Contacts of the helix formed by residues 290 - 306 (chain I) 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 GLY 290 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288I ALA* 3.6 8.4 - - - +
289I VAL* 1.3 80.0 - - - +
291I ASP* 1.3 68.1 + - - +
292I ALA* 3.8 8.1 - - - -
294I GLY* 3.3 13.3 + - - -
392I ARG* 5.5 1.1 - - - +
393I VAL 2.8 17.5 + - - -
394I ALA* 3.8 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I GLY* 1.3 78.0 - - - +
292I ALA* 1.3 62.1 + - - +
294I GLY* 3.7 2.7 - - - +
295I ASP* 3.6 15.1 - - - +
392I ARG* 3.0 49.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257I PRO* 6.1 5.6 - - + -
289I VAL 4.9 1.3 - - - +
290I GLY* 3.8 5.2 - - - -
291I ASP* 1.3 74.5 + - - +
293I ALA* 1.3 69.4 + - + +
294I GLY 3.0 2.1 + - - -
295I ASP* 3.1 15.8 + - - +
296I ALA* 3.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I VAL* 4.0 17.9 - - + +
257I PRO* 4.9 12.5 - - + +
261I MET* 3.9 23.7 - - + +
288I ALA* 4.1 7.0 - - + -
289I VAL 3.8 18.2 - - - +
290I GLY 3.7 0.8 + - - +
291I ASP* 3.6 1.0 - - - +
292I ALA* 1.3 76.6 - - - +
294I GLY* 1.3 52.7 + - - +
296I ALA* 3.5 3.2 + - - +
297I LEU* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 294 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288I ALA* 3.5 20.6 - - - +
290I GLY 3.3 7.5 + - - -
291I ASP* 4.0 2.0 - - - -
292I ALA 3.0 1.8 + - - -
293I ALA* 1.3 74.4 - - - +
295I ASP* 1.3 66.2 + - - +
297I LEU* 3.4 2.3 + - - +
298I VAL* 3.1 22.0 + - - +
390I VAL* 5.4 1.1 - - - -
392I ARG* 3.3 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 295 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I ASP* 3.6 18.9 - - - +
292I ALA 3.1 7.9 + - - +
294I GLY* 1.3 74.3 - - - +
296I ALA* 1.3 65.9 + - - +
297I LEU 3.2 0.5 + - - -
298I VAL* 3.8 2.5 - - - +
299I SER* 2.9 25.3 + - - -
371I HIS* 5.6 0.3 + - - -
392I ARG* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261I MET* 4.2 21.3 - - + -
292I ALA 3.4 9.8 + - - +
293I ALA* 3.7 7.4 - - - +
294I GLY 3.4 0.4 - - - -
295I ASP* 1.3 79.3 - - - +
297I LEU* 1.3 62.2 + - - +
299I SER* 3.6 5.2 - - - -
300I LYS* 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I VAL* 4.4 13.0 - - + -
261I MET* 4.1 18.6 - - - -
264I ALA* 5.4 0.9 - - + -
265I VAL* 3.9 22.6 - - + +
268I LEU* 4.1 20.2 - - + -
286I ALA* 3.9 26.2 - - + -
288I ALA* 4.3 18.8 - - + -
293I ALA 2.8 21.1 + - - +
294I GLY 3.6 3.8 - - - +
296I ALA* 1.3 75.2 - - - +
298I VAL* 1.3 59.1 + - - +
300I LYS* 3.9 0.9 - - - +
301I MET* 2.8 39.0 + - + +
388I LEU* 6.2 1.6 - - + -
390I VAL* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294I GLY 3.1 15.7 + - - +
295I ASP* 4.0 3.1 - - - +
297I LEU* 1.3 79.8 - - + +
299I SER* 1.3 56.7 + - - +
301I MET* 4.1 5.4 - - - -
302I THR* 2.5 38.0 + - - +
347I VAL* 4.0 23.3 - - + -
368I LEU* 4.1 7.1 - - + +
370I ASP* 3.3 36.8 - - + +
390I VAL* 4.2 22.7 - - + -
392I ARG* 3.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 299 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295I ASP 2.9 17.5 + - - -
296I ALA* 3.6 7.2 - - - -
298I VAL* 1.3 73.6 - - - +
300I LYS* 1.3 68.5 + - - +
302I THR* 3.2 7.9 + - - -
303I GLN* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261I MET* 4.1 27.1 - - + +
262I ASP* 2.7 36.8 + - - +
265I VAL* 3.8 18.3 - - + +
296I ALA* 3.0 20.2 + - - +
299I SER* 1.3 82.8 - - - +
301I MET* 1.3 61.7 + - - +
303I GLN* 3.4 10.7 + - - +
304I ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 301 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I VAL* 3.8 28.6 - - + +
268I LEU* 4.5 11.4 - - - -
269I LEU* 3.4 42.8 - - + -
273I PHE* 4.1 7.0 - - + -
297I LEU* 2.8 25.4 + - + +
298I VAL* 4.3 0.2 - - - -
300I LYS* 1.3 76.9 - - - +
302I THR* 1.3 56.3 + - - +
304I ALA* 3.2 2.7 + - + -
305I MET* 2.9 56.9 + - + +
368I LEU* 4.0 13.2 - - + -
388I LEU* 4.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 302 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I VAL 2.5 22.9 + - - -
299I SER* 3.2 6.7 + - - -
301I MET* 1.3 78.7 - - - +
303I GLN* 1.3 61.8 + - + +
305I MET* 3.6 7.8 + - - +
306I GLN* 2.9 39.2 + - - +
347I VAL* 3.5 23.8 - - + +
348I VAL* 3.9 20.4 - - + -
368I LEU* 3.8 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 303 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I SER* 3.1 19.7 + - - +
300I LYS* 3.5 10.8 - - - +
301I MET 3.2 0.2 - - - -
302I THR* 1.3 73.8 - - + +
304I ALA* 1.3 65.8 + - - +
305I MET 3.3 0.5 + - - -
306I GLN* 3.3 24.0 + - - +
307I LYS* 4.2 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I VAL* 4.2 11.9 - - + -
266I ASN* 6.1 0.2 - - - -
269I LEU* 3.8 33.9 - - + +
300I LYS 3.1 12.9 + - - +
301I MET* 3.8 3.4 - - + +
303I GLN* 1.3 78.3 - - - +
305I MET* 1.3 61.9 + - - +
307I LYS* 3.3 29.1 + - + +
308I LEU* 4.1 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 305 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I LEU* 4.5 2.0 - - - +
273I PHE* 3.6 24.0 - - + -
301I MET* 2.9 47.9 + - + +
302I THR* 3.8 7.0 - - - +
303I GLN 3.2 0.6 - - - -
304I ALA* 1.3 76.2 - - - +
306I GLN* 1.3 65.3 + - - +
308I LEU* 3.1 46.3 + - + +
348I VAL* 4.1 24.5 - - + +
366I GLY* 4.3 4.9 - - - -
367I THR 4.2 4.9 - - - -
368I LEU* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 306 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I THR* 2.9 33.0 + - - +
303I GLN* 3.3 17.6 + - - +
304I ALA 3.3 0.8 - - - -
305I MET* 1.3 77.2 - - - +
307I LYS* 1.3 62.5 + - + +
308I LEU 3.4 5.7 + - - +
348I VAL* 4.6 20.8 - - - +
----------------------------------------------------------
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