Contacts of the helix formed by residues 256 - 265 (chain X) in PDB entry 3F6E
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 256 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254X PRO 3.0 5.3 + - - -
255X ALA* 1.4 79.9 - - - +
257X ILE* 1.4 65.8 + - - -
258X ALA 3.5 1.8 - - - -
259X ALA* 4.5 1.5 - - - +
260X ILE* 3.0 26.5 + - - +
280X TYR* 3.5 7.1 - - - -
282X GLN* 3.7 8.1 - - - +
284X ASP* 3.5 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256X GLY* 1.4 72.8 - - - +
258X ALA* 1.3 64.8 + - - +
260X ILE* 3.3 2.1 + - - +
261X SER* 3.2 20.3 + - - -
280X TYR* 3.5 39.3 + - + +
282X GLN 5.2 0.8 + - - -
284X ASP* 3.4 15.7 + - - +
285X PRO* 5.1 6.3 - - + -
286X GLY 3.6 20.4 - - - +
287X GLN 3.5 21.0 - - - +
288X TYR* 3.9 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256X GLY 3.5 0.2 - - - -
257X ILE* 1.3 75.2 - - - +
259X ALA* 1.3 67.6 + - - +
261X SER* 3.2 10.2 + - - -
262X GLN* 2.9 25.8 + - - +
284X ASP* 2.9 29.4 + - - +
285X PRO 3.6 15.0 - - - +
286X GLY* 4.2 5.2 - - - -
287X GLN 4.5 0.9 - - - -
290X LYS* 5.3 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254X PRO* 3.3 34.0 - - + +
256X GLY* 3.9 5.6 - - - +
257X ILE 3.3 0.2 - - - -
258X ALA* 1.3 76.7 - - - +
260X ILE* 1.3 58.2 + - - +
262X GLN* 3.4 5.7 + - - +
263X LEU* 2.9 28.1 + - - +
282X GLN* 5.6 0.9 - - - +
284X ASP* 3.0 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235X PRO* 3.7 31.2 - - + -
253X MET* 3.7 22.7 - - + -
254X PRO* 3.2 29.6 - - + +
256X GLY 3.0 13.1 + - - +
257X ILE 4.0 2.5 - - - +
259X ALA* 1.3 76.3 - - - +
261X SER* 1.3 60.9 + - - +
263X LEU* 3.3 5.3 + - - +
264X LEU* 2.9 49.6 + - + +
278X PHE* 3.8 20.9 - - + -
280X TYR* 3.9 20.4 - - + +
288X TYR 5.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257X ILE 3.2 5.6 + - - -
258X ALA* 3.2 14.0 + - - -
260X ILE* 1.3 76.7 - - - +
262X GLN* 1.3 61.9 + - - +
264X LEU* 3.3 6.2 + - - +
265X GLU* 3.0 24.1 + - - +
287X GLN* 2.7 32.6 + - - +
288X TYR 3.5 17.5 + - - -
289X LEU* 3.8 10.5 - - - +
290X LYS* 3.7 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258X ALA 2.9 17.8 + - - +
259X ALA* 3.6 6.1 - - - +
261X SER* 1.3 79.8 + - - +
263X LEU* 1.3 64.1 + - - +
265X GLU* 3.2 35.4 + - - +
290X LYS* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232X TRP* 3.6 45.5 - - + +
253X MET* 3.6 26.0 - - + -
254X PRO* 3.9 25.1 - - + -
259X ALA 2.9 16.5 + - - +
260X ILE* 3.5 5.4 - - - +
262X GLN* 1.3 79.4 - - - +
264X LEU* 1.3 60.3 + - + +
265X GLU 3.5 3.1 + - - +
267X HIS* 4.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204X ALA* 4.4 13.5 - - + -
206X VAL* 4.4 3.8 - - + -
232X TRP* 4.4 10.1 - - + -
253X MET* 4.2 17.5 - - + -
260X ILE* 2.9 39.1 + - + +
261X SER* 3.7 5.2 - - - +
262X GLN 3.2 0.4 - - - -
263X LEU* 1.3 75.8 - - + +
265X GLU* 1.3 66.9 + - - +
267X HIS* 3.0 24.1 + - + +
270X VAL* 3.8 43.5 - - + -
278X PHE* 4.8 7.0 - - + -
289X LEU* 4.1 18.6 - - + -
293X THR* 3.2 13.6 + - + -
295X LEU* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261X SER 3.0 11.4 + - - +
262X GLN* 3.2 35.9 + - - +
263X LEU 4.2 4.5 - - - +
264X LEU* 1.3 79.8 - - - +
266X GLY* 1.3 63.3 + - - +
267X HIS* 3.3 5.7 + - - -
290X LYS* 3.3 28.1 + - + +
291X PRO 5.4 3.5 - - - +
293X THR* 4.2 5.4 - - - -
----------------------------------------------------------
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