Contacts of the helix formed by residues 367 - 380 (chain A) in PDB entry 3DYQ
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 ARG 367 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 4.6 7.4 + - - -
358A THR 5.1 0.8 + - - -
361A LEU* 3.4 39.9 + - - +
362A ALA* 3.9 4.9 - - - +
364A ASP* 2.9 21.7 + - - +
366A ALA* 1.3 81.5 - - + +
368A HIS* 1.3 64.2 + - - +
369A ALA 3.3 2.7 - - - -
370A GLU* 3.1 46.6 + - - +
371A ILE* 2.9 36.6 + - + +
395A MET* 4.1 19.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
364A ASP 4.0 1.0 + - - -
365A MET* 3.0 36.0 + - + +
366A ALA 3.4 1.0 - - - -
367A ARG* 1.3 76.7 - - - +
369A ALA* 1.3 63.3 + - + +
371A ILE* 3.2 1.6 + - - +
372A MET* 2.9 57.0 + - + +
399A LYS* 2.9 34.3 + - - +
403A ILE* 5.1 0.2 - - + -
459A PHE 5.3 1.4 + - - -
460A VAL* 3.7 40.2 + - + +
464A MET* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ALA 5.0 1.4 + - - -
367A ARG 3.3 0.4 - - - -
368A HIS* 1.3 83.9 - - + +
370A GLU* 1.3 57.4 + - - +
372A MET* 3.5 5.5 + - - +
373A ASP* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ARG* 3.1 60.5 + - - +
369A ALA* 1.3 78.8 - - - +
371A ILE* 1.3 64.7 + - - +
373A ASP* 3.3 8.4 + - - +
374A SER* 3.0 32.0 + - - +
395A MET* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA* 3.3 34.1 - - + +
367A ARG* 2.9 37.6 + - + +
368A HIS 3.8 2.7 - - - +
370A GLU* 1.3 83.5 - - - +
372A MET* 1.3 61.3 + - - +
374A SER* 3.2 6.6 + - - -
375A PHE* 2.9 28.2 + - - +
392A LEU* 3.9 7.9 - - + +
395A MET* 3.8 36.8 - - + -
396A ILE* 3.9 20.2 - - + -
399A LYS* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A HIS* 2.9 46.4 + - + +
369A ALA* 3.7 6.5 - - - +
371A ILE* 1.3 76.5 - - - +
373A ASP* 1.3 57.9 + - - +
375A PHE* 3.4 6.1 + - + +
376A LYS* 2.9 60.5 + - + +
396A ILE* 3.7 23.3 - - + -
399A LYS* 5.0 0.4 - - - -
463A PRO* 4.4 6.5 - - + +
464A MET* 3.8 39.0 - - + +
467A THR* 3.9 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA* 2.9 25.2 + - - +
370A GLU* 3.6 8.1 - - - +
371A ILE 3.2 0.2 - - - -
372A MET* 1.3 73.6 - - - +
374A SER* 1.3 65.6 + - - +
376A LYS* 3.2 23.3 + - - +
377A GLU* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLU* 3.0 22.4 + - - +
371A ILE* 3.7 3.8 - - - -
373A ASP* 1.3 74.2 - - - +
375A PHE* 1.3 65.4 + - - +
377A GLU* 3.3 15.3 + - - +
378A LYS* 3.2 26.4 + - - +
392A LEU* 3.6 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ILE 2.9 16.3 + - - +
372A MET* 3.6 6.3 - - - +
373A ASP 3.1 0.2 - - - -
374A SER* 1.3 77.9 - - - +
376A LYS* 1.3 60.2 + - + +
378A LYS* 2.9 9.3 + - + +
379A MET* 2.8 54.3 + - + +
382A PHE* 3.9 16.6 - + - -
392A LEU* 3.9 20.3 - - + +
393A LEU* 4.0 22.0 - - + -
396A ILE* 3.5 37.0 - - + -
467A THR* 4.0 33.7 - - - -
468A VAL* 4.8 1.8 - - + -
471A LEU* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A MET* 2.9 42.9 + - + +
373A ASP* 3.7 26.2 + - - +
375A PHE* 1.3 77.1 - - + +
377A GLU* 1.3 62.5 + - - +
379A MET* 3.1 19.2 + - + +
380A GLU* 3.1 16.3 + - - +
463A PRO* 6.3 2.2 - - - -
467A THR* 4.2 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASP* 3.0 16.0 + - - +
374A SER* 3.3 17.5 + - - +
376A LYS* 1.3 75.2 - - - +
378A LYS* 1.3 71.2 + - + +
380A GLU* 3.2 42.1 - - - +
381A ASN 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 3.2 16.6 - - - +
375A PHE* 2.9 7.5 + - + +
377A GLU* 1.3 84.1 - - + +
379A MET* 1.3 59.2 + - + +
381A ASN 2.9 20.8 + - - +
382A PHE* 3.1 22.4 + - + -
388A GLU* 3.8 22.7 + - - -
389A HIS* 3.9 45.0 + - + +
392A LEU* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PHE* 2.8 57.9 + - + +
376A LYS* 3.1 16.8 + - + +
378A LYS* 1.3 77.4 - - - +
380A GLU* 1.3 60.4 + - - +
381A ASN* 3.0 1.7 + - - -
382A PHE* 3.4 21.2 + - + +
467A THR* 5.0 8.7 - - + +
470A LYS* 4.5 25.1 - - + -
471A LEU* 3.4 34.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LYS 3.1 11.4 + - - +
377A GLU* 3.2 37.1 - - - +
378A LYS 3.1 0.2 - - - -
379A MET* 1.3 76.5 - - - +
381A ASN* 1.3 62.1 + - + +
----------------------------------------------------------
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