1 - - + -
220A CYS* 3.4 36.6 - - - +
221A SER 2.9 18.3 + - - +
222A PHE* 3.5 16.6 - - + +
224A THR* 1.3 72.7 - - - +
226A ALA* 1.3 58.2 + - - +
228A LEU* 3.9 4.5 - - + +
229A GLY* 3.0 24.8 + - - -
255A PHE* 3.5 27.0 - - - +
256A ALA* 3.8 20.4 - - + -
257A PRO* 5.2 4.5 - - + -
263A LEU* 4.1 16.4 - - + +
267A VAL* 4.5 1.2 - - - +
----------------------------------------------------------
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 PHE* 3.0 18.7 + - + +
223A VAL* 3.6 6.5 - - - +
224A THR 3.1 0.2 - - - -
225A LEU* 1.3 74.1 - - - +
227A LEU* 1.3 61.0 + - - +
229A GLY 3.5 0.3 + - - -
230A SER* 3.0 28.9 + - - -
263A LEU* 3.7 18.2 - - + -
266A LYS* 3.6 33.2 - - + -
267A VAL* 3.6 11.2 - - - +
270A LEU* 3.9 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A VAL* 3.1 20.6 + - + +
224A THR* 3.2 7.6 + - + +
226A ALA* 1.3 76.2 - - - +
228A LEU* 1.3 65.1 + - + +
230A SER* 2.9 26.8 + - - +
231A TYR* 3.1 46.2 + - + +
270A LEU* 3.9 19.2 - - + +
274A HIS* 4.4 7.2 - - + -
289A ASN* 3.7 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 3.4 32.1 - - + -
220A CYS* 4.4 4.5 - - - -
224A THR* 2.8 39.8 + - + +
225A LEU* 3.9 5.4 - - + +
227A LEU* 1.3 73.3 - - + +
229A GLY* 1.3 61.2 + - - +
231A TYR* 3.2 4.8 + - + +
232A THR* 3.1 23.1 + - - -
286A PHE* 3.3 54.4 - - + +
289A ASN* 3.8 18.6 - - + +
290A ALA* 4.0 5.8 - - + +
293A LEU* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU 3.0 17.2 + - - -
226A ALA 3.8 1.8 - - - -
227A LEU 3.3 0.2 - - - -
228A LEU* 1.3 74.3 - - - +
230A SER* 1.3 50.5 + - - +
232A THR* 3.0 9.4 + - - -
233A VAL* 2.8 36.6 + - - +
255A PHE* 3.6 27.1 - - - -
267A VAL* 4.0 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA 3.0 16.2 + - - -
227A LEU* 2.9 17.8 + - - +
228A LEU 3.3 0.2 - - - -
229A GLY* 1.3 75.4 - - - +
231A TYR* 1.3 54.7 + - - +
233A VAL* 3.9 3.6 - - - +
234A GLN* 3.0 28.2 + - - +
267A VAL* 3.6 18.5 - - - +
270A LEU* 3.5 24.5 - - - +
271A HIS* 3.7 6.1 - - - +
274A HIS* 2.6 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.1 44.3 + - + +
228A LEU* 3.2 8.6 + - - +
230A SER* 1.3 74.1 + - - +
232A THR* 1.3 64.4 + - - +
233A VAL 3.2 0.2 - - - -
234A GLN* 4.4 2.0 - - - -
235A SER* 2.9 26.4 + - - -
274A HIS* 3.5 29.5 - + - -
277A MET* 3.9 18.0 - - + +
282A ALA* 3.5 22.3 - - - +
285A HIS* 3.3 41.3 + + + +
286A PHE* 3.8 22.2 - - + -
289A ASN* 3.9 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ARG* 3.6 40.3 + - - +
228A LEU 3.1 11.8 + - - -
229A GLY* 3.0 13.0 + - - -
231A TYR* 1.3 75.6 - - - +
233A VAL* 1.3 58.2 + - - +
235A SER* 3.3 6.1 + - - -
236A GLU* 2.9 36.1 + - + +
253A PHE* 3.9 25.8 - - + -
255A PHE* 4.8 4.9 - - + -
286A PHE* 3.5 20.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLY 2.8 19.0 + - - +
230A SER* 3.9 6.1 - - - +
232A THR* 1.3 77.1 - - - +
234A GLN* 1.3 56.6 + - - +
237A LEU* 2.8 51.2 + - + +
238A GLY 4.1 0.2 - - - +
249A TYR* 4.2 0.4 - - + +
250A ILE* 4.0 17.7 - - + -
253A PHE* 4.2 14.6 - - + -
255A PHE* 3.7 26.7 - - + -
267A VAL* 4.1 6.1 - - + -
271A HIS* 3.3 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A SER 3.0 19.6 + - - +
231A TYR 3.8 3.6 - - - +
233A VAL* 1.3 76.5 - - - +
235A SER* 1.3 59.4 + - - +
238A GLY* 3.0 41.0 + - - +
239A ASP* 3.0 28.3 + - - -
271A HIS* 3.0 28.7 + - + +
274A HIS* 3.6 28.5 + - + +
275A ARG 4.4 0.2 + - - -
277A MET* 3.0 42.0 + - + +
279A PRO* 5.1 2.1 - - - +
282A ALA* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 4.9 0.2 - - - -
210A ARG* 4.6 3.3 + - - -
231A TYR 2.9 18.2 + - - -
232A THR* 3.5 6.7 - - - -
234A GLN* 1.3 79.6 - - - +
236A GLU* 1.3 70.3 + - - +
238A GLY* 4.2 1.9 + - - -
279A PRO* 3.7 30.1 - - - +
282A ALA* 3.9 10.7 - - - +
283A GLU* 2.6 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 2.9 29.1 + - - -
210A ARG* 3.1 32.9 + - - +
232A THR 2.9 21.2 + - - +
235A SER* 1.3 79.8 - - - +
237A LEU* 1.3 66.1 + - + +
253A PHE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 2.8 24.1 + - + +
236A GLU* 1.3 84.8 - - + +
238A GLY* 1.3 62.5 + - - +
239A ASP 4.0 3.8 + - - +
244A GLU* 5.0 6.6 - - - +
245A CYS* 6.0 0.4 - - - -
249A TYR* 3.8 36.6 - - + +
250A ILE* 4.1 0.4 - - + -
253A PHE* 3.6 40.8 - - + -
271A HIS* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLN* 3.0 29.3 + - - +
235A SER 4.2 2.1 + - - -
236A GLU 3.7 1.0 - - - -
237A LEU* 1.3 79.3 - - - +
239A ASP* 1.3 56.8 + - - +
271A HIS* 2.7 30.8 + - - -
277A MET 5.5 0.9 - - - -
279A PRO* 6.4 0.4 - - - -
----------------------------------------------------------
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