Contacts of the helix formed by residues 393 - 397 (chain E) in PDB entry 3SZ9
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 MET 393 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E GLU* 3.3 37.0 - - + +
364E GLY 3.8 6.3 - - - +
365E ALA* 3.6 35.7 - - - +
388E ASP 4.1 4.5 - - - +
389E VAL* 4.0 4.9 - - - -
390E GLN* 3.0 51.7 + - + +
392E GLY* 1.3 79.6 - - - +
394E THR* 1.3 66.3 + - - +
395E ILE* 4.2 12.8 - - + +
396E ALA* 3.0 14.5 + - + +
397E LYS* 3.3 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 394 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E TYR* 3.9 16.8 - - + -
359E THR* 3.6 18.5 - - + +
363E GLU* 2.6 33.6 + - - -
392E GLY 3.7 1.6 + - - -
393E MET* 1.3 70.5 - - - +
395E ILE* 1.3 57.8 + - - +
397E LYS* 2.9 13.7 + - - +
398E GLU* 2.9 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LYS* 2.6 28.7 + - - +
356E TYR* 3.5 31.6 - - + +
359E THR* 4.9 2.5 - - - -
360E GLY* 3.8 16.8 - - - +
363E GLU* 4.6 0.4 + - - +
365E ALA* 3.8 19.3 - - + -
386E PHE* 3.6 41.1 - - + -
389E VAL* 4.1 5.6 - - + -
393E MET* 4.2 13.7 - - + -
394E THR* 1.3 76.7 - - - +
396E ALA* 1.3 55.3 + - - +
397E LYS 3.3 0.2 - - - -
398E GLU 4.9 0.7 - - - -
400E ILE* 4.0 23.3 - - + -
406E GLN* 3.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LYS* 3.6 10.8 - - - +
307E ARG* 3.4 28.8 + - + -
389E VAL* 3.8 15.9 - - + -
390E GLN 3.4 25.8 - - - +
391E ASP* 3.8 12.4 - - - +
393E MET 3.0 7.1 + - - +
395E ILE* 1.3 79.5 - - - +
397E LYS* 1.3 61.6 + - - +
406E GLN* 4.7 0.9 - - - -
408E LEU* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 397 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LYS* 4.0 10.8 - - - +
391E ASP 3.5 22.0 - - - +
392E GLY* 3.2 26.7 + - - +
393E MET 3.5 7.0 - - - +
394E THR* 2.9 10.6 + - - +
396E ALA* 1.3 80.5 - - - +
398E GLU* 1.3 70.2 + - + +
425E TYR* 4.0 16.6 - - - -
----------------------------------------------------------
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