Contacts of the helix formed by residues 490 - 507 (chain A) 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 ILE 490 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A ASP* 4.4 13.2 - - + +
489A ASP* 1.3 79.0 - - + +
491A GLN* 1.3 63.9 + - + +
492A LYS 3.2 5.2 + - - -
493A GLU* 3.6 19.5 + - + +
494A LYS* 3.7 17.5 - - - +
544A TRP* 4.4 4.6 - - + -
549A PHE 3.9 9.0 - - - +
550A LYS* 3.7 25.1 - - - +
551A GLY 3.5 31.0 - - - +
552A PRO* 4.4 7.6 - - + -
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Residues in contact with GLN 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP* 3.5 29.9 + - + +
415A HIS* 3.6 39.0 - - + +
418A MET* 5.3 2.9 - - - +
486A LYS 5.0 0.6 + - - -
487A MET* 3.6 10.5 - - + +
488A ASP* 3.3 42.7 + - + +
490A ILE* 1.3 82.8 - - + +
492A LYS* 1.3 59.4 + - - +
493A GLU 3.5 0.4 - - - -
494A LYS* 4.2 15.3 - - + +
495A ALA* 3.6 17.8 + - - +
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Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLU* 3.5 39.0 + - + -
481A LEU* 4.2 19.0 - - + +
482A THR* 4.5 16.0 + - - -
487A MET* 3.7 26.2 - - + +
488A ASP 3.0 17.0 + - - +
489A ASP* 3.9 12.1 + - - +
491A GLN* 1.3 77.1 - - - +
493A GLU* 1.3 79.1 + - - +
494A LYS 3.4 0.7 - - - -
495A ALA* 3.7 1.4 - - - +
496A PHE* 2.9 37.1 + - - +
533A LYS* 5.5 2.3 - - - +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ASP 3.1 21.7 - - - +
490A ILE* 3.6 13.5 - - + +
492A LYS* 1.3 92.6 + - - +
494A LYS* 1.3 59.8 + - - +
496A PHE* 3.9 2.5 - - - +
497A ALA* 2.9 32.0 + - - +
533A LYS* 5.1 10.7 - - - +
537A LEU* 3.2 32.9 - - + +
544A TRP* 3.9 16.2 - - + -
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Residues in contact with LYS 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP* 5.6 1.8 + - - -
418A MET* 4.0 4.7 - - + +
490A ILE* 3.7 17.3 + - - +
491A GLN* 4.4 12.4 - - + +
493A GLU* 1.3 75.8 - - - +
495A ALA* 1.3 62.2 + - - +
497A ALA* 3.5 2.2 + - - +
498A LEU* 3.0 24.4 + - - +
544A TRP* 3.3 50.2 + - + +
545A VAL* 3.4 41.8 - - - +
547A SER 3.3 20.6 + - - +
548A LEU* 4.0 1.6 - - - +
549A PHE* 2.5 35.3 + - - +
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Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A MET* 3.7 18.6 - - - -
421A LEU* 4.5 4.4 - - + +
481A LEU* 4.0 11.0 - - + -
487A MET* 3.5 39.5 - - + -
491A GLN 3.6 7.2 + - - +
492A LYS 3.5 4.0 + - - +
493A GLU 3.3 0.4 - - - -
494A LYS* 1.3 81.2 - - - +
496A PHE* 1.3 61.3 + - - +
498A LEU* 3.4 3.1 + - - +
499A CYS* 3.1 27.0 + - - -
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Residues in contact with PHE 496 (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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474A LEU* 3.7 38.1 - - + -
477A ILE* 4.1 21.1 - - + -
478A GLU* 3.2 33.7 - - + -
481A LEU* 3.6 13.4 - - + +
492A LYS* 2.9 23.9 + - - +
493A GLU* 4.0 3.6 - - - +
495A ALA* 1.3 72.5 - - - +
497A ALA* 1.3 60.5 + - - +
499A CYS* 3.1 3.9 + - + -
500A ILE* 2.9 40.8 + - + +
533A LYS* 4.8 4.3 - - - -
534A ILE* 3.8 30.3 - - + -
537A LEU* 3.6 19.3 - - + -
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Residues in contact with ALA 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLU 2.9 19.3 + - - +
494A LYS* 3.8 4.7 - - - +
496A PHE* 1.3 76.7 - - - +
498A LEU* 1.3 51.3 + - - +
500A ILE* 3.2 3.9 + - - +
501A LYS* 2.8 41.4 + - - +
537A LEU* 3.5 41.1 - - + +
540A ALA* 4.5 2.2 - - + -
544A TRP* 5.1 0.7 - - + -
545A VAL* 4.3 16.2 - - + -
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 3.5 36.8 - - + +
418A MET* 3.6 23.6 - - + -
421A LEU* 3.9 12.8 - - + -
422A TYR* 3.7 31.2 - - + +
494A LYS 3.0 17.9 + - - +
495A ALA 3.6 4.3 - - - +
497A ALA* 1.3 76.2 - - - +
499A CYS* 1.3 58.1 + - - +
501A LYS* 3.7 6.4 - - - +
502A GLN* 2.8 52.0 + - - +
542A ILE* 4.3 13.2 - - + -
545A VAL* 4.5 6.9 - - + +
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Residues in contact with CYS 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 3.6 26.7 - - - -
