Contacts of the helix formed by residues 489 - 507 (chain E) in PDB entry 4KYI
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 489 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488E ASP* 1.3 83.3 + - - +
490E ILE* 1.3 58.8 + - + +
492E LYS* 3.4 10.0 + - - +
493E GLU* 3.0 35.0 + - + +
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Residues in contact with ILE 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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414E ASP* 5.9 0.7 - - - +
488E ASP* 2.6 16.3 + - - +
489E ASP* 1.3 71.5 - - + +
491E GLN* 1.3 57.5 + - + +
492E LYS 3.0 4.7 - - - -
493E GLU* 3.1 9.2 + - + +
494E LYS* 2.9 57.1 + - + +
544E TRP* 4.6 3.4 - - + -
549E PHE 4.0 2.9 - - - +
550E LYS* 3.1 33.2 - - - +
551E GLY* 3.6 18.6 - - - +
552E PRO* 3.9 18.2 - - + -
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Residues in contact with GLN 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414E ASP* 3.3 38.4 + - + +
415E HIS* 3.6 25.9 - - + +
418E MET* 4.8 4.3 - - + +
486E LYS 4.3 1.6 - - - +
487E MET* 3.1 33.7 - - + +
488E ASP* 3.2 42.9 + - - +
490E ILE* 1.3 78.0 - - + +
492E LYS* 1.3 56.4 + - - +
494E LYS* 4.3 10.9 - - + +
495E ALA* 3.4 13.0 + - - +
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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
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478E GLU* 3.2 36.3 + - + -
481E LEU* 4.5 14.1 - - + +
482E THR* 4.3 21.5 - - - +
487E MET* 4.3 14.6 - - + +
488E ASP 3.2 17.8 + - - +
489E ASP* 3.6 8.7 + - - +
490E ILE 3.0 0.6 - - - -
491E GLN* 1.3 77.6 - - - +
493E GLU* 1.3 86.8 + - - +
494E LYS 3.1 1.3 - - - -
495E ALA* 3.7 1.3 - - - +
496E PHE* 2.8 43.6 + - + +
533E LYS* 4.6 4.8 - - - +
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Residues in contact with GLU 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 ASP* 3.0 21.4 + - + +
490E ILE* 3.1 11.6 + - + +
492E LYS* 1.3 102.5 + - - +
494E LYS* 1.3 56.3 + - - +
496E PHE* 4.9 1.3 - - - -
497E ALA* 3.2 26.0 + - - +
533E LYS* 4.6 14.5 - - - +
537E LEU* 3.3 32.3 - - - +
544E TRP* 3.8 18.1 - - + -
552E PRO* 6.2 3.4 - - + -
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Residues in contact with LYS 494 (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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414E ASP* 3.9 11.0 + - - +
418E MET* 3.7 9.2 - - + -
490E ILE* 2.9 30.6 + - + +
491E GLN* 4.3 8.1 - - + -
493E GLU* 1.3 76.1 - - - +
495E ALA* 1.3 65.4 + - - +
497E ALA* 3.4 2.9 + - - +
498E LEU* 3.0 22.9 + - - +
544E TRP* 3.3 47.1 - - + +
545E VAL* 3.5 33.4 - - - +
547E SER 2.7 24.2 + - - +
549E PHE 2.6 32.8 + - - +
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Residues in contact with ALA 495 (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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418E MET* 3.5 14.3 - - + +
421E LEU* 4.8 6.7 - - + +
481E LEU* 3.9 13.2 - - + -
487E MET* 3.7 25.4 - - + -
491E GLN 3.4 19.1 + - - +
492E LYS 3.3 3.5 + - - +
494E LYS* 1.3 78.9 - - - +
496E PHE* 1.3 57.6 + - - +
498E LEU* 3.2 5.3 + - - +
499E CYS* 2.9 32.2 + - - -
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Residues in contact with PHE 496 (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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474E LEU* 3.2 38.6 - - + -
475E ASP* 5.4 0.9 - - - -
477E ILE* 4.1 11.9 - - + -
478E GLU* 3.3 40.2 - - + -
481E LEU* 3.6 19.0 - - + +
492E LYS* 2.8 27.0 + - + +
493E GLU* 4.9 0.2 - - - -
495E ALA* 1.3 70.6 - - - +
497E ALA* 1.3 64.3 + - - +
499E CYS* 3.4 2.2 + - + -
500E ILE* 3.0 42.3 + - + +
533E LYS* 4.6 4.5 - - - -
534E ILE* 3.8 29.6 - - + -
537E LEU* 3.5 22.4 - - + -
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Residues in contact with ALA 497 (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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493E GLU 3.2 19.6 + - - +
494E LYS 3.5 5.2 - - - +
495E ALA 3.2 0.2 - - - -
496E PHE* 1.3 80.0 - - - +
498E LEU* 1.3 55.6 + - - +
500E ILE* 3.4 2.9 + - - +
501E LYS* 2.9 36.8 + - - +
537E LEU* 3.3 37.9 - - + +
540E ALA* 4.6 2.5 - - + -
544E TRP* 4.7 0.7 - - + -
545E VAL* 3.9 17.3 - - + -
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Residues in contact with LEU 498 (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* 3.6 24.9 - - - +
418E MET* 3.7 25.8 - - - -
421E LEU* 4.0 25.4 - - + -
422E TYR* 4.0 20.4 - - + -
494E LYS 3.0 14.0 + - - +
495E ALA* 3.2 8.9 + - - +
497E ALA* 1.3 75.9 - - - +
499E CYS* 1.3 57.9 - - - +
501E LYS* 3.1 9.3 + - + +
502E GLN* 2.9 47.1 + - + +
542E ILE* 4.9 8.3 - - + -
