Contacts of the helix formed by residues 433 - 455 (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 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A PHE* 3.9 17.8 - - + -
395A LYS* 4.1 23.3 + - - +
431A ALA* 3.2 1.2 - - - +
432A LYS* 1.3 82.8 - - + +
434A THR* 1.3 62.3 + - - +
435A LYS* 2.9 17.7 + - - +
436A ILE* 2.9 54.7 + - + +
437A ILE* 3.3 12.8 - - - +
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Residues in contact with THR 434 (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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432A LYS 3.2 6.2 + - - -
433A ASP* 1.3 72.9 + - - +
435A LYS* 1.3 66.9 + - - +
437A ILE* 3.3 8.8 + - - +
438A GLN* 3.2 29.9 + - - +
479A HIS* 3.5 30.4 + - + -
481A ASN* 3.6 30.1 - - + +
484A VAL* 4.3 1.8 - - + -
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Residues in contact with LYS 435 (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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395A LYS* 6.0 0.9 - - - -
399A TRP* 3.4 29.1 - - + +
433A ASP* 2.9 10.6 + - - +
434A THR* 1.3 79.8 - - - +
436A ILE* 1.3 61.7 + - - +
438A GLN* 3.3 21.0 + - - +
439A VAL* 3.1 26.4 + - + +
18C PHE* 3.3 40.9 - - + -
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Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE* 4.3 9.6 - - + -
395A LYS* 3.7 40.2 - - + +
398A ALA* 4.1 13.5 - - + -
399A TRP* 6.2 1.3 - - + +
428A LEU* 3.9 29.8 - - + +
431A ALA* 4.0 15.5 - - + -
433A ASP* 2.9 36.8 + - + +
435A LYS* 1.3 74.3 - - - +
437A ILE* 1.3 70.9 + - + +
439A VAL* 3.2 8.2 + - + +
440A ILE* 2.9 36.3 + - + +
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Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 3.9 38.6 - - + +
431A ALA 3.3 24.2 - - - +
432A LYS 4.4 1.3 - - - +
433A ASP 3.3 15.5 - - - +
434A THR* 3.3 8.6 + - - +
436A ILE* 1.3 80.7 - - + +
438A GLN* 1.3 56.5 + - - +
440A ILE* 3.3 3.1 + - - +
441A LEU* 3.0 30.5 + - + +
476A LEU* 4.1 17.5 - - + -
479A HIS* 4.4 21.1 - - + +
484A VAL* 4.0 26.7 - - + -
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Residues in contact with GLN 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 3.2 32.5 + - - +
435A LYS* 3.6 19.2 - - + +
436A ILE 3.2 0.4 - - - -
437A ILE* 1.3 75.0 - - - +
439A VAL* 1.3 65.9 + - + +
441A LEU* 3.5 5.1 + - - +
442A ASP* 3.0 32.9 + - - +
481A ASN* 3.8 8.2 - - - +
483A SER* 2.7 32.2 + - - +
484A VAL* 3.6 17.5 - - + +
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Residues in contact with VAL 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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398A ALA* 3.7 28.0 - - + +
399A TRP* 3.4 47.3 - - + +
402A THR* 2.8 45.4 + - + +
435A LYS* 3.1 19.5 + - + +
436A ILE* 3.5 11.2 - - + +
438A GLN* 1.3 76.0 - - + +
440A ILE* 1.3 63.1 + - - +
442A ASP* 3.2 7.6 + - - +
443A ALA 3.1 11.6 + - - -
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Residues in contact with ILE 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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398A ALA* 4.6 6.7 - - + -
402A THR* 4.9 0.2 - - - -
425A LEU* 3.8 35.9 - - + +
428A LEU* 3.4 46.9 - - + +
429A LEU* 3.7 22.7 - - + +
436A ILE* 2.9 34.8 + - + +
437A ILE* 3.7 3.8 - - - +
439A VAL* 1.3 76.6 - - - +
441A LEU* 1.3 64.3 + - - +
443A ALA* 3.0 10.0 + - - +
