Contacts of the helix formed by residues 395 - 406 (chain G) 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 THR 395 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487E ARG 4.0 11.8 + - - -
488E GLU* 4.9 6.0 - - - +
289G VAL* 3.6 9.9 - - - -
393G VAL* 3.7 5.7 - - - +
394G ALA* 1.3 76.2 - - + +
396G MET* 1.3 75.2 + - - +
397G GLN* 3.4 13.9 + - + +
398G ASP* 3.0 44.8 + - - +
399G ALA 3.2 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487E ARG* 3.7 35.4 + - + +
254G ILE* 4.5 8.3 - - + -
256G MET* 3.7 37.9 - - + +
289G VAL* 3.6 11.2 - - - +
395G THR* 1.3 76.3 + - - +
397G GLN* 1.3 56.1 + - - +
399G ALA* 2.9 24.9 + - - +
400G MET* 2.9 37.3 + - + +
414G ILE* 3.8 14.4 - - + -
421G ALA* 3.5 32.3 - - + +
424G TYR* 4.4 4.5 - - + -
425G PHE* 3.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 397 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487E ARG* 4.1 11.8 + - - +
395G THR* 3.3 14.3 + - + +
396G MET* 1.3 77.6 - - - +
398G ASP* 1.3 59.4 + - - +
400G MET* 3.2 17.1 + - + +
401G ASP* 2.7 68.4 + - - +
424G TYR* 3.1 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 398 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G VAL* 4.1 18.0 - - + +
394G ALA* 3.5 19.6 + - - +
395G THR* 3.0 31.0 + - - +
397G GLN* 1.3 75.0 - - - +
399G ALA* 1.3 66.2 + - - +
401G ASP* 3.6 12.1 + - - +
402G LEU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 399 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G ILE* 3.7 26.0 - - + -
287G VAL* 3.5 33.0 - - + +
289G VAL* 5.4 1.1 - - + -
393G VAL* 4.0 8.4 - - + +
395G THR 3.2 3.2 + - - +
396G MET* 2.9 16.7 + - - +
398G ASP* 1.3 79.2 - - - +
400G MET* 1.3 59.9 + - - +
402G LEU* 3.1 7.3 + - - +
403G ILE* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 400 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487E ARG* 5.3 0.9 - - - +
254G ILE* 3.9 7.4 - - + -
396G MET* 2.9 29.1 + - + +
397G GLN* 3.7 32.5 - - - +
399G ALA* 1.3 76.0 - - - +
401G ASP* 1.3 57.8 + - - +
403G ILE* 3.3 3.3 + - - +
404G ASP* 3.0 37.4 + - - +
424G TYR* 3.5 32.1 - - + +
425G PHE* 3.8 39.9 - - + +
428G ASN* 5.3 5.2 - - - -
429G ILE* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 401 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397G GLN* 2.7 52.2 + - - +
398G ASP* 3.9 11.7 - - - +
400G MET* 1.3 76.0 - - - +
402G LEU* 1.3 57.3 + - - +
404G ASP* 3.9 8.0 - - - +
405G ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252G HIS* 4.7 1.6 - - + +
287G VAL* 4.3 17.5 - - + -
374G PRO* 3.8 31.2 - - + -
379G TYR* 3.2 31.8 + - + +
391G VAL* 3.7 34.8 - - + -
393G VAL* 4.6 8.1 - - + -
398G ASP 3.1 14.8 + - - +
399G ALA 3.1 8.5 + - - +
401G ASP* 1.3 75.8 - - - +
403G ILE* 1.3 65.1 + - - +
405G ALA* 3.4 10.0 + - + +
406G HIS* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G LYS 6.0 0.2 - - - +
252G HIS* 3.5 41.3 - - + +
254G ILE* 4.1 24.0 - - + -
287G VAL* 5.1 2.0 - - + -
399G ALA 3.0 18.7 + - - +
400G MET 3.7 5.4 - - - +
402G LEU* 1.3 75.9 - - - +
404G ASP* 1.3 58.7 + - - +
406G HIS* 3.0 24.7 + - - +
408G TYR 4.4 2.3 - - - +
409G GLY* 6.2 0.2 - - - -
412G THR* 3.6 21.8 - - - +
425G PHE* 4.3 0.4 - - + -
429G ILE* 3.9 18.6 - - + -
431G VAL* 3.7 30.5 - - + -
453G LYS* 3.4 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 404 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400G MET* 3.0 23.6 + - - +
401G ASP* 3.9 9.1 - - - +
403G ILE* 1.3 75.8 - - - +
405G ALA* 1.3 58.5 + - - +
406G HIS 3.7 0.5 - - - +
428G ASN 4.4 6.9 - - - +
429G ILE* 3.8 8.1 - - - +
430G GLN* 3.0 45.5 + - + +
453G LYS* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401G ASP 3.0 19.1 + - - +
402G LEU* 3.6 12.6 - - + +
403G ILE 3.2 0.2 - - - -
404G ASP* 1.3 75.1 - - - +
406G HIS* 1.3 64.7 + - - +
407G GLU* 3.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 406 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G LYS* 3.4 26.0 - - + +
252G HIS* 4.2 15.3 - + + -
379G TYR* 3.2 52.7 + + - -
380G GLN* 3.2 25.2 + - + -
402G LEU 3.3 7.2 + - - +
403G ILE* 3.0 15.4 + - + +
404G ASP 3.7 0.5 - - - +
405G ALA* 1.3 81.6 - - - +
407G GLU* 1.3 77.1 + - + +
408G TYR* 3.4 24.8 + + - +
453G LYS* 2.9 24.6 + - - +
----------------------------------------------------------
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