Contacts of the helix formed by residues 224 - 239 (chain A) in PDB entry 2V3V
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 THR 224 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 3.8 4.2 - - - +
221A ARG* 2.8 60.9 + - + +
222A PRO 4.1 0.9 - - - +
223A GLY* 1.3 78.1 - - - +
225A ASP* 1.3 63.3 + - - +
226A LEU 3.3 2.6 + - - -
227A ALA* 3.4 7.1 + - - +
228A PHE 3.1 16.1 + - - -
281A ILE* 3.8 16.6 - - + +
282A CYS* 3.2 32.8 - - - +
599A LYS 5.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 3.9 8.7 - - + -
220A PHE* 3.6 27.2 - - + -
221A ARG 4.7 1.0 + - - -
223A GLY 3.8 0.3 - - - -
224A THR* 1.3 74.1 + - - +
226A LEU* 1.3 64.6 + - - +
228A PHE* 3.4 7.7 - - - +
229A MET* 2.8 36.0 + - + +
310A ILE* 3.5 9.4 - - - +
313A ARG* 2.8 36.0 + - - -
812A MGD 2.8 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLY 4.4 4.0 - - - +
224A THR 3.3 0.8 - - - -
225A ASP* 1.3 82.9 + - - +
227A ALA* 1.3 57.4 + - - +
229A MET* 3.2 3.1 + - - -
230A HIS* 2.9 26.9 + - - -
313A ARG* 3.5 27.1 - - - +
315A GLN* 3.8 31.6 - - + +
318A PHE* 3.8 28.0 - - + -
319A ALA* 3.9 22.4 - - + +
322A LEU* 3.5 33.8 - - + +
596A ARG 4.8 2.2 - - - +
597A PRO 4.5 1.8 - - - +
598A ALA* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A THR* 3.4 10.7 + - - +
225A ASP 3.4 0.4 - - - -
226A LEU* 1.3 76.3 - - - +
228A PHE* 1.3 62.1 + - - +
230A HIS* 3.4 2.1 + - - +
231A SER* 2.9 25.1 + - - -
273A TYR* 3.9 28.7 - - + -
278A VAL* 3.6 19.1 - - + +
281A ILE* 4.5 20.2 - - + -
598A ALA* 3.7 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 4.8 8.1 - + - -
173A ILE* 5.7 0.2 - - + -
203A ALA* 5.5 0.2 - - + -
218A VAL* 3.7 35.9 - - + -
220A PHE* 4.1 15.3 - + + -
224A THR 3.1 13.8 + - - +
225A ASP* 3.4 14.1 - - - +
226A LEU 3.2 0.2 - - - -
227A ALA* 1.3 76.3 - - - +
229A MET* 1.3 61.3 + - + +
231A SER* 3.3 4.3 + - - -
232A MET* 3.0 54.2 + - + +
278A VAL* 3.9 7.7 - - - +
282A CYS* 3.9 15.5 - - - -
284A VAL* 4.1 9.6 - - + -
288A GLN 3.9 20.0 - - - -
289A ILE* 3.4 35.1 - - + +
292A ALA* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 4.2 22.7 - - + -
173A ILE* 4.0 15.5 - - + -
225A ASP* 2.8 28.8 + - + +
226A LEU* 3.2 5.4 + - - +
228A PHE* 1.3 72.6 - - + +
230A HIS* 1.3 65.6 + - - +
232A MET* 3.5 9.8 + - - +
233A ALA* 3.2 18.2 + - - +
310A ILE* 4.0 16.8 - - + -
319A ALA* 3.5 27.8 - - + +
322A LEU* 3.9 20.4 - - + +
323A ILE* 3.4 31.2 - - + -
326A LEU* 3.8 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU 2.9 21.3 + - - +
227A ALA 3.8 0.9 - - - +
229A MET* 1.3 75.3 - - - +
231A SER* 1.3 58.4 + - - +
233A ALA* 3.2 7.4 + - - +
234A TRP* 2.9 24.3 + - - +
266A TYR* 5.2 3.5 + + - -
269A PHE* 3.4 21.2 - + - -
270A LEU* 3.4 16.8 - - + +
273A TYR* 3.4 51.4 - + + -
322A LEU* 3.5 32.8 - - + +
325A ASN* 4.5 4.9 + - - -
594A TRP 4.3 3.1 - - - -
595A MET* 4.7 0.2 - - - -
596A ARG 2.6 29.2 + - - -
598A ALA* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA 2.9 17.4 + - - -
228A PHE 3.5 5.8 - - - -
229A MET 3.3 0.2 - - - -
