Contacts of the helix formed by residues 441 - 456 (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 GLN 441 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393E TRP* 3.8 2.5 - - - -
439E ASN* 3.0 29.6 + - - +
440E LEU* 1.3 76.7 + - - +
442E GLY* 1.3 61.0 + - - +
443E GLU* 3.2 15.7 - - + +
444E GLU* 3.0 27.0 + - + +
445E PHE* 2.8 26.7 + - - +
503E ARG* 5.2 0.7 - - - +
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Residues in contact with GLY 442 (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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320E LEU* 4.5 7.6 - - - -
393E TRP* 3.4 28.2 - - - -
441E GLN* 1.3 74.2 + - - +
443E GLU* 1.3 66.1 + - - +
445E PHE* 3.2 4.8 + - - +
446E VAL* 3.1 30.1 + - - +
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Residues in contact with GLU 443 (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* 3.6 23.6 - - + +
320E LEU* 4.4 14.9 - - + +
441E GLN* 3.7 13.2 - - + +
442E GLY* 1.3 84.5 + - - +
444E GLU* 1.3 61.7 + - + +
446E VAL* 3.2 21.8 - - - +
447E CYS* 3.4 16.1 - - - -
489E LEU* 3.5 28.1 - - + +
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Residues in contact with GLU 444 (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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440E LEU* 3.5 12.2 - - + +
441E GLN* 3.0 31.7 + - + +
443E GLU* 1.3 76.2 - - + +
445E PHE* 1.3 65.9 + - - +
447E CYS* 3.3 4.5 + - - +
448E LEU* 3.0 27.6 + - - +
486E LEU* 4.0 21.8 - - + +
489E LEU* 4.3 14.2 - - + +
490E MET* 3.9 16.2 + - + +
503E ARG* 2.7 48.4 + - - -
507E LEU* 4.3 7.2 - - + -
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Residues in contact with PHE 445 (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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323E GLU* 3.6 22.0 - - - -
389E ILE* 3.4 43.1 - - + -
390E GLY* 3.9 14.4 - - - -
393E TRP* 3.4 56.1 - + + -
440E LEU* 4.2 13.4 - - + +
441E GLN 2.8 12.3 + - - +
442E GLY* 3.2 9.4 + - - +
444E GLU* 1.3 76.7 - - - +
446E VAL* 1.3 67.1 + - + +
448E LEU* 3.0 6.6 + - - +
449E LYS* 2.9 48.9 + - + +
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Residues in contact with VAL 446 (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* 4.8 2.9 - - + +
319E LEU* 3.8 32.5 - - + +
320E LEU* 4.1 17.3 - - + +
323E GLU* 3.4 41.5 - - + +
360E TRP* 5.4 1.0 - - - +
442E GLY 3.1 12.1 + - - +
443E GLU* 3.2 22.7 - - - +
445E PHE* 1.3 85.3 - - + +
447E CYS* 1.3 59.6 - - - +
449E LYS* 4.0 6.4 - - - +
450E SER* 3.0 28.9 + - - -
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Residues in contact with CYS 447 (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* 5.1 2.0 - - - -
319E LEU* 4.2 15.3 - - - -
443E GLU 3.4 15.3 - - - -
444E GLU 3.3 8.9 + - - +
445E PHE 3.1 0.2 - - - -
446E VAL* 1.3 80.1 - - - +
448E LEU* 1.3 65.3 + - - +
450E SER* 3.4 3.3 + - - -
451E ILE* 3.0 28.9 + - - +
482E ILE* 3.7 14.2 - - + +
485E THR* 3.7 31.2 - - - -
486E LEU* 3.7 21.1 - - + -
489E LEU* 4.2 8.1 - - - -
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Residues in contact with LEU 448 (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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389E ILE* 4.0 13.0 - - + -
435E PHE* 4.2 21.1 - - + -
440E LEU* 4.0 26.0 - - + -
444E GLU 3.0 17.8 + - - +
445E PHE* 3.0 7.7 + - - +
447E CYS* 1.3 75.0 - - - +
449E LYS* 1.3 62.6 + - - +
451E ILE* 3.2 7.8 + - + +
452E ILE* 3.0 26.3 + - - +
486E LEU* 4.2 19.1 - - + -
507E LEU* 4.0 37.0 - - + +
508E LEU* 4.3 13.9 - - + -
511E LEU* 4.6 10.6 - - + +
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Residues in contact with LYS 449 (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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323E GLU* 2.7 38.9 + - - -
324E PRO* 3.7 18.6 - - - +
360E TRP* 3.7 29.5 - - + +
386E ILE* 3.9 28.4 - - + +
389E ILE* 4.1 22.3 - - + +
390E GLY* 5.4 1.7 - - - -
445E PHE* 2.9 38.3 + - + +
