Contacts of the helix formed by residues 358 - 366 (chain D) in PDB entry 3JXI
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 SER 358 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D HIS* 3.5 3.6 - - - -
349D GLU 3.6 15.0 - - - -
351D LEU 4.5 0.4 - - - -
352D LEU* 3.7 17.6 - - - +
356D GLY 4.1 0.2 + - - -
357D LEU* 1.3 74.7 - - - +
359D PRO* 1.3 76.4 - - - +
360D LEU* 3.8 5.7 + - - +
361D MET* 3.1 28.5 + - - +
362D MET* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D THR* 4.6 0.2 - - - +
311D LEU* 3.6 32.1 - - + -
312D HIS* 3.5 27.8 - - + +
315D VAL* 3.8 16.1 - - + +
332D TYR* 3.5 30.1 - - + +
348D LEU 4.9 0.9 - - - +
349D GLU* 3.9 15.3 - - + +
351D LEU 4.2 2.5 - - - +
358D SER* 1.3 86.3 - - - +
360D LEU* 1.3 57.6 + - - +
362D MET* 3.3 3.0 + - + +
363D ALA* 2.8 29.6 + - - +
375D ILE* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D TYR* 4.9 0.6 + - - +
349D GLU* 5.8 0.4 - - - +
358D SER* 3.2 7.2 + - - +
359D PRO* 1.3 78.3 - - - +
361D MET* 1.3 77.5 + - + +
363D ALA* 3.1 6.9 + - - +
364D ALA* 2.9 25.5 + - - +
372D PHE* 3.3 42.9 - - + +
375D ILE* 3.5 43.8 - - + +
376D ILE* 4.0 21.8 - - + -
379D GLU* 4.8 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D LEU* 3.9 21.2 - - + +
358D SER* 3.1 24.4 + - - +
360D LEU* 1.3 101.5 - - + +
362D MET* 1.3 57.3 + - - +
364D ALA* 3.7 11.4 + - + +
365D LYS* 3.1 26.7 + - - +
372D PHE* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ASN* 3.6 9.6 - - - +
312D HIS* 3.0 45.5 - - + +
315D VAL* 3.8 12.6 - - + -
316D ALA* 5.0 5.2 - - - -
353D ASN* 2.9 34.1 - - - +
357D LEU* 3.9 21.9 - - + +
358D SER 2.9 12.9 + - - +
359D PRO* 3.6 4.0 - - + +
361D MET* 1.3 76.3 - - - +
363D ALA* 1.3 55.4 + - - +
365D LYS* 4.2 0.7 - - - -
366D THR* 2.6 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D VAL* 3.5 20.1 - - + +
359D PRO 2.8 14.0 + - - +
360D LEU* 3.4 11.0 - - - +
362D MET* 1.3 76.3 - - - +
364D ALA* 1.3 56.8 + - - +
366D THR* 3.7 1.3 - - - -
367D GLY* 3.1 8.3 + - - -
368D LYS* 2.8 46.2 + - - +
369D ILE* 5.3 0.2 - - - +
371D ILE* 3.9 9.2 - - + -
372D PHE* 3.8 14.3 - - + +
375D ILE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D LEU 2.9 10.5 + - - +
361D MET* 3.9 12.6 - - - +
363D ALA* 1.3 73.6 - - - +
365D LYS* 1.3 66.5 + - - +
366D THR 3.4 0.2 + - - -
367D GLY* 3.5 10.0 + - - -
369D ILE* 5.7 4.4 - - - +
372D PHE* 3.4 33.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ASP* 5.6 3.8 - - - +
357D LEU* 3.7 30.3 - - + -
361D MET 3.1 18.2 + - - +
362D MET* 3.8 6.3 - - - +
363D ALA 3.4 0.2 - - - -
364D ALA* 1.3 77.0 - - - +
366D THR* 1.3 67.5 + - + +
367D GLY 3.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 366 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D VAL* 4.4 0.9 - - - +
357D LEU* 6.1 0.4 - - + -
362D MET* 2.6 33.6 + - + +
365D LYS* 1.3 88.9 - - + +
367D GLY* 1.3 61.0 + - - +
368D LYS* 3.2 34.2 + - - +
----------------------------------------------------------
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