230A HIS* 1.3 73.4 - - - +
232A MET* 1.3 62.9 + - - +
234A TRP* 3.2 4.5 + - - +
235A VAL* 3.1 26.3 + - - +
273A TYR 2.5 27.5 + - - -
274A ARG 3.4 0.7 - - - -
275A PRO* 3.2 24.8 - - - +
278A VAL* 3.5 12.6 - - - +
289A ILE* 3.8 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.8 24.5 - - + -
228A PHE* 3.0 48.0 + - + +
229A MET* 3.7 8.7 - - - +
230A HIS 3.3 0.2 - - - -
231A SER* 1.3 72.0 - - - +
233A ALA* 1.3 58.8 + - - +
235A VAL 3.3 1.9 + - - -
236A ILE* 2.9 34.7 + - + +
289A ILE* 4.2 7.9 - - + +
292A ALA* 3.9 24.2 - - + +
293A ALA* 3.6 23.7 - - + +
296A PHE* 4.1 16.6 - - + -
326A LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A MET 3.2 11.3 + - - +
230A HIS* 3.2 10.5 + - - +
232A MET* 1.3 78.3 - - - +
234A TRP* 1.3 59.1 + - - +
236A ILE* 3.4 7.0 + - - +
237A ILE* 3.0 30.4 + - + +
266A TYR* 3.5 26.9 - - + +
270A LEU* 4.1 12.6 - - + -
325A ASN* 5.9 0.7 - - + -
326A LEU* 3.8 14.3 - - + +
329A ILE* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A HIS 2.9 13.4 + - - +
231A SER* 3.2 14.8 + - - +
233A ALA* 1.3 73.7 - - - +
235A VAL* 1.3 74.4 + - + +
237A ILE* 3.3 3.7 + - - +
238A ASN* 2.8 73.1 + - + +
239A GLU* 6.2 0.2 - - + -
267A LYS 5.3 0.7 - - - -
270A LEU* 3.5 37.6 - - + +
271A GLU* 2.8 27.4 + - - -
273A TYR 4.1 7.6 - - - +
274A ARG* 3.5 42.5 - - + +
275A PRO* 3.3 34.3 - - + -
276A GLU* 5.6 0.4 - - - -
290A TYR* 4.1 15.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A SER 3.1 14.3 + - - +
232A MET 3.6 0.7 - - - +
234A TRP* 1.3 78.2 - - + +
236A ILE* 1.3 67.1 + - - +
238A ASN* 4.3 2.0 - - - -
239A GLU* 2.9 51.0 + - + +
241A LEU* 5.1 1.1 - - + -
275A PRO* 3.8 18.6 - - + -
289A ILE* 4.2 10.8 - - + -
290A TYR* 3.7 29.2 - - + -
293A ALA* 3.6 25.4 - - + -
294A ARG* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A MET* 2.9 22.4 + - + +
233A ALA* 3.6 6.5 - - - +
235A VAL* 1.3 77.8 - - - +
237A ILE* 1.3 59.8 + - + +
240A GLU 3.4 0.3 + - - -
241A LEU* 2.8 53.9 + - + +
242A ASP* 3.6 9.3 + - + +
293A ALA* 3.9 23.6 - - + +
296A PHE* 4.4 8.7 - - + -
297A ALA* 4.0 10.3 - - + -
326A LEU* 4.2 22.2 - - + -
329A ILE* 4.2 7.9 - - + -
330A THR* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA* 3.0 21.7 + - + +
234A TRP* 4.0 2.7 - - - +
236A ILE* 1.3 77.2 - - + +
238A ASN* 1.3 65.9 + - - +
240A GLU* 3.2 16.6 + - - +
242A ASP* 4.2 11.9 - - + +
263A PHE* 3.9 24.2 - - + -
266A TYR* 3.7 24.2 - - + -
267A LYS* 3.7 36.3 - - + +
270A LEU* 3.6 23.6 - - + -
329A ILE* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TRP* 2.8 62.6 + - + +
235A VAL 3.9 2.7 - - - +
237A ILE* 1.3 75.5 - - - +
239A GLU* 1.3 69.2 + - - +
240A GLU* 3.3 7.6 + - - +
274A ARG* 5.5 0.5 + - - -
290A TYR* 5.9 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 2.9 24.9 + - + +
238A ASN* 1.3 88.4 + - - +
240A GLU* 1.3 70.8 + - - +
241A LEU* 3.2 22.8 + - + +
290A TYR* 3.7 14.4 - - - -
294A ARG* 2.8 52.0 + - - +
----------------------------------------------------------
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