Contacts of the helix formed by residues 246 - 260 (chain A) in PDB entry 2VXO
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 GLY 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A SER* 3.3 10.9 + - - -
245A GLY* 1.3 77.8 - - - +
247A VAL* 1.3 62.7 + - - -
249A SER* 3.8 0.2 - - - -
250A THR* 2.7 32.6 + - - -
276A ARG* 6.4 0.2 - - - -
432A LEU* 5.7 0.7 - - - -
438A PHE* 6.1 4.9 - - - -
1697A SO4 3.1 19.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
246A GLY* 1.3 71.2 - - - +
248A ASP* 1.3 63.4 + - - +
250A THR* 3.3 5.8 + - - -
251A VAL* 3.0 39.8 + - + +
416A LYS* 4.4 15.9 - - - +
419A VAL* 4.5 6.5 - - + -
420A ARG* 4.4 7.6 - - + +
432A LEU* 3.6 25.9 - - + +
433A VAL* 3.8 27.1 - - + +
435A ARG* 3.9 29.6 - - + +
436A HIS 5.3 1.3 - - - +
1697A SO4 3.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 1.3 75.5 - - - +
249A SER* 1.3 58.6 + - - +
251A VAL 3.5 0.2 + - - -
252A CYS* 2.9 31.4 + - - +
367A GLY* 3.1 26.0 - - - +
368A THR* 5.3 0.5 - - - -
369A LEU* 4.0 15.3 + - - +
411A LEU* 3.2 12.8 - - + +
416A LYS* 3.5 35.7 + - - +
419A VAL* 3.8 13.9 - - - +
1697A SO4 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 4.3 4.8 - - - +
242A LEU 3.2 23.9 + - - -
243A LEU* 3.4 18.3 - - - -
244A SER* 3.4 5.0 + - - -
246A GLY 3.8 4.0 - - - -
248A ASP* 1.3 75.3 - - - +
250A THR* 1.3 55.7 + - - +
252A CYS* 3.5 6.6 + - - +
253A THR* 2.7 37.5 + - - -
367A GLY* 4.3 9.3 + - - +
1697A SO4 3.0 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.5 16.5 - - - +
245A GLY 3.8 6.9 + - - -
246A GLY 2.7 23.5 + - - -
247A VAL 3.7 3.6 - - - -
249A SER* 1.3 75.3 - - - +
251A VAL* 1.3 60.4 + - - +
253A THR* 3.3 4.9 + - - -
254A ALA* 2.9 27.5 + - - +
283A VAL* 3.9 9.3 - - + +
287A LEU* 3.9 26.8 - - + +
428A LEU* 3.9 20.9 - - + -
432A LEU* 4.0 20.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
247A VAL* 3.0 27.4 + - + +
248A ASP 3.9 3.6 - - - +
250A THR* 1.3 72.1 - - - +
252A CYS* 1.3 56.5 + - - +
254A ALA* 3.1 3.2 + - - +
255A LEU* 2.7 34.2 + - + +
411A LEU* 4.2 8.7 - - + -
419A VAL* 3.7 34.8 - - + +
422A LEU* 3.9 28.3 - - + -
423A GLY* 3.8 14.6 - - - +
426A LEU* 3.8 8.9 - - + +
428A LEU* 4.1 12.6 - - + -
432A LEU* 6.3 0.4 - - + -
433A VAL* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 4.8 2.9 - - + -
248A ASP 2.9 20.5 + - - +
249A SER* 3.6 6.3 - - - +
251A VAL* 1.3 75.8 - - - +
253A THR* 1.3 57.7 + - - +
255A LEU* 3.2 7.0 + - - +
256A LEU* 2.8 46.7 + - - +
365A ALA* 4.4 4.3 - - - -
366A GLN* 3.3 27.6 - - - -
367A GLY* 3.9 10.1 - - - +
410A PRO* 3.8 25.4 - - - -
411A LEU* 4.2 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 3.4 28.2 - - + +
243A LEU* 4.2 8.3 - - - +
249A SER 2.7 23.6 + - - -
