Contacts of the helix formed by residues 473 - 493 (chain E) in PDB entry 5KRA
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 473 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472E LYS* 1.3 77.4 - - - +
474E HIS* 1.3 65.2 + - - +
476E HIS* 3.4 9.2 + - - +
477E ARG* 3.1 45.5 + - - +
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Residues in contact with HIS 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E SER* 3.6 24.8 + - - -
308E LEU* 4.7 10.7 - - + +
366E GLY* 3.5 25.1 - - - -
369E ASP* 3.8 15.4 + - + +
370E LEU* 3.5 19.2 - - + +
472E LYS* 3.2 1.9 - - - +
473E ASP* 1.3 76.9 - - - +
475E ILE* 1.3 66.9 + - + +
477E ARG* 3.1 27.0 + - - +
478E VAL* 3.0 48.3 + - + +
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Residues in contact with ILE 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370E LEU* 3.8 38.1 - - + -
374E ASP* 5.5 2.5 - - + +
378E LEU* 4.3 4.9 - - + -
454E LEU* 3.4 40.4 - - + +
458E VAL* 3.9 12.1 - - + -
461E PHE* 3.6 32.8 - - + -
472E LYS* 3.4 15.5 + - - +
473E ASP 3.4 0.2 - - - -
474E HIS* 1.3 78.5 - - + +
476E HIS* 1.3 58.8 + - - +
478E VAL* 3.4 7.5 + - - +
479E LEU* 3.0 30.1 + - + +
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Residues in contact with HIS 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458E VAL* 4.0 28.8 - - + +
459E TYR* 4.5 9.0 - + - -
472E LYS* 3.1 24.8 + - + -
473E ASP* 3.8 10.7 - - - +
474E HIS 3.2 0.8 - - - -
475E ILE* 1.3 77.9 - - - +
477E ARG* 1.3 59.5 + - + +
479E LEU* 3.4 22.8 + - + +
480E ASP* 3.0 33.5 + - - +
434F ARG* 3.3 50.9 + - - +
437F MET* 4.9 5.2 - - + +
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Residues in contact with ARG 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A PRO* 6.6 0.2 - - - -
308E LEU* 3.6 33.7 - - + +
473E ASP* 3.1 44.8 + - - +
474E HIS* 3.1 34.5 + - - +
476E HIS* 1.3 74.5 - - + +
478E VAL* 1.3 59.7 + - - +
480E ASP* 3.3 14.2 + - - +
481E LYS* 3.1 20.4 + - - +
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Residues in contact with VAL 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E ALA* 4.5 13.0 - - + -
308E LEU* 4.0 14.8 - - + -
315E MET* 5.7 2.7 - - + -
365E PRO 3.9 17.3 - - - +
366E GLY* 4.8 2.9 - - - +
454E LEU* 3.6 25.1 - - + -
474E HIS* 3.0 42.7 + - + +
475E ILE* 3.6 7.9 - - - +
477E ARG* 1.3 74.8 - - - +
479E LEU* 1.3 60.1 + - - +
481E LYS* 3.0 7.0 + - + +
482E ILE* 3.0 34.2 + - + +
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Residues in contact with LEU 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 4.0 38.4 - - + +
454E LEU* 3.8 31.0 - - + +
455E ASN* 4.2 25.1 - - + +
458E VAL* 5.2 1.3 - - + -
459E TYR* 5.8 0.4 - - - +
475E ILE* 3.0 20.6 + - + +
476E HIS* 3.5 28.3 - - + +
478E VAL* 1.3 77.3 - - - +
480E ASP* 1.3 57.9 + - - +
482E ILE* 3.2 6.2 + - + +
483E THR* 2.9 31.6 + - - -
509F LEU* 4.5 13.5 - - + -
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Residues in contact with ASP 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E HIS* 3.0 21.4 + - - +
477E ARG* 3.4 17.4 - - - +
478E VAL 3.2 0.2 - - - -
479E LEU* 1.3 76.1 - - - +
481E LYS* 1.3 57.0 + - - +
483E THR* 3.2 8.0 + - - -
484E ASP* 2.9 36.4 + - - +
502F GLN* 4.0 29.5 - - - +
506F GLN* 2.9 37.0 + - - +
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Residues in contact with LYS 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E ALA 3.1 25.9 + - - +
308E LEU* 3.7 23.6 + - + +
310E LEU* 2.3 35.0 + - - +
311E THR 4.3 7.9 + - - -
312E ALA* 5.1 2.7 - - - +
315E MET* 4.0 16.0 - - + +
477E ARG 3.1 12.8 + - - +
478E VAL* 3.0 14.9 + - + +
480E ASP* 1.3 77.7 - - - +
482E ILE* 1.3 50.7 + - - +
484E ASP* 3.4 16.9 + - - +
485E THR* 2.7 37.4 + - - +
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Residues in contact with ILE 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E MET* 5.0 15.3 - - + -
319E LEU* 5.4 3.4 - - + -
364E VAL* 5.9 1.3 - - + -
447E CYS* 3.7 27.6 - - + +
450E SER* 3.9 24.0 - - - -
451E ILE* 3.7 32.1 - - + +
454E LEU* 4.3 20.4 - - + -
478E VAL* 3.0 20.6 + - + +
479E LEU* 3.2 7.8 + - - +
481E LYS* 1.3 74.9 - - + +
483E THR* 1.3 59.7 + - - +
485E THR* 3.1 8.2 + - - -
486E LEU* 2.8 28.2 + - - +
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Residues in contact with THR 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 5.3 5.3 - - - +
479E LEU* 2.9 17.7 + - - +