444A ILE* 2.9 37.6 + - + +
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Residues in contact with LEU 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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429A LEU* 4.2 7.0 - - + -
437A ILE* 3.0 22.7 + - + +
438A GLN* 3.9 5.6 - - - +
440A ILE* 1.3 75.0 - - - +
442A ASP* 1.3 64.0 + - - +
444A ILE* 3.3 17.2 + - + +
445A SER* 3.0 23.7 + - - -
473A ILE* 5.0 3.8 - - + -
476A LEU* 3.6 35.0 - - + -
484A VAL* 4.0 21.1 - - + +
487A ALA* 3.9 29.8 - - + -
488A SER* 4.1 5.6 - - - +
491A LEU* 4.1 23.0 - - + +
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Residues in contact with ASP 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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402A THR* 4.1 14.7 - - + +
438A GLN* 3.0 21.2 + - - +
439A VAL* 3.3 11.3 - - - +
441A LEU* 1.3 78.0 - - - +
443A ALA* 1.3 62.6 + - - +
445A SER* 3.2 6.2 + - - -
446A ASN* 3.0 32.5 + - - +
487A ALA* 5.6 4.3 - - - +
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Residues in contact with ALA 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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401A ILE* 4.4 7.0 - - + -
402A THR* 3.8 23.5 + - - +
405A THR* 3.6 20.6 + - + +
425A LEU* 4.3 19.3 - - + -
439A VAL 3.1 6.0 + - - +
440A ILE* 3.0 11.7 + - - +
442A ASP* 1.3 75.6 - - - +
444A ILE* 1.3 63.5 + - - +
446A ASN* 3.2 3.2 + - - +
447A ILE* 3.0 30.0 + - + +
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Residues in contact with ILE 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ILE* 6.3 1.1 - - + -
425A LEU* 4.9 5.6 - - + -
426A MET* 3.4 36.3 - - + -
429A LEU* 4.3 4.3 - - + -
440A ILE* 2.9 32.4 + - + +
441A LEU* 3.6 23.6 - - + +
443A ALA* 1.3 75.4 - - - +
445A SER* 1.3 64.1 + - - +
447A ILE* 3.2 10.2 + - + +
448A PHE* 2.9 48.0 + - + -
464A ILE* 4.2 10.8 - - + -
473A ILE* 4.4 7.9 - - + -
491A LEU* 3.9 13.2 - - + -
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Residues in contact with SER 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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441A LEU 3.0 13.6 + - - -
442A ASP* 3.2 10.3 + - - -
444A ILE* 1.3 78.6 - - - +
446A ASN* 1.3 58.1 + - - +
448A PHE* 3.2 4.9 + - - +
449A GLN* 2.9 45.8 + - - +
490A ASN* 5.1 6.7 + - - -
491A LEU* 4.1 20.9 - - - +
495A TYR* 4.8 3.5 + - - -
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Residues in contact with ASN 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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402A THR* 4.0 6.3 + - - +
405A THR* 3.2 42.4 + - - +
406A SER* 3.4 26.1 - - - -
413A ILE* 4.3 4.0 - - - +
442A ASP* 3.0 24.0 + - - +
443A ALA* 3.2 1.7 + - - +
445A SER* 1.3 77.9 + - - +
447A ILE* 1.3 62.2 + - - +
449A GLN* 3.1 23.1 + - - +
450A ALA* 3.1 20.8 + - - +
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Residues in contact with ILE 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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405A THR* 3.8 24.2 - - + -
413A ILE* 3.9 23.6 - - + -
416A LEU* 4.5 3.4 - - + -
417A VAL* 3.9 17.0 - - + -
421A ILE* 4.4 14.4 - - + -
422A ILE* 4.4 19.3 - - + -
425A LEU* 4.8 10.1 - - + -
443A ALA 3.0 20.0 + - - +
444A ILE* 3.7 7.6 - - + +
446A ASN* 1.3 75.5 - - - +
448A PHE* 1.3 58.0 + - - +
