Contacts of the helix formed by residues 384 - 396 (chain A) in PDB entry 6DWZ
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 PHE 384 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 5.5 16.6 - - + +
374A LEU* 5.1 4.0 - - + -
380A PRO* 3.9 24.7 - - + -
381A SER* 2.9 14.4 + - - +
383A CYS* 1.3 100.0 - - - +
385A VAL* 1.3 57.9 + - - +
387A PRO* 3.2 22.6 - - + +
388A SER* 2.2 34.7 + - - +
433A PHE* 6.1 0.7 - + - -
436A TYR* 3.9 40.8 - + - -
540A VAL* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A SER* 3.4 29.2 - - - +
374A LEU* 4.0 22.0 - - + -
381A SER 3.7 1.0 + - - +
382A LEU* 2.8 28.9 + - - +
384A PHE* 1.3 79.2 - - - +
386A VAL* 1.3 68.9 - - + +
388A SER* 3.1 6.2 + - - -
389A ILE* 3.0 21.7 + - + +
421A TRP* 3.8 14.5 - - + +
425A LEU* 3.9 7.4 - - + -
429A HIS* 3.6 29.2 - - + +
566A ALA* 4.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU 4.6 0.4 + - - +
383A CYS 4.5 0.6 + - - +
385A VAL* 1.3 79.0 - - + +
387A PRO* 1.4 63.8 - - + +
389A ILE* 2.7 32.9 + - + +
390A LEU* 3.3 22.8 + - + +
425A LEU* 5.1 4.9 - - + -
429A HIS* 3.8 31.9 - - + +
430A TYR* 4.4 11.4 - - + -
433A PHE* 3.7 28.3 - - + -
442A MET* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A CYS 3.4 12.3 - - - +
384A PHE* 3.2 39.9 - - + +
386A VAL* 1.4 90.2 - - + +
388A SER* 1.3 55.4 + - - +
390A LEU* 3.3 20.9 - - + +
391A LYS* 2.8 26.7 + - - +
433A PHE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 3.6 25.8 - - - +
373A GLU* 5.8 3.1 - - - +
374A LEU* 3.9 12.7 - - - +
384A PHE* 2.2 28.8 + - - +
385A VAL 3.2 8.5 - - - -
386A VAL 3.0 0.4 - - - -
387A PRO* 1.3 77.9 - - - +
389A ILE* 1.3 53.9 + - - +
391A LYS* 2.7 14.3 + - - +
392A VAL* 2.6 40.1 + - - +
421A TRP* 4.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 3.0 17.5 + - + +
386A VAL* 2.7 19.0 + - + +
388A SER* 1.3 69.2 - - - +
390A LEU* 1.3 62.9 + - + +
392A VAL* 2.8 26.4 + - - +
393A LYS* 2.9 15.8 + - + +
417A VAL* 3.6 21.5 - - + +
421A TRP* 3.5 46.7 - - + +
422A GLU* 3.7 23.6 - - + +
425A LEU* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 3.3 29.2 - - + +
387A PRO* 3.3 28.3 - - + +
389A ILE* 1.3 79.2 - - + +
391A LYS* 1.3 55.2 + - - +
393A LYS* 3.2 20.2 + - + +
394A GLU* 2.9 47.7 + - + +
422A GLU* 5.9 1.1 - - - +
433A PHE* 5.5 1.3 - - + -
441A HIS* 5.2 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLY* 4.1 14.5 + - - -
369A ARG* 4.7 10.1 - - - +
370A ILE* 3.7 27.1 - - + +
373A GLU* 4.4 18.3 + - - -
387A PRO 2.8 17.6 + - - +
388A SER* 2.7 18.8 + - - +
390A LEU* 1.3 77.2 - - - +
392A VAL* 1.3 56.2 + - - -
394A GLU* 3.1 10.7 + - + +
395A ILE* 2.8 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.5 6.5 - - + -
274A LEU* 5.4 0.4 - - + -
367A PHE* 3.4 35.4 - - + -
370A ILE* 4.2 12.1 - - + -
388A SER 2.6 25.3 + - - +
389A ILE 2.8 7.8 + - - +
391A LYS* 1.3 69.5 - - - +
393A LYS* 1.3 65.8 + - - +
394A GLU 2.9 1.7 + - - -
395A ILE* 3.0 19.2 + - - +
396A CYS* 3.1 13.0 + - - +
413A ILE* 4.4 5.4 - - + -
417A VAL* 4.3 21.3 - - + -
421A TRP* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 2.9 15.2 + - + +
390A LEU* 3.2 23.1 + - + +
392A VAL* 1.3 73.5 - - - +
394A GLU* 1.3 59.2 + - + +
396A CYS* 3.4 2.9 - - - +
397A SER* 2.9 25.1 + - - -
414A ILE* 4.3 29.1 - - + +
417A VAL* 4.4 15.4 - - + +
418A ARG* 4.2 14.3 - - - +
422A GLU* 3.2 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 2.9 38.1 + - + +
391A LYS* 3.6 9.6 + - + +
392A VAL 2.9 0.6 + - - -
393A LYS* 1.3 79.4 - - + +
395A ILE* 1.3 60.1 + - - +
396A CYS 3.2 1.1 - - - -
397A SER* 2.7 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASN 5.7 0.9 - - - +
363A ILE* 4.5 20.7 - - + +
366A GLY* 4.8 12.3 - - - +
367A PHE* 4.3 20.0 - - + -
370A ILE* 4.4 11.4 - - + -
391A LYS* 2.8 44.0 + - + +
392A VAL* 3.1 19.3 - - + +
394A GLU* 1.3 74.1 - - - +
396A CYS* 1.3 62.3 + - - +
397A SER* 3.3 2.4 + - - -
410A LYS* 3.5 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 5.3 4.7 - - - -
367A PHE* 4.2 11.9 - - - -
392A VAL 3.1 13.7 + - - +
393A LYS 3.4 2.0 - - - -
395A ILE* 1.3 76.9 - - - +
397A SER* 1.3 67.3 + - - +
398A PRO* 3.3 5.4 - - - +
410A LYS* 3.4 32.5 - - - +
413A ILE* 3.6 42.6 - - - -
414A ILE* 3.5 29.1 - - + +
----------------------------------------------------------
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