Contacts of the helix formed by residues 431 - 454 (chain B) in PDB entry 3KSA
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 431 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ILE* 5.1 4.0 - - - +
429B ASN* 3.6 12.9 + - - +
430B THR* 1.3 76.6 - - - +
432B VAL* 1.3 60.4 + - - +
433B VAL* 2.8 37.2 + - - +
434B VAL* 2.9 42.6 + - + +
435B LEU* 3.8 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 3.7 44.9 - - + +
382B ILE* 4.0 18.3 - - + +
383B SER* 5.4 1.1 - - - +
431B ASP* 1.3 70.3 + - - +
433B VAL* 1.3 62.8 + - + +
435B LEU* 4.1 9.1 - - + +
436B GLN* 3.0 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ASP* 2.8 26.0 + - - +
432B VAL* 1.3 74.2 - - - +
434B VAL* 1.3 56.2 + - - +
436B GLN* 3.2 7.6 + - - +
437B GLU* 2.9 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ASN* 4.2 16.6 - - - +
431B ASP* 2.9 39.0 - - + +
433B VAL* 1.3 71.9 - - + +
435B LEU* 1.3 73.4 + - + +
437B GLU* 3.0 31.1 + - + +
438B GLU* 3.2 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ARG* 5.5 8.3 - - - +
375B VAL* 3.8 14.3 - - + +
378B LEU* 3.6 38.4 - - + +
379B ILE* 3.5 32.1 - - + +
382B ILE* 5.6 4.0 - - + -
429B ASN* 5.7 7.2 - - - +
431B ASP 4.3 9.9 - - - +
432B VAL* 3.7 6.9 + - + +
433B VAL 3.4 0.2 - - - -
434B VAL* 1.3 86.3 - - + +
436B GLN* 1.3 57.2 + - - +
438B GLU* 3.1 10.4 + - + +
439B GLU* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 3.9 3.7 - - + +
432B VAL* 3.0 27.0 + - + +
433B VAL* 3.4 6.5 - - - +
435B LEU* 1.3 76.4 - - - +
437B GLU* 1.3 62.1 + - - +
439B GLU* 3.2 18.5 + - - +
440B ALA* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B VAL* 2.9 38.5 + - + +
434B VAL* 3.0 23.3 + - + +
436B GLN* 1.3 77.7 - - - +
438B GLU* 1.3 61.9 + - - +
440B ALA* 3.3 7.7 + - - +
441B GLU* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ARG* 5.9 4.9 - - + +
375B VAL* 5.1 12.6 - - + -
434B VAL 3.2 6.7 + - - +
435B LEU* 3.1 11.2 + - + +
437B GLU* 1.3 75.9 - - - +
439B GLU* 1.3 60.8 + - - +
441B GLU* 2.9 12.7 + - + +
442B LEU* 2.8 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.1 14.0 - - + +
375B VAL* 4.1 15.4 - - + +
376B GLU* 5.8 5.2 - - - +
379B ILE* 3.6 18.8 - - - +
435B LEU 2.8 17.8 + - - +
436B GLN* 3.5 14.0 - - - +
438B GLU* 1.3 72.4 - - - +
440B ALA* 1.3 62.6 + - - +
442B LEU* 3.3 7.2 + - - +
443B ARG* 2.4 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B GLN 3.0 11.5 + - - +
437B GLU* 3.4 11.0 - - - +
439B GLU* 1.3 75.7 - - - +
441B GLU* 1.3 64.5 + - - +
443B ARG* 3.0 7.5 + - - +
444B GLU* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLU 3.1 9.4 + - - +
438B GLU* 2.9 16.9 + - - +
440B ALA* 1.3 79.5 - - - +
442B LEU* 1.3 74.8 + - - +
444B GLU* 3.4 5.9 + - - +
445B LYS* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA* 3.7 17.9 - - + +
371B ARG* 3.8 18.8 - - + +
372B LEU* 3.3 49.6 - - + +
375B VAL* 4.6 6.3 - - + -
438B GLU* 2.8 28.2 + - + +
439B GLU* 3.7 4.7 - - - +
441B GLU* 1.3 86.1 - - - +
443B ARG* 1.3 65.2 + - - +
445B LYS* 2.9 9.3 + - + +
446B ILE* 2.8 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.0 30.3 - - + +
376B GLU* 5.6 5.3 - - - +
