Contacts of the helix formed by residues 300 - 311 (chain F) in PDB entry 4G7Z
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 300 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F GLU* 4.4 5.2 - - - +
292F ALA* 3.3 8.3 - - - -
298F GLY 4.0 3.7 + - - -
299F TRP* 1.3 72.6 - - - +
301F ALA* 1.3 65.5 + - - +
302F LYS* 3.4 30.5 + - - +
303F ARG* 2.7 38.2 + - - +
304F VAL* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F TYR* 3.8 32.3 - - + +
289F GLU* 3.3 28.6 + - + +
292F ALA* 3.7 0.2 - - - +
300F ASP* 1.3 76.3 - - - +
302F LYS* 1.3 57.5 + - - +
304F VAL* 3.3 2.1 + - - +
305F GLU* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F ASP* 3.2 29.2 + - - +
301F ALA* 1.3 79.1 - - - +
303F ARG* 1.3 60.5 + - - +
305F GLU* 3.7 8.9 - - - +
306F GLU* 3.1 53.6 + - + +
1287N GLU* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 303 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F THR* 5.2 4.9 + - - +
298F GLY* 3.3 27.6 + - - -
299F TRP* 3.5 53.0 - - + +
300F ASP* 2.7 26.4 + - - +
301F ALA 3.2 0.2 - - - -
302F LYS* 1.3 77.3 - - - +
304F VAL* 1.3 60.3 - - - +
306F GLU* 4.0 9.3 - - - +
307F THR* 2.7 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F LEU* 3.9 22.6 - - + +
288F TYR* 3.6 32.5 - - + +
291F ILE* 4.1 19.3 - - + -
292F ALA* 3.6 17.3 - - + +
299F TRP* 3.8 20.6 - - + -
300F ASP 3.1 15.8 + - - +
301F ALA 3.8 4.9 - - - +
303F ARG* 1.3 76.8 - - - +
305F GLU* 1.3 60.9 + - - +
307F THR* 3.7 2.9 + - - -
308F LEU* 3.1 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808C ARG* 2.4 42.0 + - - -
816C LYS 4.5 0.9 - - - +
817C PRO* 4.2 2.1 - - + +
818C GLY* 3.0 30.1 + - - +
819C VAL 4.0 1.6 + - - +
288F TYR* 3.5 43.3 - - + -
301F ALA* 2.9 17.4 + - - +
302F LYS* 3.7 10.1 - - - +
304F VAL* 1.3 75.1 - - - +
306F GLU* 1.3 69.5 + - + +
308F LEU* 3.0 16.2 + - - +
309F LYS* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F LYS* 3.1 46.5 + - + +
303F ARG* 3.5 7.5 + - - +
305F GLU* 1.3 83.2 - - + +
307F THR* 1.3 61.1 + - - +
309F LYS* 3.4 17.6 + - - +
310F ILE* 3.0 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F MET* 5.1 5.8 - - - -
267F THR* 4.6 11.6 - - + +
268F ILE* 3.7 27.8 - - + +
271F LEU* 3.5 28.0 - - + -
299F TRP* 3.7 12.8 - - - -
303F ARG* 2.7 25.9 + - - +
304F VAL 3.8 0.2 - - - -
306F GLU* 1.3 76.0 - - - +
308F LEU* 1.3 58.6 + - - +
310F ILE* 3.3 10.6 + - + +
311F ALA* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817C PRO* 4.3 15.9 - - + -
268F ILE* 5.5 4.5 - - + +
271F LEU* 3.9 21.1 - - + -
288F TYR* 3.9 29.4 - - + -
291F ILE* 5.9 3.6 - - + -
304F VAL* 3.1 22.4 - - + +
305F GLU 3.0 8.1 + - - +
307F THR* 1.3 79.1 - - + +
309F LYS* 1.3 62.8 + - - +
311F ALA* 3.1 18.1 + - + +
312F GLN* 3.3 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 309 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714C ASP* 4.7 16.8 + - - +
715C THR 5.9 0.8 + - - -
716C LYS* 3.5 28.0 - - - +
817C PRO* 4.2 13.6 - - + +
818C GLY* 4.6 14.4 - - - +
305F GLU 3.1 10.3 + - - +
306F GLU* 3.9 20.0 - - - +
307F THR 3.3 0.4 - - - -
308F LEU* 1.3 77.5 - - - +
310F ILE* 1.3 71.7 + - - +
312F GLN* 3.3 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C LYS* 5.7 3.4 - - - +
34D TYR* 3.6 51.9 - - + +
35D ARG* 5.0 10.1 - - + -
258F ILE* 5.6 4.3 - - - +
260F ILE* 3.6 17.0 - - + +
264F MET* 5.0 5.8 - - + -
268F ILE* 4.9 5.2 - - + -
306F GLU* 3.0 26.8 + - + +
307F THR* 3.6 9.4 - - - +
309F LYS* 1.3 87.3 - - - +
311F ALA* 1.3 59.1 + - - +
312F GLN 3.3 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F ARG* 2.6 31.4 + - - +
268F ILE* 3.6 37.7 - - + -
307F THR 3.0 16.1 + - - +
308F LEU* 3.1 12.4 + - + +
310F ILE* 1.3 76.9 - - - +
312F GLN* 1.3 57.9 + - - +
313F GLU* 3.3 3.8 + - - +
----------------------------------------------------------
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