Contacts of the helix formed by residues 431 - 455 (chain A) in PDB entry 4KPF
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A ILE* 4.2 3.7 - - - +
429A ASN* 3.1 24.9 + - - +
430A THR* 1.3 73.9 + - - +
432A VAL* 1.3 60.8 + - - +
433A VAL* 3.7 18.0 + - - +
434A VAL* 2.7 48.0 + - + +
435A LEU* 4.5 4.2 - - - +
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ILE* 3.9 26.0 - - + +
382A ILE* 3.4 33.9 - - + -
383A SER 5.8 0.2 - - - +
430A THR 3.2 6.0 + - - +
431A ASP* 1.3 72.8 - - - +
433A VAL* 1.3 61.5 + - + +
435A LEU* 3.6 6.4 + - - +
436A GLN* 3.0 54.4 + - + +
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ASP* 3.3 13.1 + - - +
432A VAL* 1.3 76.7 - - + +
434A VAL* 1.3 74.2 + - - +
436A GLN* 2.7 29.0 + - + +
437A GLU* 2.8 25.6 + - + -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ASN* 5.9 2.2 - - - +
431A ASP* 2.7 34.5 + - + +
433A VAL* 1.3 78.5 - - - +
435A LEU* 1.3 84.2 + - + +
437A GLU* 3.2 12.3 + - + +
438A GLU* 3.0 19.6 + - - +
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ARG* 4.9 5.8 - - - +
375A VAL* 4.0 21.7 - - + +
378A LEU* 3.9 33.2 - - + -
379A ILE* 3.9 17.9 - - + -
382A ILE* 4.1 23.6 - - + -
429A ASN* 5.4 3.6 - - - +
431A ASP 4.5 4.3 - - - +
432A VAL 3.6 9.8 + - - +
433A VAL 3.1 0.4 - - - -
434A VAL* 1.3 90.1 - - + +
436A GLN* 1.3 54.5 + - - +
438A GLU* 2.8 39.2 + - - +
439A GLU* 2.8 11.8 + - - +
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Residues in contact with GLN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ILE* 4.1 19.1 - - + +
432A VAL* 3.0 40.9 + - + +
433A VAL* 2.7 24.0 + - + +
435A LEU* 1.3 69.7 - - - +
437A GLU* 1.3 62.9 + - - +
439A GLU* 2.9 19.8 + - - +
440A ALA* 2.9 23.0 + - - +
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A VAL* 2.8 33.7 + - + +
434A VAL* 3.4 11.9 - - + +
436A GLN* 1.3 71.3 - - - +
438A GLU* 1.3 61.9 + - - +
440A ALA* 3.2 6.5 + - - +
441A GLU* 3.0 22.9 + - - +
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ARG* 2.8 48.1 + - - -
375A VAL* 3.5 11.0 - - + +
434A VAL 3.0 9.7 + - - +
435A LEU* 2.8 24.2 + - - +
437A GLU* 1.3 70.8 - - - +
439A GLU* 1.3 64.7 + - - +
441A GLU* 3.4 6.9 + - + +
442A LEU* 3.0 37.5 + - + +
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 3.5 19.5 - - + +
375A VAL* 4.4 11.2 - - + +
376A GLU* 3.8 16.9 - - + +
379A ILE* 3.7 22.9 - - + +
435A LEU 2.8 14.7 + - - +
436A GLN* 3.2 19.7 + - - +
438A GLU* 1.3 71.7 - - - +
440A ALA* 1.3 62.2 + - - +
442A LEU* 3.4 3.1 + - - +
443A ARG* 2.9 60.9 + - - +
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Residues in contact with ALA 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A GLN 2.9 10.1 + - - +
437A GLU* 3.5 10.3 - - - +
438A GLU 3.2 0.2 - - - -
439A GLU* 1.3 72.5 - - - +
441A GLU* 1.3 67.3 + - - +
442A LEU 2.8 3.1 + - - -
443A ARG* 2.9 19.8 + - - +
444A GLU* 3.0 14.5 + - - +
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A GLU 3.0 13.0 + - - +
438A GLU* 3.9 7.6 - - + +
440A ALA* 1.3 78.1 - - - +
442A LEU* 1.3 57.8 + - + +
444A GLU* 3.6 7.8 + - - +
445A LYS* 3.1 27.5 + - - +
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ALA* 3.9 27.8 - - + +
371A ARG* 3.5 32.1 - - + -
372A LEU* 3.7 28.5 - - + +
375A VAL* 4.5 1.8 - - + -
438A GLU* 3.0 35.6 + - + +
439A GLU 3.7 4.3 - - - +
440A ALA 2.8 5.7 + - - -
441A GLU* 1.3 75.0 - - + +
443A ARG* 1.3 64.9 + - - +
445A LYS* 3.3 12.5 + - + +
446A ILE* 3.0 31.1 + - + +
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Residues in contact with ARG 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU* 4.0 15.0 - - + +
376A GLU* 3.5 19.5 + - - -
439A GLU* 2.9 58.3 + - - +
440A ALA* 2.9 9.5 + - - +
442A LEU* 1.3 76.4 - - - +
444A GLU* 1.3 63.3 + - - +
446A ILE* 3.3 10.8 + - + +
447A ALA* 3.1 22.9 + - - +
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ALA 3.0 15.0 + - - +
441A GLU* 3.8 7.4 - - - +
443A ARG* 1.3 78.0 - - - +
445A LYS* 1.3 63.2 + - - +
