Contacts of the helix formed by residues 239 - 250 (chain A) in PDB entry 1V9P
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 239 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 4.8 0.2 - - - +
238A LYS* 1.3 85.7 + - - +
240A GLN* 1.3 62.8 + - - +
241A TYR* 3.0 12.6 + - - +
242A GLU* 3.2 21.1 + - - +
243A LEU* 3.0 17.2 + - - +
260A LYS* 4.9 3.5 + - - -
293A ASP* 2.4 41.0 + - - -
295A LEU* 3.4 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.5 26.2 - - + +
116A GLU* 3.1 21.1 - - - +
226A TYR 3.8 7.2 + - - +
227A ALA* 6.2 0.2 - - - +
239A SER* 1.3 72.3 + - - +
241A TYR* 1.3 66.6 + - - +
243A LEU* 2.8 39.9 + - - +
244A LEU* 3.2 18.1 + - + +
291A LYS* 3.4 20.5 - - + +
292A LEU 4.4 3.6 - - - +
293A ASP* 3.0 21.9 + - - +
295A LEU* 3.1 13.9 - - + +
298A TRP* 4.0 20.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.8 7.4 - - + +
239A SER* 3.0 10.7 + - - +
240A GLN* 1.3 83.4 - - - +
242A GLU* 1.3 69.6 + - + +
244A LEU* 3.4 9.8 + - - +
245A LEU* 3.4 40.6 + - + +
258A TYR* 3.4 35.4 + + - -
259A GLU* 4.4 3.1 - - - -
260A LYS* 3.4 50.9 - - + +
293A ASP* 3.0 8.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
237A LEU* 5.0 10.8 - - + -
238A LYS* 4.6 19.7 - - + +
239A SER* 3.2 28.1 + - - +
241A TYR* 1.3 81.9 - - + +
243A LEU* 1.3 55.3 + - - +
245A LEU* 2.9 19.8 + - - +
246A TRP* 2.6 36.3 + - - +
260A LYS* 5.5 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR 2.9 35.2 - - - +
227A ALA* 3.8 10.8 - - - -
228A LEU* 4.1 8.5 - - + +
232A LEU* 3.8 25.1 - - + -
237A LEU* 3.1 34.9 - - + +
239A SER 3.0 8.3 + - - +
240A GLN* 2.8 28.6 + - - +
242A GLU* 1.3 74.4 - - - +
244A LEU* 1.3 51.0 + - - +
246A TRP* 2.8 5.5 + - - +
247A LEU* 2.6 43.3 + - + +
295A LEU* 4.1 12.8 - - + -
298A TRP* 6.4 0.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
114A THR* 4.0 9.0 - - + -
116A GLU* 3.6 16.6 - - - +
225A PHE 4.2 5.2 - - - +
226A TYR* 3.7 36.3 - - + +
240A GLN* 3.2 25.0 + - - +
241A TYR 3.7 3.4 - - - +
243A LEU* 1.3 75.8 - - - +
245A LEU* 1.3 60.4 + - - +
247A LEU* 3.7 7.2 - - - +
248A LYS* 3.2 20.8 + - - +
254A VAL* 3.8 15.6 - - + +
256A HIS* 4.6 2.2 - - + -
258A TYR* 3.3 55.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.4 31.6 + - + +
242A GLU* 2.9 22.9 + - - +
244A LEU* 1.3 76.3 - - - +
246A TRP* 1.3 66.9 + - - +
248A LYS* 3.2 20.7 + - + +
249A GLU* 3.0 24.1 + - - +
258A TYR* 3.3 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLY 4.7 3.1 + - - -
165A VAL* 3.7 29.6 - - + -
166A PRO* 4.5 6.5 - - + -
169A LEU* 4.0 14.4 - - + -
228A LEU* 4.0 27.1 - - + -
235A SER* 4.6 16.3 + - - -
237A LEU* 3.8 36.7 - - + +
242A GLU 2.6 17.1 + - - +
243A LEU* 3.2 7.9 - - - +
245A LEU* 1.3 69.8 - - - +
247A LEU* 1.3 86.7 + - + +
248A LYS 3.0 1.4 + - - -
249A GLU* 3.0 25.8 + - - +
250A LYS* 3.1 55.9 + - + +
252A PHE* 5.3 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 4.5 7.6 - - + -
225A PHE* 3.4 31.2 - - + +
226A TYR* 3.5 26.5 - - - +
227A ALA 3.8 2.7 - - - +
228A LEU* 3.8 24.0 - - + -
243A LEU* 2.6 29.4 + - + +
244A LEU* 3.7 9.2 - - - +
246A TRP* 1.3 84.3 - - + +
248A LYS* 1.3 59.6 + - - +
250A LYS* 3.6 2.0 + - - -
252A PHE* 3.0 60.0 + - + +
254A VAL* 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 3.2 10.8 + - - +
245A LEU* 3.2 25.2 + - + +
246A TRP 3.1 0.2 - - - -
247A LEU* 1.3 75.7 - - - +
249A GLU* 1.3 67.1 + - - +
250A LYS 3.1 1.6 - - - -
251A GLY* 3.0 16.1 + - - -
252A PHE 3.5 12.5 - - - +
254A VAL* 3.6 24.0 - - + +
258A TYR* 5.5 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU 3.0 10.4 + - - +
246A TRP* 3.0 22.0 + - - +
248A LYS* 1.3 77.4 - - - +
250A LYS* 1.3 74.5 + - + +
251A GLY* 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO* 4.6 7.1 - - - +
161A ARG 4.9 1.9 - - - +
162A LEU* 4.8 15.8 - - + +
163A LYS 2.8 32.7 + - - +
164A GLY* 4.0 10.7 + - - -
165A VAL* 4.1 7.0 - - + -
246A TRP* 3.1 68.0 + - + +
248A LYS 3.1 1.4 + - - -
249A GLU* 1.3 90.3 + - + +
251A GLY* 1.3 57.8 + - - +
252A PHE* 3.5 25.1 - - + -
----------------------------------------------------------
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