Contacts of the helix formed by residues 491 - 510 (chain F) in PDB entry 4YJL
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 491 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441F PRO* 6.0 0.7 - - - +
489F THR* 3.0 22.0 - - + +
490F ASN* 1.3 75.5 - - - +
492F HIS* 1.3 60.7 + - - +
493F TYR* 3.2 15.8 + - - +
494F SER* 2.9 33.5 + - - -
495F ILE* 3.0 26.0 + - - +
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Residues in contact with HIS 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D LYS* 4.1 19.3 - - - -
490F ASN* 3.0 20.2 + - + -
491F ASP* 1.3 72.8 + - - +
493F TYR* 1.3 60.1 + - - +
495F ILE* 4.0 10.2 - - + +
496F THR* 2.7 34.6 + - - +
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Residues in contact with TYR 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D ASP 4.4 2.2 - - - -
435D LYS* 3.6 47.3 + - + +
441F PRO* 3.7 20.0 - - + -
442F VAL* 3.5 49.4 - - + +
445F GLN* 3.7 2.8 - - - -
446F ILE 3.2 11.8 + - - -
447F CYS* 3.0 39.3 + - + +
448F PRO* 3.6 5.4 - - - +
491F ASP* 3.2 13.3 + - - +
492F HIS* 1.3 77.5 - - - +
494F SER* 1.3 63.3 + - - +
496F THR* 3.8 2.8 - - - -
497F LEU* 3.1 29.8 + - + +
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Residues in contact with SER 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F PRO* 5.6 2.5 - - - -
482F ASP* 2.7 26.3 + - - -
486F TYR* 5.0 5.2 - - - +
489F THR* 5.2 7.5 + - - +
491F ASP* 2.9 28.2 + - - -
493F TYR* 1.3 75.4 - - - +
495F ILE* 1.3 65.9 + - - +
497F LEU* 3.4 12.4 - - - +
498F ARG* 3.0 43.5 + - - +
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Residues in contact with ILE 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489F THR 3.8 11.7 - - - +
490F ASN* 3.5 41.5 - - + +
491F ASP 3.0 10.8 + - - +
492F HIS* 4.0 11.0 - - + +
493F TYR 3.4 0.2 - - - -
494F SER* 1.3 74.6 - - - +
496F THR* 1.3 60.3 + - - +
498F ARG* 3.2 9.0 + - - +
499F ARG* 2.9 42.6 + - + +
537F SER* 3.5 36.1 - - - +
540F LEU* 4.4 8.2 - - + +
803F EDO 4.1 10.1 - - - +
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Residues in contact with THR 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D GLY 5.8 1.1 - - - +
431D MET* 4.3 2.0 - - - -
435D LYS* 3.5 25.6 + - + +
447F CYS* 3.4 23.8 - - - -
492F HIS* 2.7 22.0 + - - +
493F TYR 3.8 0.9 - - - -
495F ILE* 1.3 78.2 - - - +
497F LEU* 1.3 57.7 + - - +
499F ARG* 3.1 22.5 + - - +
500F TYR* 2.9 52.3 + - + +
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Residues in contact with LEU 497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441F PRO* 3.6 38.8 - - + -
446F ILE* 4.2 12.3 - - + -
447F CYS* 3.7 14.1 - - - +
450F VAL* 3.7 23.5 - - + +
478F LEU* 4.7 12.8 - - + +
479F LEU* 5.5 2.2 - - - -
482F ASP* 4.2 17.9 - - + +
493F TYR* 3.1 26.7 + - + +
494F SER* 3.4 14.4 - - - +
496F THR* 1.3 75.5 - - - +
498F ARG* 1.3 71.3 + - + +
501F ALA* 3.0 32.8 + - + +
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Residues in contact with ARG 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F LEU* 3.7 27.0 - - + +
482F ASP* 2.8 46.8 + - + +