545E VAL* 4.3 17.9 - - + +
546E VAL* 5.3 0.2 - - + -
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Residues in contact with CYS 499 (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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421E LEU* 3.6 29.2 - - - -
451E ILE* 3.8 19.3 - - - -
455E GLN* 2.8 30.0 + - - +
474E LEU* 5.9 0.7 - - - -
477E ILE* 4.1 23.8 - - + -
481E LEU* 4.4 5.2 - - - -
495E ALA 2.9 22.3 + - - +
496E PHE* 3.8 7.4 - - + +
497E ALA 3.4 0.2 - - - -
498E LEU* 1.3 75.5 - - - +
500E ILE* 1.3 62.0 + - - +
502E GLN* 4.3 1.8 - - - -
503E VAL* 3.2 17.4 + - - +
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Residues in contact with ILE 500 (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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474E LEU* 4.3 11.4 - - + -
496E PHE* 3.0 37.6 + - + +
497E ALA* 3.7 3.8 - - - +
499E CYS* 1.3 74.8 - - - +
501E LYS* 1.3 65.4 + - - +
503E VAL* 3.2 8.7 + - - +
504E ASN* 3.1 21.3 + - - +
511E LEU* 3.9 16.9 - - + +
515E LEU* 5.2 0.2 - - + -
534E ILE* 3.6 47.3 - - + +
537E LEU* 4.0 19.5 - - + -
538E LEU* 3.9 28.3 - - + -
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Residues in contact with LYS 501 (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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362E GLU* 2.4 38.3 + - - +
364E VAL* 3.6 18.4 - - + +
497E ALA 2.9 25.9 + - - +
498E LEU* 3.4 9.9 - - - +
500E ILE* 1.3 75.3 - - - +
502E GLN* 1.3 61.8 + - - +
504E ASN* 3.5 3.1 + - - +
505E PHE* 3.3 21.7 + - - +
537E LEU 3.8 13.5 - - - +
538E LEU* 3.2 32.6 + - + +
539E TRP 4.8 0.2 - - - -
540E ALA 2.9 30.1 + - - -
542E ILE* 4.2 24.2 - - + +
545E VAL* 4.4 9.0 - - + -
602E GOL 4.6 3.3 - - - -
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Residues in contact with GLN 502 (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* 3.4 27.3 + - + -
365E TYR* 3.5 32.3 + - + +
421E LEU* 2.5 39.5 + - - +
452E LEU* 5.7 0.3 - - - +
455E GLN* 3.0 31.5 + - - +
498E LEU* 2.9 36.1 + - + +
499E CYS* 4.3 1.3 - - - -
501E LYS* 1.3 75.0 - - - +
503E VAL* 1.3 65.2 + - - +
505E PHE* 3.1 3.5 + - - +
506E LEU* 3.0 30.2 + - + +
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Residues in contact with VAL 503 (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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455E GLN* 3.7 35.6 - - + +
458E ILE* 4.0 33.4 - - + -
459E VAL* 3.8 17.3 - - + +
462E MET* 4.2 5.2 - - + -
474E LEU* 5.2 2.5 - - + -
477E ILE* 5.1 2.0 - - + -
499E CYS 3.2 15.5 - - - +
500E ILE* 3.2 9.7 + - - +
502E GLN* 1.3 77.1 - - - +
504E ASN* 1.3 53.5 + - - +
506E LEU* 3.4 2.6 + - - -
507E SER* 2.4 34.1 + - - -
511E LEU* 3.9 17.7 - - + -
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Residues in contact with ASN 504 (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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357E SER* 4.3 7.3 - - - -
500E ILE 3.1 12.5 + - - +
501E LYS 3.7 9.0 - - - +
503E VAL* 1.3 76.5 - - - +
505E PHE* 1.3 59.2 + - - +
507E SER* 3.0 8.9 + - - -
508E GLU 3.2 0.2 + - - -
509E GLY* 2.9 53.8 + - - -
511E LEU* 3.6 9.5 - - + +
512E GLU* 3.2 42.1 + - - +
538E LEU* 3.9 23.2 - - + +
602E GOL 4.4 13.2 + - - -
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Residues in contact with PHE 505 (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* 4.7 7.6 - - + -
365E TYR* 4.0 23.8 - + - -
501E LYS 3.3 10.1 + - - +
502E GLN* 3.1 8.3 + - - +
504E ASN* 1.3 75.4 - - - +
506E LEU* 1.3 80.7 + - + +
507E SER 3.0 9.8 + - - -
508E GLU* 3.1 16.0 + - - +
602E GOL 3.8 30.4 - - - +
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Residues in contact with LEU 506 (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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365E TYR* 3.4 27.1 - - + +
452E LEU* 5.8 2.9 - - + -
455E GLN* 5.4 9.4 - - + +
456E GLU* 5.1 14.8 - - + +
459E VAL* 3.2 33.2 - - + +
463E ASN* 5.2 1.0 + - - -
502E GLN* 3.0 23.5 + - + +
503E VAL* 3.4 1.3 + - - -
505E PHE* 1.3 96.3 - - + +
507E SER* 1.3 56.3 + - - +
508E GLU* 3.5 3.4 - - - +
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Residues in contact with SER 507 (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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459E VAL* 4.0 11.9 - - - -
462E MET* 3.6 28.3 - - - +
463E ASN* 4.8 4.0 - - - -
503E VAL 2.4 25.9 + - - -
504E ASN* 3.0 14.9 + - - -
506E LEU* 1.3 80.6 - - - +
508E GLU* 1.3 70.8 + - - +
510E LYS* 3.1 31.1 - - - +
511E LEU 4.0 4.0 + - - -
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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