Contacts of the helix formed by residues 260 - 274 (chain E) in PDB entry 4ZZ7
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 260 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ASP 4.0 0.8 + - - -
259E ALA* 1.3 73.1 - - - +
261E MET* 1.3 63.8 + - - +
262E ASP* 3.3 17.8 + - - +
263E ASN* 3.2 31.4 + - + +
264E ALA* 3.1 21.0 + - - +
415E PHE* 5.8 0.3 - - - +
417E ARG* 5.1 4.4 - - - +
482F PRO* 6.2 0.2 - - + -
483F SER* 3.6 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 261 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E VAL* 3.8 25.1 - - + -
256E MET 5.2 3.8 - - - +
257E PRO* 5.9 2.2 - - + +
259E ALA* 3.5 9.2 + - - +
260E ASP* 1.3 74.1 + - - +
262E ASP* 1.3 57.9 + - - +
264E ALA* 3.4 4.5 + - - +
265E VAL* 3.0 38.2 + - + +
293E ALA* 4.0 29.2 - - + +
296E ALA* 4.3 14.1 - - + -
297E LEU* 3.7 39.7 - - - +
300E LYS* 4.1 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 262 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E ASP* 3.2 14.6 + - - +
261E MET* 1.3 77.0 - - - +
263E ASN* 1.3 62.6 + - - +
264E ALA 3.3 0.2 + - - -
265E VAL* 3.3 4.8 + - - +
266E ASN* 3.1 27.0 + - - +
300E LYS* 2.6 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E ASP* 3.2 27.6 + - + +
262E ASP* 1.3 77.8 - - - +
264E ALA* 1.3 61.8 + - - +
266E ASN* 4.2 7.0 - - - +
267E GLN* 3.2 50.6 + - - +
415E PHE* 5.0 2.9 - - - -
437E ASN* 5.0 3.1 - - - +
480F ARG* 3.7 19.6 + - - +
482F PRO* 3.6 27.1 - - + +
483F SER* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E VAL* 4.4 14.1 - - + -
260E ASP 3.1 16.6 + - - +
261E MET* 3.6 11.0 - - - +
262E ASP 3.2 0.2 - - - -
263E ASN* 1.3 75.6 - - - +
265E VAL* 1.3 59.5 + - + +
267E GLN* 3.5 2.1 + - - +
268E LEU* 2.8 40.3 + - + +
297E LEU* 5.3 0.4 - - + -
415E PHE* 4.1 37.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E MET* 3.0 24.3 + - + +
262E ASP* 3.3 3.8 + - - +
264E ALA* 1.3 73.9 - - - +
266E ASN* 1.3 66.5 + - - +
268E LEU* 3.1 8.3 + - - +
269E LEU* 3.1 22.7 + - - +
297E LEU* 4.0 29.8 - - + +
300E LYS* 3.9 29.2 - - + +
301E MET* 3.8 27.6 - - + +
304E ALA* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ASP 3.1 16.9 + - - +
263E ASN* 4.2 7.7 - - - +
265E VAL* 1.3 77.8 - - - +
267E GLN* 1.3 65.8 + - + +
269E LEU* 3.2 32.7 - - - +
270E GLY 3.8 2.8 + - - -
304E ALA* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E ASN* 3.2 41.0 + - - +
264E ALA 3.9 2.2 - - - +
266E ASN* 1.3 82.4 - - + +
268E LEU* 1.3 62.2 + - - +
269E LEU 3.4 0.2 + - - -
270E GLY* 3.5 2.8 + - - +
271E ALA* 3.2 22.2 + - - +
415E PHE* 3.7 19.4 - - + -
437E ASN 3.5 18.6 + - - +
438E ILE* 4.8 3.3 - - - +
439E PRO* 3.5 30.8 - - + +
480F ARG* 3.6 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E ALA* 4.3 7.0 - - + -
255E VAL* 4.7 4.5 - - + -
264E ALA 2.8 24.5 + - - +
265E VAL* 3.1 5.8 + - - +
267E GLN* 1.3 75.8 - - - +
269E LEU* 1.3 58.7 + - - +
271E ALA* 4.3 1.8 - - - -
272E ALA* 2.9 34.1 + - - +
273E PHE* 4.6 0.3 - - - -
283E LEU* 3.9 45.5 - - + +
286E ALA* 4.1 18.4 - - + -
297E LEU* 3.9 28.3 - - + -
301E MET* 4.5 10.5 - - - +
388E LEU* 4.9 10.3 - - + -
415E PHE* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E VAL 3.1 11.2 + - - +
266E ASN* 3.2 27.1 - - - +
268E LEU* 1.3 75.2 - - - +
270E GLY* 1.3 58.4 + - - +
273E PHE* 2.9 48.4 + - + +
274E GLY 3.7 0.5 + - - -
301E MET* 3.3 27.8 - - + +
304E ALA* 3.8 30.7 - - + +
305E MET 4.5 0.2 - - - +
308E LEU* 4.1 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 270 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E ASN 3.8 3.0 + - - -
267E GLN 3.5 5.8 + - - -
268E LEU 3.4 0.2 - - - -
269E LEU* 1.3 79.8 - - - +
271E ALA* 1.3 51.6 + - - +
274E GLY* 2.9 17.2 + - - -
279E ARG* 2.7 29.7 + - - -
440E LEU* 5.1 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E GLN 3.2 16.1 + - - +
268E LEU* 3.9 4.7 - - - +
269E LEU 3.2 0.8 - - - -
270E GLY* 1.3 79.7 - - - +
272E ALA* 1.3 62.2 + - - +
274E GLY 4.5 0.5 + - - +
279E ARG* 3.9 9.4 + - - +
282E ALA* 3.3 13.0 - - - +
283E LEU* 3.2 38.7 + - + -
439E PRO* 3.7 19.7 - - + -
440E LEU* 4.1 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E LEU* 2.9 18.9 + - + +
271E ALA* 1.3 78.5 - - - +
273E PHE* 1.3 71.7 + - + +
277E GLY* 3.2 23.0 - - - -
282E ALA* 4.6 2.1 - - - +
283E LEU 3.4 24.2 + - - +
284E SER* 5.5 0.2 - - - +
385E GLY 4.4 4.9 - - - +
386E PRO* 4.5 0.2 - - - +
387E VAL 4.7 4.7 + - - +
388E LEU* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E LEU 4.7 0.2 - - - -
269E LEU* 2.9 27.5 + - + +
272E ALA* 1.3 81.5 - - + +
274E GLY* 1.3 61.4 + - - +
276E SER* 2.9 24.9 + - - -
277E GLY 3.7 4.0 - - - +
301E MET* 4.2 15.0 - - + -
305E MET* 3.8 37.2 - - + -
308E LEU* 4.0 17.3 - - + -
320E PHE* 3.3 32.7 - - + -
366E GLY* 4.2 5.6 - - - -
367E THR 3.9 15.0 - - - -
386E PRO* 3.8 33.9 - - + -
387E VAL 4.2 0.2 - - - -
388E LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E ASP* 4.4 4.0 - - - -
269E LEU 3.7 1.8 + - - -
270E GLY* 2.9 25.8 + - - -
271E ALA 4.7 0.7 - - - +
272E ALA 3.6 0.6 - - - +
273E PHE* 1.3 76.7 - - - +
275E SER* 1.3 62.6 - - - -
277E GLY* 3.0 18.4 + - - -
279E ARG* 3.3 22.4 + - - -
319E ASP 5.2 2.9 - - - -
320E PHE* 5.0 2.0 - - - -
----------------------------------------------------------
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