483F CYS* 3.5 15.3 - - - +
486F TYR* 3.9 6.5 - - - +
487F GLY 2.9 29.9 + - - -
488F LEU* 4.5 0.4 - - - +
489F THR* 4.7 2.5 - - - +
494F SER* 3.0 30.3 + - - +
495F ILE* 3.6 5.4 - - - +
496F THR 3.2 0.2 - - - -
497F LEU* 1.3 82.0 - - + +
499F ARG* 1.3 54.4 + - - +
501F ALA* 3.9 1.2 - - - +
502F GLY* 3.0 25.8 + - - -
532F GLN* 2.7 42.5 + - - +
540F LEU* 3.9 22.0 - - + +
543F VAL* 4.6 0.3 - - - +
544F ILE* 5.1 0.7 - - - +
803F EDO 4.4 9.1 + - - -
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Residues in contact with ARG 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F ILE* 2.9 30.8 + - - +
496F THR* 3.4 31.7 + - - +
498F ARG* 1.3 76.1 - - - +
500F TYR* 1.3 72.6 + - + +
502F GLY 3.2 1.2 + - - -
503F MET* 2.9 45.0 + - - +
537F SER* 4.5 0.2 - - - -
539F ASP* 3.9 22.4 + - - +
540F LEU* 3.8 35.4 - - + +
543F VAL* 3.5 17.0 - - + +
506L TYR* 5.7 2.6 + - - -
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Residues in contact with TYR 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D GLU* 4.1 6.6 - - + +
429D PRO 3.8 14.6 + - - -
430D GLY 5.3 0.3 - - - -
431D MET* 3.5 26.7 - - - +
447F CYS* 3.9 8.3 - - - -
450F VAL* 3.7 23.1 - - + +
451F CYS* 3.6 35.0 - - + -
454F MET* 3.3 33.0 - - + +
496F THR* 2.9 41.8 + - + +
499F ARG* 1.3 90.1 + - + +
501F ALA* 1.3 63.5 + - - +
503F MET* 3.3 20.1 + - + +
504F ALA* 3.1 18.9 + - - +
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Residues in contact with ALA 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F VAL* 4.2 15.6 - - + +
475F ILE* 3.5 26.7 - - + +
478F LEU* 5.1 2.2 - - + -
479F LEU* 4.2 23.6 - - + +
497F LEU* 3.0 19.4 + - + +
498F ARG 3.9 3.8 - - - +
500F TYR* 1.3 77.0 - - - +
502F GLY* 1.3 56.6 + - - +
504F ALA* 3.2 2.9 + - - -
505F LEU* 2.9 32.5 + - - +
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Residues in contact with GLY 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F LEU* 4.8 6.4 - - - +
498F ARG 3.0 13.6 + - - -
501F ALA* 1.3 73.8 - - - +
503F MET* 1.3 58.7 - - - +
505F LEU* 3.3 8.2 + - - -
506F THR* 2.8 31.7 + - - -
543F VAL* 3.5 21.1 - - - -
544F ILE* 5.1 2.7 - - - -
547F VAL* 3.2 12.3 - - - +
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Residues in contact with MET 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454F MET* 3.6 34.3 - - + -
458F PHE* 4.6 4.5 - - + -
499F ARG* 2.9 33.3 + - - +
500F TYR* 3.5 27.6 - - + +
501F ALA 3.3 0.2 - - - -
502F GLY* 1.3 73.9 - - - +
504F ALA* 1.3 59.7 + - - +
506F THR* 3.3 5.5 + - - -
507F ASN* 3.0 34.8 + - - +
543F VAL* 4.1 6.1 - - + -
506L TYR* 3.5 57.8 - - + +
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Residues in contact with ALA 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F VAL* 5.4 0.9 - - + +
453F LEU* 4.5 1.1 - - + +
454F MET* 4.0 14.7 - - - +
457F SER* 3.5 22.0 - - - +
475F ILE* 4.0 25.8 - - + -
500F TYR 3.1 13.3 + - - +
501F ALA* 3.2 8.9 + - - +
503F MET* 1.3 75.4 - - - +
505F LEU* 1.3 57.3 + - - +
507F ASN* 3.2 2.8 + - - +
508F LEU* 2.8 35.8 + - + +
