Contacts of the helix formed by residues 239 - 261 (chain A) in PDB entry 1VI9
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 239 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 5.3 0.4 - - - -
237A GLY 3.6 2.4 + - - +
238A ALA* 1.3 77.2 - - - +
240A LEU* 1.3 66.4 + - - +
241A GLN* 3.5 6.8 + - - +
242A GLU* 2.9 47.0 + - - +
243A ALA* 2.9 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ILE* 4.4 17.0 - - + -
198A LEU* 3.4 33.4 - - + +
200A THR* 3.9 31.9 - - + +
203A GLU* 3.8 36.3 - - + +
205A TRP* 3.9 20.4 - - + +
234A LEU* 4.5 8.3 - - + -
239A THR* 1.3 74.9 - - - +
241A GLN* 1.3 56.4 + - - +
243A ALA* 3.8 1.5 - - - +
244A LEU* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TRP* 3.5 50.8 - - + -
239A THR* 3.3 6.5 + - - +
240A LEU* 1.3 77.2 - - - +
242A GLU* 1.3 58.8 + - + +
244A LEU* 3.3 3.9 + - - +
245A GLU* 2.7 71.7 + - + +
281A TYR* 5.6 0.8 + - - -
283A SER* 5.5 0.8 + - - -
284A ALA* 4.2 6.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LYS* 4.5 3.9 + - - +
237A GLY 4.6 1.0 - - - +
238A ALA* 3.5 12.8 - - + +
239A THR* 2.9 49.5 + - - +
241A GLN* 1.3 75.7 - - + +
243A ALA* 1.3 61.2 + - - +
245A GLU* 4.2 4.7 - - - +
246A HIS* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.8 18.8 - - + -
233A LYS* 3.7 28.9 - - + -
234A LEU* 4.1 11.2 - - + -
238A ALA* 3.9 4.9 - - + +
239A THR 2.9 18.5 + - - +
240A LEU* 3.8 4.5 - - - +
242A GLU* 1.3 77.0 - - - +
244A LEU* 1.3 58.0 + - - +
246A HIS* 3.8 0.5 - - - +
247A VAL* 2.9 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.2 18.4 - - + -
196A MSE 4.0 19.3 - - + +
198A LEU* 4.1 16.4 - - + +
205A TRP* 3.7 40.2 - - + +
206A HIS 4.2 0.2 - - - -
207A ILE* 3.8 38.1 - - + +
230A LEU* 5.4 2.0 - - + -
240A LEU 3.0 18.2 + - - +
241A GLN* 3.8 3.4 - - - +
243A ALA* 1.3 78.0 - - - +
245A GLU* 1.3 58.4 + - - +
247A VAL* 4.1 3.4 - - + +
248A THR* 2.6 33.0 + - - -
284A ALA* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.9 7.2 - - + -
241A GLN* 2.7 53.7 + - - +
242A GLU* 4.2 4.1 - - - +
244A LEU* 1.3 71.7 - - - +
246A HIS* 1.4 63.1 + - - +
248A THR* 4.1 0.7 - - - -
249A ALA* 3.3 24.3 + - - +
281A TYR* 3.9 19.3 + - + -
282A PHE* 3.4 21.6 + - - +
283A SER* 3.7 4.1 + - - -
284A ALA* 2.8 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.8 20.5 - - + +
233A LYS* 2.7 39.8 + - + +
242A GLU 2.8 19.7 + - - +
243A ALA 3.9 1.8 - - - +
245A GLU* 1.4 78.8 - - - +
247A VAL* 1.3 62.7 + - - +
249A ALA* 3.9 2.1 - - - +
250A ALA* 2.9 23.7 + - + +
275A ILE 3.0 26.2 + - - -
276A ALA 3.5 17.0 + - - -
278A PRO* 3.9 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 5.9 0.9 - - + -
196A MSE 4.8 6.3 - - + -
226A THR* 3.7 41.5 - - + +
229A LEU* 3.6 17.5 - - + +
230A LEU* 3.5 35.0 - - + +
233A LYS* 4.0 7.9 - - + -
243A ALA 2.9 25.0 + - - +
244A LEU* 4.1 4.0 - - + +
246A HIS* 1.3 71.6 - - - +
248A THR* 1.3 65.0 + - - +
250A ALA* 3.8 4.3 - - - +
251A VAL* 3.0 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A MSE 3.3 25.7 - - + +
207A ILE* 3.4 37.8 - - + +
208A SER 4.4 1.1 - - - +
209A ARG* 3.9 37.0 + - + +
244A LEU 2.6 24.6 + - - -
245A GLU 4.1 1.1 - - - -
247A VAL* 1.3 75.4 - - - +
249A ALA* 1.3 62.7 + - - +
251A VAL* 5.1 0.2 - - - -
252A TYR* 3.1 24.3 + - - +
282A PHE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU 3.3 16.3 + - - +
246A HIS* 4.8 0.2 - - - -
248A THR* 1.3 76.3 - - - +
250A ALA* 1.3 60.8 + - - +
252A TYR* 3.2 4.0 + - - +
253A GLU* 2.9 31.7 + - - +
278A PRO* 3.5 19.1 - - + -
280A HIS* 3.3 26.2 - - - +
282A PHE* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 6.3 0.2 - - + -
229A LEU* 4.0 19.7 - - + -
246A HIS* 2.9 23.2 + - + +
