Contacts of the helix formed by residues 284 - 293 (chain A) in PDB entry 4E2I
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 ASP 284 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A CYS* 3.2 5.6 - - - +
283A ASP* 1.3 82.3 - - - +
285A VAL* 1.3 74.8 + - - +
286A LEU* 2.9 7.4 + - - +
287A LEU* 2.7 46.8 + - + -
288A LEU* 3.1 20.0 - - - +
341A VAL* 3.1 15.4 - - - +
349F ARG* 4.5 1.5 + - - -
516F LYS* 2.9 29.2 - - - +
517F ARG* 3.8 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP* 1.3 78.9 + - - +
286A LEU* 1.3 67.1 + - + +
287A LEU 3.2 0.9 - - - -
288A LEU* 3.3 3.5 + - - +
289A LEU* 3.0 23.0 + - + +
334A LYS* 4.2 31.4 - - + +
337A CYS* 4.3 3.7 - - + +
338A GLN* 3.3 48.2 - - + +
341A VAL* 3.7 15.9 - - + -
514F LEU* 5.2 10.1 - - + -
515F ASN 5.6 4.3 - - - +
516F LYS* 5.1 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP* 2.9 4.7 + - - +
285A VAL* 1.3 78.5 - - - +
287A LEU* 1.3 61.8 + - - +
289A LEU* 3.3 10.6 + - + +
290A GLY* 3.0 18.5 + - - -
334A LYS* 4.6 12.8 - - + -
342F ASP* 3.7 43.1 - - + +
345F LEU* 4.2 25.8 - - + -
346F ALA* 3.5 14.6 - - - +
349F ARG* 3.1 41.2 - - + +
511F LYS* 4.7 2.5 - - + +
516F LYS* 3.7 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A CYS* 3.8 18.4 - - - -
284A ASP* 2.7 31.6 + - + +
286A LEU* 1.3 71.0 - - - +
288A LEU* 1.3 64.7 + - - +
289A LEU 3.2 0.2 + - - -
290A GLY* 3.3 1.4 + - - -
291A MET* 3.1 44.5 + - + +
349F ARG* 3.5 29.7 - - + +
350F VAL* 4.4 4.6 - - - +
353F LEU* 3.8 28.5 - - + -
517F ARG* 3.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 5.1 4.7 - - + +
276A TYR* 4.1 22.0 - - + -
277A ALA* 3.8 21.8 - - + -
280A THR* 4.6 0.2 - - - +
282A CYS* 3.5 29.2 - - + +
284A ASP 3.1 15.8 + - - +
285A VAL 3.3 3.9 + - - +
287A LEU* 1.3 78.1 - - - +
289A LEU* 1.3 61.9 + - - +
291A MET* 4.1 3.5 - - + +
292A TYR* 3.3 22.9 + - - +
337A CYS* 3.4 23.6 - - + +
340A ALA* 3.4 33.2 - - + -
341A VAL* 3.9 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A VAL* 3.0 14.0 + - + +
286A LEU* 3.4 15.0 - - + +
287A LEU 3.1 0.2 - - - -
288A LEU* 1.3 74.0 - - - +
290A GLY* 1.3 66.2 + - - +
292A TYR* 3.3 3.6 + - - +
293A LEU* 3.0 38.0 + - + +
327A PHE* 3.7 17.0 - - + -
333A GLN* 3.2 38.4 - - + +
334A LYS* 4.6 13.5 - - + +
337A CYS* 3.6 9.4 - - + -
339F GLN* 5.5 0.9 - - + +
342F ASP* 4.0 38.1 - - + +
343F THR* 4.5 3.4 - - - +
346F ALA* 4.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU 3.0 8.7 + - - -
289A LEU* 1.3 79.8 - - - +
291A MET* 1.3 64.0 + - - +
293A LEU* 3.1 19.2 + - - +
294A GLU* 3.5 14.9 - - - +
346F ALA* 3.6 20.9 - - - -
347F LYS* 5.0 0.9 - - - -
350F VAL* 3.8 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TYR* 3.8 22.4 - - + +
282A CYS* 5.9 0.9 - - - -
287A LEU* 3.1 34.5 + - + +
288A LEU* 4.1 5.6 - - - +
290A GLY* 1.3 75.0 - - - +
292A TYR* 1.3 60.2 + - - +
294A GLU* 3.5 18.4 + - - +
295A PHE* 3.1 22.1 - - + -
310A GLN* 5.3 2.7 - - + +
312A SER* 3.1 32.5 - - - +
313A HIS* 5.5 2.5 - - + -
350F VAL* 3.5 29.7 - - + +
353F LEU* 6.3 0.7 - - - -
354F GLN* 3.8 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 4.1 1.9 - - - +
273A VAL* 3.5 31.9 - - + +
276A TYR* 3.6 27.6 - + + -
288A LEU 3.3 16.6 + - - +
289A LEU 3.3 4.4 + - - +
290A GLY 3.2 0.6 - - - -
291A MET* 1.3 74.7 - - - +
293A LEU* 1.3 57.2 + - - +
294A GLU 3.1 9.4 + - - -
295A PHE* 3.3 25.0 + + - +
320A HIS* 3.4 49.4 + + + +
323A ASN* 2.8 31.2 + - - +
324A ALA* 3.9 14.0 - - + +
327A PHE* 3.7 32.5 - + + -
337A CYS* 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 3.0 43.7 + - + +
290A GLY* 3.1 12.9 + - - +
292A TYR* 1.3 76.3 - - - +
294A GLU* 1.3 58.9 + - - +
295A PHE 3.3 0.9 - - - -
296A GLN* 3.2 44.5 - - - +
297A TYR* 3.7 9.7 + - - -
327A PHE* 3.5 26.9 - - + -
328A ALA* 4.9 0.2 - - - -
333A GLN* 3.8 18.8 - - - +
274F THR* 6.4 0.2 - - + -
278F MET* 6.2 2.2 - - + -
343F THR* 3.6 32.1 - - + -
346F ALA* 4.8 0.4 - - + -
----------------------------------------------------------
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