Contacts of the helix formed by residues 311 - 322 (chain E) in PDB entry 5KRA
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 311 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 4.4 30.5 - - + +
309E SER 5.0 2.9 - - - +
310E LEU* 1.3 76.9 - - - +
312E ALA* 1.3 58.9 + - - +
313E ASP* 3.5 7.7 + - - +
314E GLN* 3.2 40.8 + - - +
315E MET* 2.9 27.5 + - - +
481E LYS* 4.4 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E THR* 1.3 74.2 - - - +
313E ASP* 1.3 62.4 + - - +
315E MET* 3.1 9.0 + - - +
316E VAL* 3.0 28.8 + - - +
481E LYS* 5.0 4.9 - - - +
484E ASP* 5.0 1.8 - - + +
485E THR* 3.9 14.1 - - - +
488E HIS* 3.3 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E THR* 3.3 7.2 + - - +
312E ALA* 1.3 79.6 - - - +
314E GLN* 1.3 59.0 + - + +
316E VAL* 3.5 7.8 + - - +
317E SER* 3.0 32.6 + - - +
488E HIS* 3.1 22.6 + - - -
492E LYS* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 5.9 1.6 - - - +
464B SER* 3.9 33.0 - - - +
309E SER 4.9 0.7 - - - +
310E LEU* 3.4 27.5 - - + +
311E THR* 3.2 42.6 + - - +
313E ASP* 1.3 76.2 - - + +
315E MET* 1.3 61.1 + - - +
317E SER* 3.9 6.1 - - - -
318E ALA* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E ALA* 3.5 28.5 - - + +
310E LEU* 4.4 8.0 - - + +
311E THR 2.9 13.9 + - - +
312E ALA* 3.1 8.9 + - - +
314E GLN* 1.3 74.9 - - - +
316E VAL* 1.3 65.1 + - - +
318E ALA* 3.3 3.3 + - - +
319E LEU* 3.1 44.9 + - + +
365E PRO* 4.1 31.9 - - + +
447E CYS* 5.7 0.2 - - - -
478E VAL* 5.7 2.0 - - + -
481E LYS* 4.0 19.5 - - + +
482E ILE* 5.0 13.9 - - + -
485E THR* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ALA 3.0 16.4 + - - +
313E ASP* 3.7 10.3 - - - +
314E GLN 3.4 0.2 - - - -
315E MET* 1.3 76.8 - - - +
317E SER* 1.3 57.4 + - - +
319E LEU* 3.2 9.6 + - - +
320E LEU* 2.9 39.7 + - + +
443E GLU* 3.6 33.4 - - + +
446E VAL* 5.3 1.6 - - + -
447E CYS* 5.1 1.8 - - - -
485E THR* 3.6 20.4 - - + -
488E HIS* 5.5 0.4 - - + -
489E LEU* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B THR* 6.4 2.0 - - - -
313E ASP* 3.0 18.4 + - - +
314E GLN* 3.9 7.3 - - - -
315E MET 3.3 0.2 - - - -
316E VAL* 1.3 77.1 - - - +
318E ALA* 1.3 56.7 + - - +
320E LEU* 3.4 10.0 + - - +
321E ASP* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B SER 5.3 3.4 - - - +
465B THR* 5.9 4.9 - - + -
466B LEU* 4.9 11.7 - - + -
310E LEU* 4.6 7.2 - - + -
314E GLN 3.1 18.8 + - - +
315E MET* 3.6 5.8 - - - +
316E VAL 3.2 0.2 - - - -
317E SER* 1.3 77.8 - - - +
319E LEU* 1.3 61.8 + - - +
321E ASP* 3.6 5.7 + - - +
322E ALA* 3.2 23.0 + - - +
363E ARG* 4.2 7.6 + - - +
365E PRO* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E MET* 3.1 36.8 + - + +
316E VAL* 3.2 4.4 + - - +
318E ALA* 1.3 73.8 - - - +
320E LEU* 1.3 65.8 + - - +
322E ALA* 3.1 15.0 + - + +
323E GLU* 3.4 14.9 + - - +
360E TRP* 5.0 4.1 + - - +
363E ARG 5.4 0.2 - - - +
364E VAL* 4.4 10.1 - - + -
365E PRO* 3.7 27.4 - - + -
446E VAL* 3.8 39.2 - - + +
447E CYS* 4.2 20.0 - - - -
450E SER* 3.4 21.8 - - - +
482E ILE* 5.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E VAL* 2.9 39.0 + - + +
317E SER* 3.8 8.3 - - - +
318E ALA 3.4 0.2 - - - -
319E LEU* 1.3 77.2 - - - +
321E ASP* 1.3 61.5 + - - +
322E ALA 3.1 0.2 - - - -
323E GLU* 3.2 25.9 + - + +
442E GLY* 4.3 15.0 - - - +
443E GLU* 4.4 14.8 - - + +
446E VAL* 4.1 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E SER 3.0 17.3 + - - +
318E ALA* 4.0 6.1 - - - +
320E LEU* 1.3 76.0 - - - +
322E ALA* 1.3 59.6 + - - +
323E GLU 3.3 3.4 + - - +
363E ARG* 3.5 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E ALA 3.2 16.3 + - - +
319E LEU* 3.1 9.6 + - - +
320E LEU 3.1 0.8 - - - -
321E ASP* 1.3 77.2 - - - +
323E GLU* 1.3 66.7 + - - +
324E PRO* 3.3 1.2 - - - +
360E TRP* 3.1 31.7 - - + +
363E ARG* 3.5 43.4 - - + +
364E VAL* 4.9 1.8 - - + +
----------------------------------------------------------
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