Contacts of the helix formed by residues 236 - 253 (chain A) in PDB entry 3ZFW
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 HIS 236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO* 1.4 90.7 - - + +
238A ASP* 2.8 52.3 + - + +
239A VAL* 3.2 38.6 + - + +
242A MET* 6.0 0.4 - - + -
269A ILE* 3.5 18.8 - - - +
273A THR* 4.3 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 1.4 99.8 - - + +
238A ASP* 1.3 63.9 + - - +
240A ALA* 3.3 17.0 + - + +
241A THR* 3.4 12.0 + - - -
269A ILE* 4.3 5.4 - - + -
270A ARG* 4.8 2.5 + - + -
273A THR* 3.8 31.6 - - + +
274A LEU* 4.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 2.8 32.3 + - + +
237A PRO* 1.3 74.5 - - - +
239A VAL* 1.4 62.8 + - - +
240A ALA 3.3 0.2 - - - -
241A THR* 3.3 16.3 + - - +
242A MET* 3.2 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 3.2 34.7 + - + +
238A ASP* 1.4 76.1 - - - +
240A ALA* 1.4 55.5 + - - +
242A MET* 3.1 22.1 + - + +
243A LEU* 3.0 44.1 + - + +
269A ILE* 4.2 10.5 - - + -
246B LEU* 5.2 0.7 - - + -
249B VAL* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS 4.0 1.2 + - - -
237A PRO 3.3 12.6 + - - +
238A ASP 3.3 0.2 - - - -
239A VAL* 1.4 78.1 - - - +
241A THR* 1.4 50.5 + - - +
243A LEU* 3.4 7.5 + - - +
244A ASN* 2.7 34.7 + - - +
266A ALA* 3.6 30.4 - - + +
269A ILE* 3.9 14.7 - - + +
270A ARG* 3.6 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO 3.4 12.5 + - - -
238A ASP* 3.3 20.9 + - - +
239A VAL 3.3 0.4 - - - -
240A ALA* 1.4 73.6 - - - +
242A MET* 1.3 54.4 + - - +
244A ASN* 3.4 3.3 + - - +
245A ILE* 2.8 54.5 + - + +
270A ARG* 3.5 16.9 + - - +
211X ALA 4.8 1.2 + - - +
212X ILE* 4.6 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 6.0 0.2 - - + -
238A ASP* 3.2 23.1 + - + +
239A VAL* 3.1 30.0 + - + +
241A THR* 1.3 73.5 - - - +
243A LEU* 1.4 58.2 + - - +
245A ILE* 3.2 13.1 + - + +
246A LEU* 2.9 29.3 + - - +
245B ILE* 4.9 14.6 - - - -
246B LEU* 3.9 15.4 - - + +
249B VAL* 4.5 20.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
239A VAL* 3.0 30.0 + - + +
240A ALA* 3.5 8.1 - - - +
242A MET* 1.4 74.3 - - - +
244A ASN* 1.4 56.5 + - - +
246A LEU* 3.5 1.6 + - - -
247A ALA* 2.9 28.6 + - - +
262A LEU* 3.6 38.4 - - + +
265A ASP* 4.0 4.9 - - + -
266A ALA* 4.1 8.7 - - + +
269A ILE* 3.7 29.4 - - + -
246B LEU* 3.8 17.2 - - + +
249B VAL* 5.6 1.3 - - + -
250B TYR* 3.3 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA 2.7 20.7 + - - +
241A THR* 3.4 11.2 - - - +
243A LEU* 1.4 70.8 - - - +
245A ILE* 1.4 62.0 + - - +
247A ALA* 3.3 12.0 + - - +
248A LEU* 3.4 20.6 + - - +
263A LEU* 3.4 27.3 - - - +
266A ALA* 4.7 0.2 - - - +
270A ARG* 3.1 25.3 - - - +
284A THR* 4.2 2.2 + - - -
287A ASN* 5.2 3.9 + - - +
207X TRP* 5.4 5.7 + - - -
211X ALA* 3.5 20.3 - - - +
212X ILE* 3.9 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 2.8 40.9 + - + +