450A ALA* 3.2 3.6 + - - +
451A ALA* 2.9 26.4 + - + +
460A LEU* 3.6 21.8 - - + -
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Residues in contact with PHE 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 ILE* 2.9 33.8 + - + +
445A SER 3.5 8.5 - - - +
447A ILE* 1.3 78.0 - - - +
449A GLN* 1.3 56.2 + - - +
451A ALA* 3.1 3.2 + - - +
452A GLU* 2.9 31.5 + - - +
457A THR* 3.9 24.1 - - + +
460A LEU* 3.7 17.7 - - + -
461A SER* 4.3 3.1 - - - -
464A ILE* 3.4 35.0 - - + -
491A LEU* 4.0 11.0 - - + -
495A TYR* 3.3 56.5 - + + -
496A PHE* 3.8 22.7 - + - -
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Residues in contact with GLN 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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445A SER* 2.9 33.0 + - - +
446A ASN* 3.1 24.3 + - - +
448A PHE* 1.3 77.7 - - - +
450A ALA* 1.3 61.4 + - - +
452A GLU* 3.3 23.7 + - - +
453A LYS* 3.3 27.8 + - - +
494A LYS* 6.5 0.2 - - - -
495A TYR* 4.8 7.4 - - - +
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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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410A VAL* 4.0 19.7 - - + +
413A ILE* 3.7 39.7 - - + -
414A VAL* 6.2 0.7 - - + -
446A ASN 3.1 5.9 + - - -
447A ILE 3.2 8.3 + - - +
449A GLN* 1.3 75.5 - - - +
451A ALA* 1.3 62.7 + - - +
453A LYS* 3.2 27.6 + - - +
454A LEU* 3.4 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 ILE* 2.9 14.7 + - + +
448A PHE 3.1 8.7 + - - +
450A ALA* 1.3 75.6 - - - +
452A GLU* 1.3 61.1 + - - +
454A LEU* 3.2 10.6 + - - +
455A GLY 3.0 3.8 + - - -
456A GLU* 3.0 41.8 + - + +
457A THR* 3.8 13.7 - - + -
460A LEU* 3.9 20.0 - - + -
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Residues in contact with GLU 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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448A PHE 2.9 12.8 + - - +
449A GLN* 3.5 16.8 - - - +
450A ALA 3.2 0.4 - - - -
451A ALA* 1.3 74.2 - - - +
453A LYS* 1.3 66.4 + - + +
455A GLY* 3.1 13.1 + - - +
457A THR* 3.4 21.5 - - + -
494A LYS* 3.3 18.4 + - - -
495A TYR* 2.9 32.4 + - + -
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Residues in contact with LYS 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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410A VAL* 4.0 23.7 - - + +
449A GLN* 3.3 26.7 + - - +
450A ALA* 3.2 14.0 + - - +
452A GLU* 1.3 79.7 - - + +
454A LEU* 1.3 62.1 + - + +
455A GLY 3.6 0.2 + - - -
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Residues in contact with LEU 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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410A VAL* 3.8 24.5 - - + -
411A GLU* 5.8 3.8 - - - +
414A VAL* 3.7 30.1 - - + -
450A ALA 3.4 6.5 + - - +
451A ALA* 3.2 11.1 + - - +
452A GLU 3.1 0.6 - - - -
453A LYS* 1.3 78.4 - - + +
455A GLY* 1.3 62.9 + - - +
456A GLU* 3.5 33.4 + - - +
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Residues in contact with GLY 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 3.0 4.1 + - - -
452A GLU* 3.1 13.9 + - - -
453A LYS 3.4 0.6 + - - -
454A LEU* 1.3 79.7 - - - +
456A GLU* 1.3 53.3 + - - +
457A THR* 3.7 3.4 - - - -
458A GLU* 2.7 24.2 - - - +
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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