451A ILE* 3.9 13.2 - - - -
455A GLN* 3.5 25.6 + - - +
474A LEU* 5.9 1.6 - - - -
477A ILE* 4.2 20.4 - - + -
481A LEU* 4.6 2.0 - - - -
495A ALA 3.1 23.9 + - - -
496A PHE* 3.1 13.3 + - + +
498A LEU* 1.3 75.9 - - - +
500A ILE* 1.3 61.3 + - - +
502A GLN* 3.9 2.9 - - - +
503A VAL* 3.2 29.1 + - - +
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Residues in contact with ILE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU* 4.7 7.2 - - + -
496A PHE* 2.9 40.7 + - + +
497A ALA* 3.5 6.1 - - - +
499A CYS* 1.3 75.0 - - - +
501A LYS* 1.3 60.3 + - - +
503A VAL* 3.3 6.7 + - - +
504A ASN* 2.9 28.6 + - - +
511A LEU* 4.0 12.4 - - + +
515A LEU* 5.0 0.4 - - + -
534A ILE* 3.6 51.4 - - + +
537A LEU* 3.8 27.6 - - + -
538A LEU* 3.9 18.8 - - + -
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Residues in contact with LYS 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 2.4 34.1 + - - +
364A VAL* 3.6 15.2 - - + +
497A ALA* 2.8 24.9 + - - +
498A LEU* 3.7 3.1 - - - +
500A ILE* 1.3 73.2 - - - +
502A GLN* 1.3 56.8 + - - +
504A ASN* 3.4 3.1 + - - +
505A PHE* 3.0 27.7 + - - +
537A LEU 3.7 13.2 - - - +
538A LEU* 3.1 35.9 + - + +
539A TRP 4.5 0.4 - - - -
540A ALA* 2.9 27.6 + - - -
542A ILE* 3.8 28.0 - - + +
545A VAL* 4.6 5.6 - - + -
603A GOL 3.8 12.8 + - - +
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Residues in contact with GLN 502 (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 VAL* 3.4 44.4 + - + -
365A TYR* 3.8 26.6 + - + +
421A LEU* 3.0 32.1 + - - +
455A GLN* 3.7 26.3 + - - +
498A LEU* 2.8 35.8 + - - +
499A CYS* 3.9 4.8 - - - +
501A LYS* 1.3 74.3 - - - +
503A VAL* 1.3 60.2 + - - +
505A PHE* 3.2 3.6 + - - +
506A LEU* 2.9 34.4 + - - +
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Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLN* 3.6 36.8 - - + +
458A ILE* 4.1 27.8 - - + -
459A VAL* 4.1 14.6 - - + -
462A MET* 4.3 5.4 - - + -
474A LEU* 5.3 4.9 - - + -
477A ILE* 5.4 0.2 - - + -
499A CYS 3.2 18.2 + - - +
500A ILE* 3.3 5.1 + - - +
502A GLN* 1.3 73.8 - - - +
504A ASN* 1.3 66.8 + - - +
506A LEU* 3.1 8.2 + - - +
507A SER* 3.0 25.5 + - - -
511A LEU* 3.9 18.4 - - + -
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Residues in contact with ASN 504 (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 SER* 4.4 2.2 + - - -
500A ILE 2.9 16.6 + - - +
501A LYS 3.6 5.4 - - - +
503A VAL* 1.3 77.2 - - - +
505A PHE* 1.3 58.0 + - - +
507A SER* 3.4 6.3 + - - -
509A GLY* 3.0 42.7 + - - -
511A LEU* 4.1 9.4 - - + +
512A GLU* 3.7 28.3 + - - +
538A LEU* 3.3 36.1 - - + +
603A GOL 3.8 21.4 + - - -
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Residues in contact with PHE 505 (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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362A GLU 5.5 4.5 - - - -
364A VAL* 4.3 12.1 - - + -
365A TYR* 4.3 20.4 - + - -
501A LYS 3.0 13.9 + - - +
502A GLN* 3.3 10.5 - - - +
503A VAL 3.1 0.4 - - - -
504A ASN* 1.3 74.3 - - - +
506A LEU* 1.3 81.1 + - + +
507A SER 3.1 5.5 + - - -
508A GLU* 3.2 15.6 + - - +
603A GOL 4.3 30.2 - - - -
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 3.8 24.7 - - + +
452A LEU* 5.6 3.1 - - + -
455A GLN* 4.6 16.6 - - + +
456A GLU* 5.4 8.7 - - + -
459A VAL* 3.4 29.5 - - + +
463A ASN* 5.3 1.4 + - - -
502A GLN 2.9 25.1 + - - +
503A VAL* 3.1 7.6 + - - +
505A PHE* 1.3 92.7 - - + +
507A SER* 1.3 57.8 + - - +
508A GLU* 3.5 4.3 + - - +
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Residues in contact with SER 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A VAL* 4.2 13.0 - - - -
462A MET* 3.7 23.3 - - - +
463A ASN* 4.5 5.6 - - - +
503A VAL 3.0 16.3 + - - -
504A ASN* 3.4 8.3 + - - -
505A PHE 3.1 0.2 - - - -
506A LEU* 1.3 77.6 - - - +
508A GLU* 1.3 70.1 + - - +
510A LYS* 3.2 40.3 + - - +
511A LEU 3.6 8.5 + - - -
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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