Contacts of the helix formed by residues 390 - 408 (chain A) in PDB entry 5K9S
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 390 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A THR* 3.2 30.8 + - + +
352A GLN* 4.7 4.3 - - - +
353A LYS* 5.3 0.5 - - - +
389A ALA* 1.3 77.3 - - - +
391A PHE* 1.3 61.1 + - - +
392A LYS* 3.6 14.2 + - - +
393A THR* 3.0 36.9 + - - -
394A GLN* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 1.3 74.5 - - - +
392A LYS* 1.3 66.9 + - + +
394A GLN* 3.1 18.9 + - - +
395A LYS* 2.9 50.4 + - + +
428A LEU* 4.1 15.5 - - + -
431A ALA* 3.5 33.9 - - + -
432A LYS* 5.6 3.8 - - + -
433A ASP* 3.9 21.5 - - + -
436A ILE* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LYS* 4.0 23.7 - - + +
390A ASP* 3.3 10.8 + - - +
391A PHE* 1.3 81.4 - - + +
393A THR* 1.3 62.1 + - - +
395A LYS* 3.3 27.9 + - + +
396A GLU* 3.4 17.3 + - - +
19C LYS 5.6 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A THR 4.1 2.8 + - - -
352A GLN* 4.2 8.5 - - + +
353A LYS* 3.4 32.0 + - - +
356A THR* 3.6 14.1 - - - +
385A VAL* 3.4 24.9 - - + -
389A ALA* 3.8 7.0 - - + -
390A ASP* 3.0 29.2 + - - -
392A LYS* 1.3 74.6 - - - +
394A GLN* 1.3 66.7 + - - +
396A GLU* 3.0 10.0 + - - +
397A ALA* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL 3.7 10.1 - - - +
386A LEU* 3.0 31.8 + - - +
387A SER 3.8 13.1 + - - -
389A ALA 3.2 20.1 + - - +
390A ASP 2.9 11.9 + - - +
391A PHE* 3.1 34.0 + - + +
393A THR* 1.3 76.6 - - - +
395A LYS* 1.3 61.2 + - - +
397A ALA* 3.2 8.5 + - - +
398A ALA* 3.0 23.4 + - - +
428A LEU* 4.0 26.2 - - + +
436A ILE* 4.5 2.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
391A PHE* 2.9 43.3 + - + +
392A LYS* 3.4 18.8 - - + +
393A THR 3.2 0.2 - - - -
394A GLN* 1.3 76.3 - - - +
396A GLU* 1.3 67.6 + - - +
398A ALA* 3.2 5.5 + - - +
399A TRP* 3.1 28.7 + - + -
433A ASP* 4.1 20.2 + - - -
435A LYS* 6.0 0.4 - - - -
436A ILE* 3.7 29.0 - - + +
18C PHE* 3.9 24.0 - - + -
19C LYS* 3.7 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LYS* 4.1 28.0 - - + +
356A THR* 3.4 21.8 - - + +
357A TRP* 3.7 31.9 - - - +
360A SER* 4.2 4.5 + - - -
392A LYS 3.5 15.0 - - - +
393A THR 3.0 7.5 + - - +
395A LYS* 1.3 78.9 + - - +
397A ALA* 1.3 63.6 + - - +
399A TRP* 3.2 11.3 + - - +
400A ALA* 3.0 18.7 + - - +
12C LYS* 3.9 10.8 + - - -
15C ARG* 5.9 2.8 - - - +
18C PHE* 4.2 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A THR* 3.2 10.7 - - + +
382A LEU* 4.3 8.3 - - + +
385A VAL* 3.8 28.9 - - + -
386A LEU* 3.8 23.8 - - + +
393A THR 3.0 6.2 + - - +
394A GLN 3.2 6.9 + - - +
396A GLU* 1.3 76.2 - - - +
398A ALA* 1.3 63.8 + - - +
400A ALA* 3.0 8.1 + - - +
401A ILE* 3.0 26.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
386A LEU* 3.6 14.6 - - + +
394A GLN 3.0 12.6 + - - +
395A LYS 3.4 8.5 - - - +
397A ALA* 1.3 76.3 - - - +
399A TRP* 1.3 62.6 + - - +
401A ILE* 3.0 8.2 + - - +
402A THR* 2.9 25.3 + - - -
425A LEU* 5.1 3.8 - - + +
428A LEU* 4.6 2.9 - - + -
436A ILE* 4.1 22.7 - - + -
439A VAL* 3.7 11.4 - - + +
440A ILE* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 4.1 12.1 - - - +
395A LYS* 3.1 23.3 + - + -
396A GLU* 3.4 13.5 - - - +
398A ALA* 1.3 78.4 - - - +
400A ALA* 1.3 63.3 + - - +
