Contacts of the helix formed by residues 385 - 400 (chain A) in PDB entry 2KR6
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 ASP 385 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLY* 3.7 4.1 + - - -
384A GLY* 1.3 75.2 - - - +
386A PHE* 1.3 65.1 + - + +
387A ILE 2.9 4.0 - - - -
388A PHE* 2.7 30.2 + - - +
389A TYR* 3.3 17.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PRO* 4.5 21.5 - - + -
375A GLU* 5.5 5.4 - - - -
376A GLU 5.4 2.5 - - - -
377A ARG 5.0 7.2 - - - -
378A GLY* 5.6 0.4 - - - -
379A VAL* 3.3 47.9 - - + +
380A LYS* 4.8 0.7 - - - -
381A LEU* 2.9 50.0 - - + +
382A GLY* 3.1 19.1 + - - +
385A ASP* 1.3 85.6 - - + +
387A ILE* 1.3 49.1 + - - +
389A TYR* 4.1 7.8 - - + +
390A SER* 2.7 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLY 2.7 8.2 + - - +
383A LEU* 3.0 30.3 - - + +
384A GLY* 3.2 15.9 - - - +
385A ASP 2.9 0.4 + - - -
386A PHE* 1.3 76.4 - - - +
388A PHE* 1.3 62.8 + - + +
390A SER* 2.9 11.0 + - - +
391A VAL* 2.9 34.7 - - + +
415A LEU* 3.5 41.7 - - + -
416A ILE* 6.5 0.4 - - + -
439A ILE* 3.7 29.8 - - + -
440A THR 5.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLY 4.0 9.4 - - - +
385A ASP* 2.7 17.9 + - - +
387A ILE* 1.3 78.6 - - + +
389A TYR* 1.3 81.6 + + - +
391A VAL* 3.0 16.7 - - - +
392A LEU* 3.2 32.2 + - + +
408A ILE* 4.9 5.8 - - + -
412A VAL* 3.4 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASP* 3.3 17.2 + - + +
386A PHE* 4.1 8.5 - - + +
388A PHE* 1.3 98.8 - + - +
390A SER* 1.3 60.4 + - - +
392A LEU* 4.5 10.1 - - + -
393A VAL* 2.9 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY* 6.0 4.7 - - - -
379A VAL 4.3 13.0 - - - -
380A LYS* 6.2 1.6 - - - -
386A PHE 2.7 27.3 + - - -
387A ILE* 2.9 20.4 + - - +
389A TYR* 1.3 73.5 - - - +
391A VAL* 1.3 62.8 + - - +
393A VAL* 5.0 0.7 - - - -
394A GLY* 2.7 32.6 + - - +
395A LYS* 5.7 0.3 - - - -
440A THR 6.1 0.6 - - - -
441A PHE* 3.8 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 2.9 29.4 - - + +
388A PHE* 3.0 19.1 - - + +
390A SER* 1.3 85.2 + - - +
392A LEU* 1.3 71.1 + - + +
395A LYS* 2.9 37.0 + - - +
408A ILE* 4.7 0.6 - - - +
411A PHE* 3.5 44.4 - - + +
412A VAL* 4.7 11.0 - - + +
415A LEU* 4.0 23.1 - - + -
441A PHE* 5.7 1.1 - - - -
442A GLY 5.4 7.0 - - - +
446A TYR* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 3.2 31.3 + - + +
389A TYR* 4.2 14.4 - - + +
391A VAL* 1.3 83.1 - - + +
393A VAL* 1.3 91.4 + - + +
395A LYS 4.0 0.3 - - - -
396A ALA* 3.0 27.6 + - + +
403A ASP 5.4 1.1 - - - +
404A TRP 5.3 1.6 - - - +
408A ILE* 3.3 56.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY* 5.9 7.6 - - - -
389A TYR* 2.9 35.5 + - + +
390A SER* 5.0 0.4 - - - -
392A LEU* 1.3 91.0 - - + +
394A GLY* 1.3 66.9 + - - +
396A ALA* 2.9 18.1 + - + +
397A SER* 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 2.7 25.9 + - - +
393A VAL* 1.3 74.4 - - - +
395A LYS* 1.3 60.1 + - - +
397A SER* 4.2 2.7 - - - -
398A ALA* 3.0 32.1 + - - +
441A PHE* 4.4 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER 5.7 0.2 - - - -
391A VAL* 2.9 27.0 + - - +
392A LEU 4.1 1.6 - - - +
394A GLY* 1.3 77.6 + - - +
396A ALA* 1.3 59.9 + - - +
398A ALA* 3.5 27.3 - - - +
399A THR* 2.7 49.0 + - - +
401A SER 4.6 0.2 + - - -
402A GLY* 4.8 2.4 + - - -
407A THR* 4.6 13.5 - - + -
408A ILE 5.7 2.0 - - - +
411A PHE* 3.4 50.0 - - + -
441A PHE* 5.6 4.4 - - - +
442A GLY 5.4 1.8 - - - +
443A LEU* 3.6 39.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 3.0 16.8 + - + +
393A VAL* 2.9 16.2 + - + +
395A LYS* 1.3 76.5 - - - +
397A SER* 1.3 57.3 + - - +
400A ALA 2.8 36.6 + - - +
401A SER* 4.6 1.3 - - - -
402A GLY* 3.4 24.0 - - - +
408A ILE* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A VAL* 3.1 11.6 + - - -
394A GLY* 4.3 2.5 - - - -
396A ALA* 1.3 78.1 - - - +
398A ALA* 1.3 70.7 + - - +
399A THR 4.1 0.5 - - - -
400A ALA* 4.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLY 3.0 21.1 + - - +
395A LYS* 3.5 20.4 - - - +
397A SER* 1.3 80.2 - - - +
399A THR* 1.3 66.2 + - - +
443A LEU* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LYS* 2.7 41.9 + - - +
397A SER 4.1 0.6 - - - +
398A ALA* 1.3 76.0 - - - +
400A ALA* 1.3 71.2 + - + +
401A SER 4.7 4.5 - - - +
402A GLY* 6.5 0.2 - - - -
407A THR* 4.7 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA 2.8 14.9 + - - +
397A SER* 4.4 4.1 - - - -
398A ALA 3.7 0.2 - - - -
399A THR* 1.3 86.8 - - + +
401A SER* 1.3 70.6 + - - +
----------------------------------------------------------
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