480E ASP* 3.2 14.0 + - - -
482E ILE* 1.3 76.8 - - - +
484E ASP* 1.3 65.5 + - - +
486E LEU* 3.2 12.6 + - - +
487E ILE* 3.1 22.3 + - - +
504E LEU* 4.3 12.1 - - + +
508E LEU* 5.5 0.2 - - - +
501F HIS* 3.7 33.2 - - + +
502F GLN* 4.1 6.1 - - - -
505F ALA* 3.3 24.4 - - + +
509F LEU* 5.7 2.6 - - - +
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Residues in contact with ASP 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E ALA* 5.3 1.8 - - + -
480E ASP 2.9 22.5 + - - +
481E LYS* 3.5 19.1 - - + +
483E THR* 1.3 76.4 - - - +
485E THR* 1.3 57.4 + - - +
487E ILE* 3.5 7.0 + - - +
488E HIS* 2.9 29.0 + - - +
498F GLN* 3.3 27.4 + - - +
501F HIS* 5.6 1.7 - - - +
502F GLN* 3.2 34.3 + - - +
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Residues in contact with THR 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ALA* 3.9 17.5 - - + +
315E MET* 3.5 25.4 - - + +
316E VAL* 3.6 29.4 - - + -
447E CYS* 3.7 17.5 - - - -
481E LYS* 2.7 22.6 + - - +
482E ILE* 3.1 12.1 + - - -
484E ASP* 1.3 74.7 - - - +
486E LEU* 1.3 64.8 + - - +
488E HIS* 3.3 8.0 - - - +
489E LEU* 3.1 22.9 + - + +
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Residues in contact with LEU 486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444E GLU* 4.0 31.0 - - + +
447E CYS* 3.7 24.2 - - + -
448E LEU* 4.2 12.8 - - + -
451E ILE* 4.0 26.7 - - + -
482E ILE 2.8 12.7 + - - +
483E THR* 3.2 10.3 + - - +
485E THR* 1.3 75.7 - - - +
487E ILE* 1.3 61.9 + - - +
489E LEU* 3.1 15.9 + - + +
490E MET* 3.1 22.6 + - + +
504E LEU* 3.9 25.8 - - + -
507E LEU* 4.3 13.5 - - + -
508E LEU* 4.6 2.9 - - + -
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Residues in contact with ILE 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483E THR 3.1 15.3 + - - +
484E ASP* 3.9 6.5 - - - +
486E LEU* 1.3 75.7 - - - +
488E HIS* 1.3 53.3 + - - +
490E MET* 3.1 8.5 + - - +
491E ALA* 2.8 34.9 + - + +
500E GLN* 3.3 35.9 - - - +
504E LEU* 3.7 36.8 - - + -
501F HIS* 3.7 40.4 - - + +
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Residues in contact with HIS 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ALA* 3.3 30.7 - - + +
313E ASP* 3.1 34.7 + - - -
316E VAL* 5.5 0.4 - - + -
484E ASP 2.9 19.5 + - - +
485E THR 3.3 6.7 - - - +
487E ILE* 1.3 77.7 - - - +
489E LEU* 1.3 70.0 + - + +
491E ALA* 3.4 6.9 + - - +
492E LYS* 3.0 38.8 + - + +
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Residues in contact with LEU 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E VAL* 3.7 24.2 - - + -
443E GLU* 3.5 50.9 - - + +
444E GLU* 4.0 16.4 - - + +
447E CYS* 4.2 12.1 - - - -
485E THR 3.1 15.6 + - - +
486E LEU* 3.1 8.9 + - - +
488E HIS* 1.3 85.3 - - + +
490E MET* 1.3 57.8 + - - +
492E LYS* 3.4 18.8 + - - +
493E ALA* 3.0 27.5 + - - +
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Residues in contact with MET 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444E GLU* 3.9 15.7 - - - +
486E LEU* 3.3 22.9 - - + +
487E ILE* 3.1 15.8 + - - +
489E LEU* 1.3 73.6 - - - +
491E ALA* 1.3 67.0 + - - +
493E ALA* 3.2 12.7 + - - +
494E GLY 3.3 0.2 + - - -
495E LEU* 3.2 36.6 + - + +
500E GLN* 3.4 33.7 - - + +
503E ARG* 3.7 24.5 - - + -
504E LEU* 3.7 15.7 - - + +
507E LEU* 3.6 31.2 - - + -
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Residues in contact with ALA 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E ILE* 2.8 18.2 + - + +
488E HIS* 3.7 8.5 - - - +
490E MET* 1.3 78.8 - - - +
492E LYS* 1.3 60.9 + - - +
494E GLY* 3.1 14.6 + - - -
495E LEU 4.3 2.6 + - - +
500E GLN* 3.7 26.6 - - - +
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Residues in contact with LYS 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E ASP* 3.1 28.3 + - - +
488E HIS* 3.0 31.7 + - + +
489E LEU* 3.8 18.8 - - - +
491E ALA* 1.3 77.3 - - - +
493E ALA* 1.3 60.6 + - - +
494E GLY* 3.1 2.5 + - - -
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Residues in contact with ALA 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489E LEU 3.0 18.6 + - - +
490E MET* 3.5 11.2 - - - +
491E ALA 3.2 0.4 - - - -
492E LYS* 1.3 76.4 - - - +
494E GLY* 1.3 58.2 + - - +
495E LEU* 3.5 11.3 + - + +
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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
------------------------------------------------------------
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