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Residues in contact with LEU 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472F LEU* 3.8 38.8 - - + +
475F ILE* 3.8 15.7 - - + -
476F ALA* 3.9 17.5 - - + +
479F LEU* 3.8 28.3 - - + -
501F ALA 2.9 17.4 + - - +
502F GLY* 3.6 9.0 - - - +
503F MET 3.3 0.2 - - - -
504F ALA* 1.3 74.0 - - - +
506F THR* 1.3 62.5 + - - +
508F LEU* 3.4 4.1 + - + +
509F THR* 2.8 32.7 + - - +
519F LEU* 4.3 22.2 - - + -
525F CYS* 5.1 0.9 - - - -
529F LEU* 4.6 6.5 - - + -
547F VAL* 4.1 9.2 - - + -
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Residues in contact with THR 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502F GLY 2.8 20.9 + - - -
503F MET* 3.3 9.4 + - - -
505F LEU* 1.3 72.0 - - - +
507F ASN* 1.3 62.9 + - - +
509F THR* 3.0 10.0 + - - -
510F PHE* 3.2 3.6 + - - +
543F VAL 3.9 0.7 + - - -
546F SER* 3.5 23.0 - - - +
547F VAL* 3.3 23.8 + - - +
550F ASN* 2.7 36.0 + - - +
504L ALA 3.5 11.9 - - - +
505L LEU 4.1 0.2 - - - -
506L TYR* 3.8 24.1 - - - +
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Residues in contact with ASN 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454F MET 4.0 0.2 + - - -
457F SER* 3.0 42.5 + - - +
458F PHE* 3.4 38.1 - - - -
463F ARG* 3.3 16.9 + - - -
503F MET 3.0 15.9 + - - -
504F ALA 3.2 3.1 + - - +
506F THR* 1.3 75.5 - - - +
508F LEU* 1.3 60.8 + - - +
509F THR 3.5 0.9 + - - -
510F PHE* 3.5 15.4 + - - +
505L LEU* 3.4 17.3 - - + +
506L TYR* 2.7 31.3 + - - -
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Residues in contact with LEU 508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457F SER* 4.7 2.7 - - - -
463F ARG* 4.0 28.9 - - + +
466F MET* 4.0 30.7 - - + -
467F ASN* 3.7 21.7 + - - +
472F LEU* 3.7 45.8 - - + +
475F ILE* 4.1 12.6 - - + -
504F ALA 2.8 24.9 + - - +
505F LEU* 4.0 2.2 - - + +
507F ASN* 1.3 72.9 - - - +
509F THR* 1.3 59.5 + - - +
510F PHE 3.4 0.7 - - - -
512F ASP* 3.5 9.2 - - - +
515F ASN* 2.8 27.1 + - - +
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Residues in contact with THR 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472F LEU* 4.0 17.9 - - + -
505F LEU 2.8 19.1 + - - +
506F THR* 3.0 11.6 + - - -
508F LEU* 1.3 79.6 - - - +
510F PHE* 1.3 66.5 + - - +
511F GLY 3.1 3.3 + - - -
512F ASP 3.2 4.9 + - - -
515F ASN* 4.1 15.5 - - - +
516F LYS* 3.1 26.8 - - - +
519F LEU* 4.2 8.1 - - + -
547F VAL* 4.7 3.0 + - + -
550F ASN* 3.2 22.4 + - - +
551F LEU* 4.0 21.8 - - + -
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Residues in contact with PHE 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463F ARG* 4.7 12.6 + - - -
506F THR 3.2 10.6 + - - +
507F ASN 3.6 15.4 - - - +
508F LEU 3.4 1.3 - - - +
509F THR* 1.3 74.3 - - - +
511F GLY* 1.3 70.0 + - - +
512F ASP* 3.0 7.2 + - - +
550F ASN* 3.5 5.8 - - - +
503L ASP* 3.6 20.6 - - - -
504L ALA* 3.5 35.0 - - - +
505L LEU* 3.6 34.5 - - + -
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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
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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