446A ILE 3.1 0.5 + - - -
447A ALA* 3.1 8.0 + - + +
448A MET* 3.0 26.7 + - + +
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Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ASP* 5.7 2.9 - - + +
368A ALA* 4.8 13.5 - - + -
441A GLU 3.1 16.8 + - - +
442A LEU* 3.3 13.2 + - + +
444A GLU* 1.3 79.2 - - - +
446A ILE* 1.3 58.2 + - + +
448A MET* 3.4 6.9 + - + +
449A LEU* 2.8 50.8 + - + +
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Residues in contact with ILE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LYS* 3.8 22.8 - - + +
368A ALA* 3.8 19.7 - - + +
369A GLU* 4.0 34.3 - - + +
372A LEU* 4.5 14.1 - - + -
442A LEU 3.0 20.8 + - - +
443A ARG* 3.7 7.0 - - - +
444A GLU 3.1 0.8 - - - -
445A LYS* 1.3 74.8 - - - +
447A ALA* 1.3 58.2 + - - +
449A LEU* 3.2 5.7 + - - +
450A ALA* 2.7 37.1 + - + +
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ARG 3.1 13.1 + - - +
444A GLU* 3.5 10.8 - - + +
446A ILE* 1.3 79.0 - - - +
448A MET* 1.3 63.1 + - + +
450A ALA* 3.8 4.8 - - - +
451A ALA* 3.1 24.3 + - - +
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Residues in contact with MET 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A GLU* 3.0 15.5 + - + +
445A LYS* 3.8 10.3 - - + +
447A ALA* 1.3 79.7 - - - +
449A LEU* 1.3 62.8 + - + +
451A ALA* 3.5 6.2 + - - +
452A ILE* 3.3 25.3 + - + +
458A THR* 5.3 0.2 - - - +
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A ARG* 5.9 1.6 - - - +
361A SER* 3.6 43.9 - - - +
364A ASP* 3.9 20.4 - - + +
365A LYS* 4.3 23.6 - - + +
368A ALA* 5.4 1.1 - - + -
445A LYS* 2.8 48.0 + - + +
446A ILE* 3.2 3.6 + - - +
448A MET* 1.3 76.5 - - + +
450A ALA* 1.3 66.5 + - - +
452A ILE* 3.4 13.0 + - + +
453A ILE* 3.1 27.7 + - - +
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LYS* 4.4 17.5 - - + +
446A ILE* 2.7 25.8 + - + +
447A ALA* 3.8 6.3 - - - +
448A MET 3.3 0.2 - - - -
449A LEU* 1.3 73.2 - - - +
451A ALA* 1.3 54.7 + - - +
453A ILE* 2.8 26.5 + - - +
454A GLY* 2.8 13.9 + - - -
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ALA 3.1 12.6 + - - +
448A MET* 3.5 11.7 - - - +
450A ALA* 1.3 74.9 - - - +
452A ILE* 1.3 65.0 + - - +
453A ILE 3.0 0.3 + - - -
454A GLY* 3.0 1.7 + - - -
455A ASP* 2.7 31.8 + - + +
458A THR* 4.0 16.2 - - + +
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Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ILE* 4.0 19.5 - - + +
358A LEU* 3.9 4.9 - - + +
360A ARG* 5.5 0.2 - - - +
361A SER* 3.9 21.8 - - - +
448A MET* 3.3 17.0 - - + +
449A LEU* 3.5 15.3 - - + +
450A ALA 3.3 0.2 - - - -
451A ALA* 1.3 77.3 - - - +
453A ILE* 1.3 62.0 + - - +
455A ASP 3.7 4.3 + - - +
458A THR* 3.5 19.7 - - + +
459A MET* 3.4 30.8 - - + +
462A LEU* 3.2 32.5 - - + -
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Residues in contact with ILE 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A LEU* 3.7 26.3 - - + +
361A SER* 3.9 17.5 - - - +
362A ARG* 3.9 47.3 - - + +
365A LYS* 4.2 20.9 - - + +
449A LEU 3.1 17.3 - - - +
450A ALA* 2.8 11.9 + - - +
452A ILE* 1.3 76.8 - - - +
454A GLY* 1.3 61.6 + - - +
455A ASP 3.8 0.9 + - - -
456A GLU* 5.4 3.5 - - - +
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A ALA 2.8 11.8 + - - -
451A ALA* 3.6 2.5 - - - -
453A ILE* 1.3 79.2 - - - +
455A ASP* 1.3 57.1 + - - +
456A GLU 4.1 1.5 + - - -
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A ALA* 2.7 20.0 + - + +
452A ILE 3.7 3.8 - - - +
453A ILE 3.5 0.8 - - - -
454A GLY* 1.3 73.2 - - - +
456A GLU* 1.3 64.9 + - - +
457A ARG* 2.9 15.0 + - - +
458A THR* 2.4 43.4 + - - +
459A MET* 3.0 21.1 + - - +
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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
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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) + - + + + + + -
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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