439B GLU* 2.4 54.1 + - - +
440B ALA* 3.7 6.3 - - - +
442B LEU* 1.3 76.5 - - - +
444B GLU* 1.3 58.0 + - - +
446B ILE* 3.4 12.2 + - + +
447B ALA* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA 2.9 16.1 + - - +
441B GLU* 3.7 5.6 - - - +
443B ARG* 1.3 73.5 - - - +
445B LYS* 1.3 64.3 + - - +
447B ALA* 3.9 3.9 - - - +
448B MET* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA* 5.3 6.3 - - + -
441B GLU 3.0 13.1 + - - +
442B LEU* 2.9 12.0 + - + +
444B GLU* 1.3 72.4 - - - +
446B ILE* 1.3 68.4 + - + +
448B MET* 3.2 8.6 + - - +
449B LEU* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS* 4.2 26.9 - - + +
368B ALA* 3.6 19.1 - - + -
369B GLU* 4.0 30.3 - - + +
372B LEU* 4.4 17.3 - - + -
442B LEU 2.8 24.3 + - - +
443B ARG* 3.7 11.4 - - + +
445B LYS* 1.3 71.3 - - - +
447B ALA* 1.3 60.4 + - - +
449B LEU* 3.1 11.7 + - - +
450B ALA* 2.8 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ARG 3.0 17.5 + - - +
444B GLU* 4.0 5.4 - - - +
446B ILE* 1.3 75.6 - - - +
448B MET* 1.3 68.0 + - - +
450B ALA* 3.6 7.3 + - - +
451B ALA* 3.3 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLU 3.0 15.0 + - - +
445B LYS* 3.2 12.1 + - - +
447B ALA* 1.3 76.0 - - - +
449B LEU* 1.3 65.4 + - + +
451B ALA* 3.0 27.1 - - - +
452B ILE* 3.3 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B SER* 3.8 30.2 - - - +
364B ASP* 3.7 17.9 - - + +
365B LYS* 3.4 45.5 - - + +
368B ALA* 5.3 1.6 - - + -
445B LYS* 2.9 27.5 + - + +
446B ILE* 3.4 7.0 - - - +
448B MET* 1.3 75.7 - - + +
450B ALA* 1.3 66.3 + - - +
451B ALA 3.0 1.6 - - - -
452B ILE* 2.9 27.7 + - + +
453B ILE* 3.0 16.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS* 4.3 20.4 - - + +
446B ILE* 2.8 21.4 + - + +
447B ALA* 3.9 8.5 - - - +
449B LEU* 1.3 72.5 - - - +
451B ALA* 1.3 64.7 + - - +
453B ILE* 3.5 11.5 + - - +
454B GLY* 3.2 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ALA 3.3 8.9 + - - +
448B MET* 3.0 15.6 + - - +
450B ALA* 1.3 74.6 - - - +
452B ILE* 1.3 68.4 + - + +
454B GLY 2.9 10.8 + - - -
455B ASP* 2.8 29.6 + - + +
458B THR* 5.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ILE* 4.1 15.9 - - + -
358B LEU* 3.7 11.2 - - + +
360B ARG* 5.6 0.4 - - - +
361B SER* 3.9 18.4 - - - +
448B MET* 3.4 22.0 - - + +
449B LEU* 2.9 22.7 + - + +
451B ALA* 1.3 72.3 - - + +
453B ILE* 1.3 63.8 + - - +
454B GLY 3.3 0.2 + - - -
455B ASP* 3.6 9.9 + - - -
456B GLU* 4.7 0.7 + - - -
458B THR* 4.6 6.8 - - - +
459B MET* 3.6 43.2 - - + +
462B LEU* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B LEU* 4.2 25.2 - - + +
361B SER* 4.4 13.7 - - - -
362B ARG* 3.5 46.4 - - + +
365B LYS* 4.2 27.6 - - + -
449B LEU 3.0 12.2 + - - +
450B ALA* 3.6 11.0 - - - +
451B ALA 2.9 0.2 + - - -
452B ILE* 1.3 79.6 - - - +
454B GLY* 1.3 61.6 + - - +
455B ASP 4.0 0.2 + - - -
456B GLU* 5.4 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ALA 3.2 5.6 + - - -
451B ALA* 2.9 11.3 + - - -
453B ILE* 1.3 81.0 - - - +
455B ASP* 1.3 55.5 + - - +
456B GLU 3.8 2.0 - - - -
----------------------------------------------------------
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