Contacts of the helix formed by residues 364 - 378 (chain A) in PDB entry 6EJ9
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 364 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A HIS* 3.7 11.9 - - - +
336A GLY* 3.1 38.6 + - - -
337A ARG* 6.3 1.3 - - - +
360A VAL* 3.5 15.4 - - - +
361A ASP* 2.9 14.3 + - - +
362A LYS 3.3 0.4 - - - -
363A ARG* 1.3 78.5 + - - +
365A ASN* 1.3 64.1 + - - +
366A TYR 3.4 2.9 - - - -
367A LEU* 3.4 3.6 + - - -
368A HIS 3.1 16.6 + - - -
387A ARG* 3.5 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 6.1 0.2 - - - +
362A LYS* 3.5 13.1 + - - +
363A ARG 3.6 4.7 + - - -
364A SER* 1.3 72.9 - - - +
366A TYR* 1.3 65.8 + - - +
368A HIS* 3.2 4.2 + - - +
369A ARG* 3.1 33.1 + - + +
387A ARG* 3.1 29.7 + - - +
639A ASP* 3.7 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 3.7 55.0 - - - +
339A SER* 3.3 26.9 + - - -
364A SER 3.4 0.8 - - - -
365A ASN* 1.3 79.3 - - - +
367A LEU* 1.3 65.8 + - - +
369A ARG* 3.2 25.7 + - - +
370A GLN* 3.2 46.2 + - + +
633A ASN* 3.3 40.0 + - + +
636A ASP* 3.7 26.7 - - + -
639A ASP* 4.0 5.5 + - - +
687A HIS* 4.9 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 3.8 24.0 - - + -
335A HIS* 3.7 25.8 - - - +
336A GLY 3.5 26.3 + - - +
337A ARG 5.1 0.7 - - - -
338A ALA 4.7 2.5 - - - +
339A SER* 3.7 35.9 - - - +
342A LEU* 4.2 16.4 - - + -
360A VAL* 4.3 4.5 - - + -
364A SER* 3.4 9.9 + - - +
365A ASN 3.3 0.4 - - - -
366A TYR* 1.3 85.4 - - + +
368A HIS* 1.3 63.3 + - - +
370A GLN* 3.2 4.7 + - + +
371A VAL* 2.9 34.0 + - + +
424A ALA* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A VAL* 3.8 24.0 - - + +
364A SER 3.1 14.9 + - - +
365A ASN 3.2 8.7 + - - +
367A LEU* 1.3 76.1 - - - +
369A ARG* 1.3 60.5 + - - +
371A VAL* 3.1 4.5 + - + +
372A LEU* 2.9 60.7 + - + +
383A VAL* 4.6 14.7 - - + +
384A THR 4.9 3.8 + - - -
387A ARG* 3.7 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASN* 3.1 18.8 + - - +
366A TYR* 3.6 18.4 - - - +
368A HIS* 1.3 79.9 - - - +
370A GLN* 1.3 69.1 + - - +
372A LEU* 3.4 22.1 + - + +
373A GLN* 3.5 16.8 + - - +
376A ARG* 5.4 0.3 + - - -
636A ASP* 2.8 32.7 + - - +
638A PRO* 3.7 24.8 - - - +
639A ASP* 3.0 40.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 4.1 17.5 + - - -
343A GLN* 4.5 16.0 + - - +
366A TYR* 3.4 53.1 + - + +
367A LEU* 3.2 7.6 + - + +
368A HIS 3.2 0.8 - - - -
369A ARG* 1.3 84.6 + - - +
371A VAL* 1.3 61.8 + - + +
373A GLN* 3.3 24.1 + - - +
374A VAL* 3.6 10.8 + - - +
636A ASP* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.1 26.5 - - + -
358A ILE* 3.7 35.7 - - + -
360A VAL* 4.1 17.9 - - + -
367A LEU* 2.9 26.2 + - + +
368A HIS* 3.6 5.2 - - + +
370A GLN* 1.3 73.5 - - + +
372A LEU* 1.3 66.7 + - - +
374A VAL* 3.0 18.7 + - + +
375A SER* 3.1 11.3 + - - -
383A VAL* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A HIS* 2.9 43.1 + - + +
369A ARG* 3.6 17.3 - - + +
370A GLN 3.3 0.2 - - - -
371A VAL* 1.3 76.8 - - - +
373A GLN* 1.3 61.2 + - - +
375A SER* 3.0 21.0 + - - +
376A ARG* 3.1 49.0 + - + +
383A VAL* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG 3.5 12.8 + - - +
370A GLN* 3.3 16.5 + - - +
371A VAL 3.2 0.8 - - - -
372A LEU* 1.3 77.9 - - - +
374A VAL* 1.3 62.5 + - + +
376A ARG* 2.9 35.3 + - - +
377A GLN* 3.3 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLN* 4.8 19.3 - - + +
346A PHE* 3.8 40.2 - - + -
358A ILE* 5.3 3.4 - - + -
370A GLN 3.8 13.2 - - - +
371A VAL* 3.0 13.6 + - + +
373A GLN* 1.3 76.5 - - + +
375A SER* 1.3 66.1 + - - +
376A ARG 3.1 0.2 - - - -
377A GLN* 3.0 18.7 + - - +
378A TYR* 3.3 23.2 + - + +
381A VAL* 4.3 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL 3.1 5.2 + - - -
372A LEU* 3.0 25.8 + - - +
374A VAL* 1.3 76.6 - - - +
376A ARG* 1.3 62.1 + - - +
378A TYR 3.2 16.8 - - - +
381A VAL* 3.6 31.5 - - - +
382A ARG* 4.4 2.7 - - - -
383A VAL* 3.7 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG 5.4 0.4 + - - -
372A LEU* 3.1 51.7 + - + +
373A GLN* 2.9 37.9 + - - +
374A VAL 3.1 0.2 - - - -
375A SER* 1.3 81.2 - - - +
377A GLN* 1.3 60.7 + - + +
378A TYR 3.5 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLN* 3.3 31.6 + - - +
374A VAL* 3.0 11.9 + - - +
376A ARG* 1.3 80.8 - - + +
378A TYR* 1.3 94.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 4.4 12.5 - + - -
350A TYR* 4.1 20.9 - + - +
374A VAL* 3.3 32.3 + - + -
375A SER 3.2 16.2 - - - +
376A ARG 3.5 0.6 - - - -
377A GLN* 1.3 112.3 + - + +
379A SER* 1.3 63.9 + - - +
380A ASN* 3.3 15.9 - - - +
381A VAL* 3.4 24.3 + - + +
----------------------------------------------------------
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