250A THR* 3.5 7.4 - - - -
252A CYS* 1.3 75.7 - - - +
254A ALA* 1.3 58.3 + - - +
256A LEU* 3.8 3.6 - - - +
257A ASN* 3.0 27.9 + - - +
265A VAL* 4.4 4.3 - - + +
267A ALA* 3.8 27.4 - - + -
287A LEU* 4.4 12.1 - - + -
292A ILE* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR 2.9 16.9 + - - +
251A VAL 3.7 3.4 - - - +
253A THR* 1.3 76.6 - - - +
255A LEU* 1.3 58.0 + - - +
257A ASN* 3.5 2.3 + - - +
258A ARG* 2.9 29.6 + - - +
287A LEU* 4.5 4.7 - - + +
290A LEU* 4.7 5.4 - - + -
292A ILE* 4.0 19.2 - - + +
426A LEU* 3.7 24.3 - - + +
428A LEU* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 4.1 22.2 - - + +
226A CYS* 3.9 16.4 - - - -
227A ILE* 4.0 23.8 - - + -
230A ILE* 4.1 8.7 - - + -
251A VAL 2.7 21.5 + - - +
252A CYS 3.5 3.8 - - - +
254A ALA* 1.3 71.2 - - - +
256A LEU* 1.3 60.1 + - - +
258A ARG* 3.2 3.1 + - - +
259A ALA* 2.9 28.1 + - - +
410A PRO* 3.8 21.8 - - + -
411A LEU* 3.8 26.9 - - + -
422A LEU* 4.7 7.9 - - + -
426A LEU* 3.7 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 4.1 24.0 - - + -
239A VAL* 3.9 15.0 - - + -
241A VAL* 4.3 14.4 - - + -
252A CYS* 2.8 30.8 + - - +
253A THR 3.8 3.6 - - - +
255A LEU* 1.3 71.9 - - + +
257A ASN* 1.3 66.3 + - - +
259A ALA* 3.3 3.3 + - - +
260A LEU* 3.0 34.2 + - + +
265A VAL* 3.7 14.1 - - + -
365A ALA* 3.4 28.5 - - + -
408A ILE* 4.2 13.0 - - + -
410A PRO* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR 3.0 16.6 + - - +
254A ALA 3.8 1.6 - - - +
256A LEU* 1.3 79.3 - - - +
258A ARG* 1.3 56.3 + - - +
260A LEU 2.8 24.3 - - - +
262A GLN* 4.0 32.8 + - - +
265A VAL* 3.8 21.5 + - + +
290A LEU 4.3 6.6 - - - +
291A GLY 4.4 3.3 + - - +
292A ILE* 3.3 41.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 4.2 3.8 + - - +
224A LEU* 4.0 23.6 - - - +
227A ILE* 3.7 34.0 - - + +
231A LYS* 5.7 3.0 - - - +
254A ALA 2.9 18.1 + - - +
255A LEU 3.2 4.9 + - - +
257A ASN* 1.3 76.4 - - - +
259A ALA* 1.3 59.1 + - - +
260A LEU 3.6 1.6 + - - +
426A LEU* 3.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ILE* 3.7 29.4 - - + +
230A ILE* 3.7 35.0 - - + -
231A LYS* 3.4 32.4 - - - +
255A LEU 2.9 16.4 + - - +
256A LEU 3.3 2.9 + - - +
258A ARG* 1.3 76.9 - - - +
260A LEU* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 4.1 25.6 - - + -
231A LYS* 4.4 11.7 - - + -
234A VAL* 4.2 13.5 - - + -
235A GLY 4.3 4.9 - - - +
239A VAL* 3.7 29.8 - - + -
256A LEU* 3.0 21.6 + - + +
257A ASN 2.8 17.6 - - - +
258A ARG 4.4 1.7 - - - +
259A ALA* 1.3 86.4 - - - +
261A ASN* 1.3 70.7 + - - +
262A GLN 3.9 0.2 + - - -
264A GLN* 3.7 28.9 - - + +
265A VAL* 4.1 9.4 - - + -
----------------------------------------------------------
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