446E VAL* 4.0 5.6 - - - +
448E LEU* 1.3 75.1 - - - +
450E SER* 1.3 62.7 + - - +
452E ILE* 3.3 7.8 + - - +
453E LEU* 3.2 19.6 + - - +
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Residues in contact with SER 450 (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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319E LEU* 3.4 25.3 - - - +
360E TRP* 4.3 10.0 + - - -
364E VAL* 3.9 18.8 - - - +
446E VAL 3.0 17.3 + - - -
447E CYS 3.6 4.7 - - - -
449E LYS* 1.3 80.1 - - - +
451E ILE* 1.3 61.2 + - - +
453E LEU* 3.2 15.6 + - - +
454E LEU* 3.2 17.7 + - - +
482E ILE* 3.9 19.1 - - - -
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Residues in contact with ILE 451 (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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447E CYS 3.0 20.1 + - - +
448E LEU* 3.2 11.0 + - - +
450E SER* 1.3 76.1 - - - +
452E ILE* 1.3 53.1 + - - +
454E LEU* 3.2 1.6 + - - -
455E ASN* 2.8 40.6 + - + +
479E LEU* 4.0 16.0 - - + +
482E ILE* 3.7 27.6 - - + -
483E THR* 5.3 5.4 - - - +
486E LEU* 4.0 23.1 - - + -
508E LEU* 4.0 14.1 - - + -
511E LEU* 3.9 8.5 - - + -
509F LEU* 3.7 39.5 - - + -
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Residues in contact with ILE 452 (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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382E ALA* 3.7 8.8 - - + +
385E GLU* 3.6 26.5 - - + +
386E ILE* 4.2 7.2 - - + -
389E ILE* 3.7 43.3 - - + -
448E LEU 3.0 10.2 + - - +
449E LYS* 3.5 7.6 - - - +
451E ILE* 1.3 76.4 - - - +
453E LEU* 1.3 63.7 + - - +
455E ASN* 4.8 2.2 - - - +
456E SER* 2.9 45.0 + - - +
511E LEU* 3.9 24.9 - - + -
514E ILE* 4.2 14.8 - - + -
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Residues in contact with LEU 453 (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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360E TRP* 3.9 22.4 - - + -
361E ALA* 4.0 12.6 - - + -
364E VAL* 4.3 13.2 - - + -
367E PHE* 3.7 36.8 - - + -
378E LEU* 3.4 34.6 - - + +
379E LEU* 3.7 29.6 - - + -
382E ALA* 4.2 6.6 - - - +
386E ILE* 4.2 12.6 - - + -
449E LYS 3.2 7.6 + - - +
450E SER 3.2 9.7 + - - +
452E ILE* 1.3 81.7 - - - +
454E LEU* 1.3 60.7 + - + +
456E SER 4.6 0.7 + - - -
457E GLY 5.0 0.3 + - - -
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Residues in contact with LEU 454 (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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364E VAL* 5.2 7.2 - - + -
365E PRO 5.2 3.6 - - - +
366E GLY 5.4 1.8 - - - +
367E PHE* 4.1 22.7 - - + +
370E LEU* 4.3 8.1 - - + -
378E LEU* 3.9 25.9 - - + +
450E SER 3.2 12.0 + - - +
451E ILE 3.2 2.0 + - - -
453E LEU* 1.3 81.0 - - + +
455E ASN* 1.3 58.6 + - - +
458E VAL* 3.4 13.5 - - - +
475E ILE* 3.4 32.1 - - + +
478E VAL* 3.6 34.8 - - + -
479E LEU* 3.8 19.0 - - + +
482E ILE* 4.3 12.3 - - + -
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Residues in contact with ASN 455 (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* 2.8 26.4 + - + +
452E ILE* 4.5 1.9 - - - +
454E LEU* 1.3 77.7 - - - +
456E SER* 1.3 69.6 + - - +
457E GLY 3.1 3.7 + - - -
458E VAL* 3.3 21.1 + - - +
459E TYR* 2.7 38.2 + - - -
479E LEU* 4.2 12.0 - - + +
511E LEU* 5.7 1.8 - - - +
515E ARG* 4.3 0.4 - - - +
509F LEU* 3.6 40.0 + - + +
512F SER* 4.1 14.1 + - - -
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Residues in contact with SER 456 (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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381E CYS* 3.3 11.7 - - - -
382E ALA* 3.8 14.4 - - - -
385E GLU* 2.7 33.8 + - - -
452E ILE* 2.9 26.0 + - - +
453E LEU 4.6 0.2 + - - -
454E LEU 3.8 0.2 - - - -
455E ASN* 1.3 79.3 + - - +
457E GLY* 1.3 57.1 + - - +
459E TYR* 4.7 3.8 + - - -
460E THR* 4.9 2.3 + - - +
515E ARG* 3.1 36.2 + - - +
512F SER* 5.1 0.9 + - - -
513F HIS* 5.0 3.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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