247A VAL* 3.8 3.1 - - - +
249A ALA* 1.3 78.6 - - - +
251A VAL* 1.3 61.3 + - - +
253A GLU* 3.2 4.9 + - - +
254A ILE* 3.1 26.3 + - - +
274A ARG 4.0 10.8 - - - -
275A ILE* 3.7 29.3 - - + +
278A PRO* 3.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 3.6 24.7 - - - +
222A VAL* 3.9 27.8 - - + +
225A VAL* 4.2 14.6 - - + -
226A THR* 3.6 33.9 - - + +
229A LEU* 4.4 5.2 - - + -
247A VAL* 3.0 22.6 + - + +
250A ALA* 1.3 75.0 - - - +
252A TYR* 1.3 61.9 + - - +
254A ILE* 3.1 11.6 + - + +
255A MSE 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 3.8 24.6 - - - +
210A PRO* 3.7 34.0 - - + +
212A VAL* 3.7 27.9 - - + +
248A THR 3.1 17.7 + - - +
249A ALA 3.5 3.8 - - - +
251A VAL* 1.3 77.3 - - - +
253A GLU* 1.3 56.8 + - - +
255A MSE 3.1 6.9 + - + +
256A VAL* 2.8 51.6 + - + +
280A HIS* 3.5 35.3 + + + -
282A PHE* 3.5 26.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 2.9 18.5 + - - +
250A ALA 3.2 7.8 + - - +
252A TYR* 1.3 76.8 - - - +
254A ILE* 1.3 62.3 + - + +
256A VAL* 3.2 8.3 - - - +
257A THR* 3.1 27.5 + - - -
271A ALA* 4.3 2.9 - - + -
274A ARG* 2.9 60.8 + - + +
278A PRO* 3.9 5.2 - - + -
279A GLU* 2.8 29.1 + - - +
280A HIS* 2.8 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 3.9 26.7 - - + -
229A LEU* 5.1 0.9 - - + -
250A ALA 3.1 14.9 + - - +
251A VAL* 3.1 11.5 + - + +
253A GLU* 1.3 77.1 - - - +
255A MSE 1.3 58.5 + - - +
257A THR* 3.3 2.6 + - - -
258A THR* 2.8 32.4 + - - -
266A LEU* 4.0 19.1 - - + -
267A GLN 4.0 27.8 + - - +
268A VAL* 4.1 14.6 - - + +
271A ALA* 3.8 12.3 - - + -
275A ILE* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 5.0 9.0 - - - +
212A VAL* 4.3 22.4 - - + -
214A PHE* 3.3 37.9 - - + -
219A PRO* 4.1 9.9 - - + -
222A VAL* 3.5 24.5 - - + -
251A VAL* 3.0 29.0 + - + +
252A TYR* 3.5 9.2 - - + +
254A ILE* 1.3 78.1 - - - +
256A VAL* 1.3 63.4 + - - +
258A THR* 3.1 3.8 + - - -
259A LYS* 2.9 24.6 + - - +
266A LEU* 3.2 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL* 4.8 6.5 - - + -
252A TYR* 2.8 60.2 + - + +
253A GLU* 3.2 31.9 - - - +
255A MSE 1.3 71.7 - - - +
257A THR* 1.3 57.8 + - - +
259A LYS* 3.3 6.2 + - - +
260A ALA* 2.9 30.9 + - - +
274A ARG* 4.4 4.0 - - - +
280A HIS* 4.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU 3.1 10.5 + - - -
254A ILE 3.6 3.4 - - - -
256A VAL* 1.3 75.7 - - - +
258A THR* 1.3 65.7 + - - +
260A ALA* 3.8 6.2 - - + +
261A MSE 3.0 47.6 + - + +
267A GLN* 4.0 6.1 - - + -
270A ALA* 3.9 16.6 - - + -
271A ALA* 3.8 7.6 - - - +
274A ARG* 2.9 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 3.8 14.4 - - + -
219A PRO* 4.2 8.1 - - + -
254A ILE* 2.8 25.4 + - - +
255A MSE 3.1 7.2 + - - -
257A THR* 1.3 77.5 - - - +
259A LYS* 1.3 60.8 - - - +
261A MSE 3.4 0.5 + - - -
262A GLN 3.3 2.1 + - - -
263A GLU* 3.0 52.1 + - + +
265A GLU 3.4 20.2 - - - +
266A LEU* 3.6 7.2 - - + +
267A GLN* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL* 3.9 18.4 - - + +
213A ASP* 3.3 38.2 + - - +
214A PHE* 3.8 18.3 - - + +
255A MSE 2.9 15.9 + - - +
256A VAL* 3.6 5.4 - - - +
258A THR* 1.3 74.2 - - - +
260A ALA* 1.3 59.1 + - - +
262A GLN* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL 2.9 17.7 + - - +
257A THR* 3.8 7.6 - - + +
259A LYS* 1.3 76.1 - - - +
261A MSE 1.3 62.2 + - + +
262A GLN* 3.3 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A THR* 3.0 38.7 + - + +
258A THR 3.4 2.9 + - - +
260A ALA* 1.3 77.1 - - + +
262A GLN* 1.3 71.7 + - - +
263A GLU* 3.2 17.0 + - + +
267A GLN* 3.2 30.1 - - + +
270A ALA* 3.7 13.7 - - + -
1B LEU* 5.7 9.2 - - + -
2B MSE 4.8 11.9 - - + +
----------------------------------------------------------
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