Contacts of the helix formed by residues 490 - 507 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414G ASP* 5.4 3.4 - - - +
488G ASP* 3.7 20.6 - - + +
489G ASP* 1.3 78.5 - - + +
491G GLN* 1.3 63.6 + - + +
492G LYS 3.0 4.3 - - - -
493G GLU* 2.9 23.8 + - - +
494G LYS* 3.2 37.8 + - + +
544G TRP* 4.2 11.0 - - + -
548G LEU 5.9 0.4 - - - +
549G PHE 4.0 4.3 - - - +
550G LYS* 3.5 36.6 - - + -
551G GLY* 3.9 8.7 - - - +
552G PRO* 5.5 4.0 - - + -
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Residues in contact with GLN 491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G ASP* 3.2 40.7 + - + +
415G HIS* 3.5 23.5 - - + +
418G MET* 4.7 3.5 - - - +
486G LYS 3.7 5.2 - - - +
487G MET* 3.3 20.9 - - + +
488G ASP* 3.1 45.8 + - + +
490G ILE* 1.3 81.6 - - + +
492G LYS* 1.3 56.7 + - - +
494G LYS* 3.8 18.0 - - + +
495G ALA* 3.4 21.7 + - - +
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Residues in contact with LYS 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478G GLU* 5.5 10.1 - - + +
481G LEU* 4.2 9.8 - - + +
482G THR* 3.7 35.3 + - - +
487G MET* 3.7 25.1 + - + +
488G ASP 3.3 15.0 + - - +
489G ASP* 3.3 37.7 + - - +
490G ILE 3.0 1.2 - - - -
491G GLN* 1.3 76.6 - - - +
493G GLU* 1.3 65.7 + - + +
494G LYS 3.2 1.6 - - - -
495G ALA* 3.8 1.5 - - - +
496G PHE* 3.0 32.2 + - + +
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Residues in contact with GLU 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489G ASP 3.8 12.3 - - - +
490G ILE* 2.9 12.8 + - - +
492G LYS* 1.3 85.1 - - + +
494G LYS* 1.3 59.8 + - + +
496G PHE* 4.7 3.1 - - - -
497G ALA* 3.2 25.7 + - - +
533G LYS* 5.2 10.3 - - + +
537G LEU* 3.9 31.9 - - + +
544G TRP* 4.8 10.3 - - + -
552G PRO* 4.3 19.5 - - - +
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Residues in contact with LYS 494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G ASP* 3.8 13.3 + - - -
418G MET* 3.6 5.6 - - + +
490G ILE* 3.2 34.6 - - + +
491G GLN* 3.8 12.8 - - + +
492G LYS 3.2 0.2 - - - -
493G GLU* 1.3 77.2 - - - +
495G ALA* 1.3 59.5 + - - +
497G ALA 3.9 0.2 - - - -
498G LEU* 3.1 26.0 + - - +
544G TRP* 3.1 48.3 + - + -
545G VAL* 3.6 33.2 - - - +
547G SER 2.6 30.5 + - - -
548G LEU 4.3 0.2 - - - -
549G PHE 3.7 15.8 + - - +
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Residues in contact with ALA 495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G MET* 3.5 15.5 - - + +
421G LEU* 4.9 7.2 - - + -
481G LEU* 3.9 14.4 - - + -
487G MET* 3.7 26.9 - - + -
491G GLN 3.4 16.9 + - - +
492G LYS 3.6 1.5 + - - +
494G LYS* 1.3 78.2 - - - +
496G PHE* 1.3 59.9 + - - +
498G LEU* 3.1 5.2 + - - +
499G CYS* 2.8 33.0 + - - -
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Residues in contact with PHE 496 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G LEU* 3.2 53.8 - - + -
477G ILE* 4.2 17.7 - - + -
478G GLU* 3.4 45.8 - - + -
481G LEU* 3.6 10.4 - - + +
492G LYS* 3.0 19.8 + - + +
493G GLU* 4.5 0.9 - - - +
495G ALA* 1.3 76.2 - - - +
497G ALA* 1.3 57.5 + - - +
499G CYS* 3.2 4.5 + - + -
500G ILE* 2.8 43.3 + - + +
533G LYS* 5.4 0.9 - - - -
534G ILE* 4.3 14.8 - - + -
537G LEU* 4.1 18.8 - - + -
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Residues in contact with ALA 497 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493G GLU 3.2 20.7 + - - +
494G LYS 3.9 0.2 - - - +
495G ALA 3.2 0.2 - - - -
496G PHE* 1.3 78.0 - - - +
498G LEU* 1.3 61.4 + - - +
500G ILE* 3.8 2.8 - - - +
501G LYS* 3.2 32.6 + - - +
537G LEU* 3.5 39.3 - - + +
540G ALA* 4.7 2.7 - - + -
544G TRP* 5.4 0.4 - - - +
545G VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G VAL* 3.8 15.9 - - + +
418G MET* 3.6 26.7 - - + -
421G LEU* 3.6 34.5 - - + -
422G TYR* 4.0 22.0 - - + +
494G LYS 3.1 16.1 + - - +
495G ALA 3.1 7.4 + - - +
497G ALA* 1.3 76.5 - - - +
499G CYS* 1.3 62.7 + - - +
501G LYS* 3.5 8.9 + - + +
502G GLN* 3.2 44.8 + - + +
542G ILE* 5.5 4.0 - - + -
545G VAL* 4.7 8.9 - - + +
546G VAL* 4.7 9.6 - - + -
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Residues in contact with CYS 499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421G LEU* 3.5 28.9 - - - -