242A MET* 3.2 10.5 + - + +
244A ASN* 1.4 71.4 - - - +
246A LEU* 1.3 64.2 + - + +
248A LEU* 3.5 22.6 + - + +
249A VAL* 3.6 10.8 + - + +
242B MET* 5.2 15.7 - - + -
212X ILE* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A MET 2.9 16.7 + - - +
243A LEU 3.7 4.0 - - - +
245A ILE* 1.3 76.8 - - + +
247A ALA* 1.4 62.7 + - - +
248A LEU 3.3 0.7 - - - -
249A VAL* 3.3 24.8 + - + +
250A TYR* 3.3 23.1 + - + -
262A LEU* 4.0 8.3 - - + -
239B VAL 4.7 0.9 - - - +
242B MET* 4.1 23.6 - - + -
243B LEU* 3.6 43.7 - - + -
246B LEU* 3.6 30.1 - - + -
262B LEU* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU 2.9 15.2 + - - +
244A ASN 3.3 11.4 + - - +
246A LEU* 1.4 75.3 - - - +
248A LEU* 1.4 56.5 + - + +
250A TYR 3.3 1.2 + - - -
251A ARG* 2.9 29.5 + - - +
259A ALA* 3.6 19.9 - - + +
262A LEU* 4.4 9.0 - - + -
263A LEU* 3.8 33.0 - - + -
207X TRP* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 3.4 23.1 + - - +
245A ILE* 3.6 17.0 - - + +
246A LEU 3.3 0.2 - - - -
247A ALA* 1.4 74.7 - - - +
249A VAL* 1.3 59.2 + - + +
251A ARG* 3.5 37.0 - - - +
252A ASP* 3.0 37.6 + - - +
207X TRP* 3.5 27.1 - - + +
209X ASP* 5.4 2.9 - - - +
212X ILE* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.6 13.7 + - + +
246A LEU* 3.3 28.2 + - + +
247A ALA 3.3 0.2 - - - -
248A LEU* 1.3 78.3 - - - +
250A TYR* 1.4 66.5 + - + +
252A ASP* 3.5 5.7 + - - +
253A GLN* 3.3 25.2 + - + +
239B VAL* 3.6 33.9 - - + -
242B MET* 4.8 14.4 - - - -
243B LEU* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.3 22.8 + - + -
247A ALA 3.3 6.5 + - - +
249A VAL* 1.4 78.7 - - + +
251A ARG* 1.4 60.9 + - - +
253A GLN* 3.1 10.0 + - - +
255A LYS* 2.9 68.5 + - + +
258A ASP* 3.6 31.9 - - + -
259A ALA* 3.8 8.3 - - + +
262A LEU* 3.7 24.5 - - + -
243B LEU* 3.4 34.2 - - + +
261B HIS 5.5 0.2 - - - -
262B LEU* 3.7 12.0 - - + +
265B ASP* 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA 2.9 17.9 + - - +
248A LEU* 3.5 26.7 + - - +
250A TYR* 1.4 74.6 - - - +
252A ASP* 1.3 83.5 + - - +
254A ASN* 2.9 27.0 + - - +
255A LYS 4.8 1.1 - - - +
256A TYR* 4.0 10.3 - - + -
259A ALA* 3.9 7.7 - - + +
290A VAL* 6.0 0.7 - - + -
291A LEU* 4.1 22.2 - - + -
294A LYS* 6.1 3.6 - - - -
207X TRP* 3.3 59.7 - - + +
209X ASP* 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.0 14.9 + - - +
249A VAL* 3.9 6.5 - - - +
250A TYR 3.3 0.4 - - - -
251A ARG* 1.3 116.8 + - - +
253A GLN* 1.3 59.8 + - - +
254A ASN* 3.2 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 3.3 14.2 + - + +
250A TYR* 3.1 10.0 + - - +
252A ASP* 1.3 76.9 - - - +
254A ASN* 1.3 69.6 + - - +
255A LYS* 3.2 40.2 + - + +
236B HIS* 5.7 7.6 + - - -
269B ILE* 5.6 5.5 - - - +
----------------------------------------------------------
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