402A THR* 3.3 9.9 + - + -
403A ASN* 2.9 49.9 + - - +
435A LYS* 3.4 30.4 - - - +
436A ILE* 6.2 0.8 - - + +
439A VAL* 3.4 37.2 - - + +
12C LYS* 4.5 19.4 - - + +
18C PHE* 3.7 27.1 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
356A THR 4.6 3.6 - - - +
359A MET 4.3 3.1 - - - -
360A SER* 3.6 34.0 - - - +
363A THR* 3.1 12.6 + - - +
382A LEU* 4.6 20.2 - - + -
396A GLU 3.0 9.0 + - - +
397A ALA* 3.0 14.8 + - - +
399A TRP* 1.3 76.3 - - - +
401A ILE* 1.3 58.7 + - + +
404A TYR* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 6.2 0.2 - - + -
382A LEU* 4.7 24.2 - - + +
383A VAL* 5.5 0.9 - - + +
386A LEU* 4.5 8.1 - - + -
397A ALA* 3.0 18.7 + - + +
398A ALA* 3.0 8.9 + - - +
400A ALA* 1.3 77.5 - - + +
402A THR* 1.3 66.8 + - - +
404A TYR* 3.0 7.1 + - + +
405A THR* 2.8 33.3 + - + +
416A LEU* 4.1 23.8 - - + -
421A ILE* 3.7 40.6 - - + -
425A LEU* 4.3 16.2 - - + -
443A ALA* 4.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ALA 2.9 5.9 + - - -
399A TRP* 3.7 16.4 - - + -
401A ILE* 1.3 76.2 - - - +
403A ASN* 1.3 67.8 + - - +
405A THR* 3.0 10.0 + - - -
406A SER* 2.9 25.6 + - - -
439A VAL* 2.8 41.4 + - + +
440A ILE* 4.9 0.2 - - - -
442A ASP* 4.1 24.5 - - + +
443A ALA* 3.8 8.9 - - - +
446A ASN* 4.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 2.8 30.4 + - - +
361A ASN* 5.2 1.4 + - - -
363A THR* 3.4 26.9 - - - +
364A ALA* 3.7 12.2 - - - +
399A TRP* 2.9 38.9 + - - +
402A THR* 1.3 77.2 - - - +
404A TYR* 1.3 64.0 + - - +
406A SER* 3.4 8.5 + - - -
407A GLY* 3.1 19.6 + - - -
10C ASN* 3.3 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A THR* 3.8 22.8 + - + -
370A ILE* 3.7 25.0 - - + +
373A VAL* 5.2 4.0 - - + -
374A VAL* 3.4 21.5 - - + +
379A VAL* 4.1 20.2 - - + -
382A LEU* 6.0 3.4 - - + -
400A ALA 3.1 19.7 + - - +
401A ILE* 3.0 10.9 + - + +
403A ASN* 1.3 76.5 - - - +
405A THR* 1.3 60.9 + - - +
408A GLY* 2.8 28.4 + - - -
412A GLN* 2.9 45.8 + - + +
413A ILE* 4.3 3.6 - - + -
415A TYR* 3.9 7.6 - - - -
416A LEU* 3.9 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE* 2.8 26.7 + - + +
402A THR 3.0 11.6 + - - -
404A TYR* 1.3 73.9 - - + +
406A SER* 1.3 59.6 + - - +
408A GLY 4.2 2.8 + - - +
413A ILE* 3.5 23.6 - - + +
416A LEU* 3.5 30.5 - - + -
443A ALA* 3.6 14.1 - - + +
446A ASN* 3.2 32.4 + - - +
447A ILE* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A THR* 2.9 14.0 + - - +
403A ASN* 3.4 10.9 + - - -
405A THR* 1.3 77.2 + - - +
407A GLY* 1.3 61.2 + - - +
408A GLY 3.6 1.0 - - - +
446A ASN* 3.4 21.3 - - - +
10C ASN* 3.8 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A THR 5.4 0.2 - - - -
365A GLY 5.3 4.9 - - - +
367A GLN* 3.1 32.2 + - - +
370A ILE* 3.7 11.9 - - - +
403A ASN 3.1 10.9 + - - -
406A SER* 1.3 82.4 + - - +
408A GLY* 1.3 60.6 + - - +
10C ASN* 5.7 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLN* 4.1 4.1 + - - -
370A ILE* 3.9 5.8 - - - -
404A TYR* 2.8 19.3 + - - -
405A THR 4.2 2.4 - - - +
406A SER 3.6 1.7 - - - +
407A GLY* 1.3 80.6 - - - +
409A THR* 1.3 68.6 + - - +
412A GLN* 3.2 16.2 - - - -
413A ILE* 4.2 11.6 - - - +
----------------------------------------------------------
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