451G ILE* 4.1 11.2 - - - -
455G GLN* 3.4 25.7 + - - +
474G LEU* 6.3 0.7 - - + -
477G ILE* 4.3 22.0 - - + -
481G LEU* 4.6 3.4 - - - -
495G ALA 2.8 28.0 + - - -
496G PHE* 3.5 11.0 - - + +
498G LEU* 1.3 73.7 - - - +
500G ILE* 1.3 62.6 + - - +
502G GLN* 3.3 3.6 + - - +
503G VAL* 3.1 27.7 + - - +
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Residues in contact with ILE 500 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G LEU* 4.4 10.8 - - + -
496G PHE* 2.8 38.5 + - + +
497G ALA* 3.8 4.7 - - - +
498G LEU 3.3 0.2 - - - -
499G CYS* 1.3 72.1 - - - +
501G LYS* 1.3 63.9 + - - +
503G VAL* 3.1 10.8 + - - +
504G ASN* 2.9 20.4 + - - +
511G LEU* 3.9 13.9 - - + +
534G ILE* 3.7 40.8 - - + -
537G LEU* 3.8 27.6 - - + -
538G LEU* 3.7 29.6 - - + -
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Residues in contact with LYS 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G GLU* 3.5 32.2 + - - +
364G VAL* 3.5 15.7 - - + +
497G ALA 3.2 19.1 + - - +
498G LEU* 3.8 7.4 - - + +
499G CYS 3.4 0.2 - - - -
500G ILE* 1.3 78.3 - - - +
502G GLN* 1.3 56.6 + - - +
504G ASN* 3.2 4.6 + - - +
505G PHE* 2.8 28.2 + - - +
537G LEU 3.9 9.4 - - - -
538G LEU* 2.8 47.3 + - + +
539G TRP* 4.2 1.0 - - - +
540G ALA 2.8 28.1 + - - +
542G ILE* 4.5 16.6 - - + -
545G VAL* 4.7 10.3 - - + -
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Residues in contact with GLN 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G VAL* 3.5 34.3 + - + +
365G TYR* 3.5 37.8 + - + +
421G LEU* 3.0 30.2 + - - +
422G TYR* 4.4 0.2 - - - +
452G LEU* 5.6 0.2 - - - +
455G GLN* 3.5 23.2 + - - +
498G LEU* 3.2 29.0 + - - +
499G CYS* 3.6 6.1 - - - +
500G ILE 3.2 0.6 - - - -
501G LYS* 1.3 74.4 - - - +
503G VAL* 1.3 60.1 + - - +
505G PHE* 3.1 4.0 + - - +
506G LEU* 2.8 36.9 + - + +
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Residues in contact with VAL 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455G GLN* 3.9 31.8 - - + -
458G ILE* 3.7 38.6 - - + -
459G VAL* 3.8 15.3 - - + +
462G MET* 4.4 3.6 - - + -
474G LEU* 5.4 5.2 - - + -
477G ILE* 5.3 3.4 - - + -
499G CYS 3.1 17.9 + - - +
500G ILE* 3.4 9.0 - - - +
502G GLN* 1.3 74.0 - - - +
504G ASN* 1.3 62.8 + - - +
506G LEU* 3.3 2.8 + - - +
507G SER* 3.0 24.1 + - - -
511G LEU* 3.8 15.9 - - + -
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Residues in contact with ASN 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357G SER* 4.6 7.3 + - - -
358G VAL* 5.1 12.7 - - - +
500G ILE 2.9 12.5 + - - +
501G LYS* 3.4 9.8 + - - +
503G VAL* 1.3 75.6 - - - +
505G PHE* 1.3 59.9 + - - +
507G SER* 3.3 6.6 + - - -
509G GLY* 2.9 55.9 + - - -
511G LEU* 4.0 12.7 - - + +
512G GLU* 3.5 23.9 + - - +
538G LEU* 4.0 24.6 - - + +
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Residues in contact with PHE 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358G VAL* 6.4 1.6 - - + -
364G VAL* 3.6 30.7 - - + -
365G TYR* 4.6 16.4 - + - -
501G LYS 2.8 13.7 + - - +
502G GLN* 3.1 8.0 + - - +
504G ASN* 1.3 77.6 - - - +
506G LEU* 1.3 82.7 + - + +
508G GLU* 3.2 17.5 + - - +
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Residues in contact with LEU 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G TYR* 4.0 26.0 - - + +
452G LEU* 5.5 2.9 - - + -
455G GLN* 4.8 17.7 - - + +
456G GLU* 5.3 9.2 - - + -
459G VAL* 3.3 36.4 - - + +
463G ASN* 5.0 3.1 + - - -
502G GLN 2.8 23.3 + - - +
503G VAL* 4.8 1.1 - - - -
505G PHE* 1.3 92.9 - - + +
507G SER* 1.3 58.5 + - - +
508G GLU* 3.4 4.1 - - - +
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Residues in contact with SER 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459G VAL* 4.1 11.2 - - - -
462G MET* 3.7 22.1 - - - +
463G ASN* 4.3 10.3 - - - +
503G VAL 3.0 16.6 + - - -
504G ASN* 3.3 8.3 + - - -
506G LEU* 1.3 77.6 - - - +
508G GLU* 1.3 69.4 + - - +
510G LYS* 3.2 31.2 + - - +
511G LEU 3.5 18.0 + - - -
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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
------------------------------------------------------------
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