Contacts of the helix formed by residues 481 - 505 (chain C) in PDB entry 5I4A
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 ASN 481 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLU* 2.8 6.4 + - + -
480C LEU* 1.3 77.7 + - - +
482C GLU* 1.3 68.4 + - - +
483C LYS* 3.1 13.9 + - - +
484C MET* 2.9 56.8 + - + +
485C ASN* 2.9 31.1 + - - -
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Residues in contact with GLU 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C HIS* 5.0 4.2 + - - -
480C LEU* 5.4 2.0 - - - +
481C ASN* 1.3 73.0 - - - +
483C LYS* 1.3 64.2 + - - +
485C ASN* 3.9 5.2 - - - +
486C LEU* 3.0 34.5 + - + +
520C ILE 4.8 3.1 - - - +
521C GLU* 3.1 32.5 - - - +
522C ASP* 2.5 40.9 + - + +
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Residues in contact with LYS 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C ASN* 3.1 10.5 + - - +
482C GLU* 1.3 78.7 - - - +
484C MET* 1.3 66.6 + - + +
486C LEU* 3.4 8.9 + - + +
487C ASP* 3.0 56.0 + - - +
525C ILE* 6.3 4.9 - - + -
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Residues in contact with MET 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLU* 3.6 35.0 - - + +
481C ASN* 2.9 39.3 + - + +
483C LYS* 1.3 77.6 - - + +
485C ASN* 1.3 66.3 + - - +
487C ASP* 3.2 12.1 + - - +
488C ILE* 3.1 31.1 + - + +
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Residues in contact with ASN 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C LEU* 5.4 9.2 - - + +
449C HIS* 3.7 15.3 - - + -
456C THR* 2.9 39.8 + - - +
458C LEU* 5.2 1.6 - - - +
478C LEU* 4.0 12.6 - - + +
479C GLU 3.2 19.6 + - - -
480C LEU* 4.2 1.2 - - - +
481C ASN 2.9 25.0 + - - +
482C GLU* 3.9 7.9 - - - +
484C MET* 1.3 79.8 - - - +
486C LEU* 1.3 56.8 + - + +
488C ILE* 3.3 7.9 + - - +
489C LEU* 2.9 28.7 + - - +
521C GLU* 6.0 0.9 - - + -
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C GLU* 3.0 47.1 + - + +
483C LYS* 3.8 9.2 - - + +
485C ASN* 1.3 73.3 - - + +
487C ASP* 1.3 67.6 + - - +
489C LEU* 3.8 11.1 - - + +
490C GLU* 3.0 25.5 + - - +
521C GLU* 4.1 13.7 - - + -
522C ASP* 3.7 18.4 - - + -
525C ILE* 4.0 21.1 - - + -
526C ILE* 3.6 32.1 - - + -
529C PHE* 4.0 12.8 - - + -
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Residues in contact with ASP 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C LYS* 3.0 53.2 + - - +
484C MET* 3.2 12.4 + - - +
486C LEU* 1.3 78.5 - - - +
488C ILE* 1.3 59.9 + - + +
490C GLU* 3.5 12.1 + - - +
491C LYS* 3.0 27.3 + - - +
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Residues in contact with ILE 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C LEU* 4.3 7.2 - - + -
475C HIS* 3.6 39.5 - - + +
478C LEU* 3.6 39.3 - - + -
484C MET* 3.1 19.6 + - + +
485C ASN* 3.8 5.6 - - - +
487C ASP* 1.3 75.0 - - + +
489C LEU* 1.3 60.2 + - - +
491C LYS* 3.1 13.5 + - + +
492C GLU* 2.8 29.5 + - + +
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Residues in contact with LEU 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ILE* 4.3 19.3 - - + -
447C LEU* 4.5 19.1 - - + -
458C LEU* 4.1 30.2 - - + +
460C ILE* 4.2 14.6 - - + -
485C ASN 2.9 17.2 + - - +
486C LEU* 3.8 17.0 - - + +
487C ASP 3.3 0.2 - - - -
488C ILE* 1.3 77.5 - - - +
490C GLU* 1.3 56.6 + - - +
492C GLU* 3.8 1.0 - - - -
493C TYR* 2.8 34.5 + - + +
515C ARG* 5.5 2.5 - - - +
519C PHE* 6.0 2.2 - - + -
521C GLU* 5.7 0.2 - - - +
526C ILE* 4.7 13.5 - - + -
529C PHE* 4.1 18.6 - - + -
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Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C LEU 3.0 18.4 + - - +
487C ASP* 3.8 11.9 - - - +
489C LEU* 1.3 76.4 - - - +
491C LYS* 1.3 57.7 + - - +
493C TYR* 3.2 1.6 + - - +
494C ILE* 2.9 55.7 + - + +
525C ILE* 6.0 0.2 - - - +
529C PHE* 3.4 54.6 - - + +
532C TYR* 6.0 0.2 - - - -
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Residues in contact with LYS 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C HIS* 6.0 4.3 - - + +
487C ASP 3.0 16.1 + - - +
488C ILE* 3.1 18.1 + - + +
490C GLU* 1.3 78.0 - - - +
492C GLU* 1.3 68.5 + - + +
494C ILE* 3.4 9.2 + - - +
495C LYS* 3.2 45.5 + - + +
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Residues in contact with GLU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C LEU* 4.5 5.6 - - + -
460C ILE* 4.0 25.2 - - + +
471C TYR* 2.3 39.0 + - - -
473C GLY* 3.6 9.5 - - - -
474C LYS 5.1 0.2 + - - -
475C HIS* 2.4 43.9 + - + +
488C ILE* 2.8 21.9 + - + +
489C LEU* 3.9 4.3 - - - +
491C LYS* 1.3 74.6 + - + +
493C TYR* 1.3 65.8 + - - +
495C LYS* 3.2 16.8 + - - +
496C ALA* 3.0 22.2 + - - +
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Residues in contact with TYR 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ILE* 3.6 32.5 - - + -
460C ILE* 5.0 4.4 - - - +
489C LEU* 2.8 23.0 + - + +
490C GLU* 3.2 6.5 + - - +
492C GLU* 1.3 76.7 - - - +
494C ILE* 1.3 64.2 + - + +
496C ALA* 3.2 5.5 + - - +
497C PHE* 2.8 53.5 + + - +
511C VAL* 3.5 19.7 - - + +
513C ILE* 4.0 3.4 - - + -
529C PHE* 3.7 19.7 - + + -
530C ILE* 2.9 59.0 + - + +
532C TYR* 3.9 11.0 - - + -
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Residues in contact with ILE 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C GLU* 2.9 42.0 + - + +
491C LYS* 3.8 8.5 - - - +
493C TYR* 1.3 81.5 - - + +
495C LYS* 1.3 52.8 + - - +
497C PHE* 3.4 6.0 - - - +
498C GLU* 2.7 48.0 + - + +
529C PHE 5.8 0.4 - - - +
532C TYR* 3.6 48.0 - - + +
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Residues in contact with LYS 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C TYR* 3.2 38.4 + - + +
491C LYS* 3.2 40.8 + - + +
492C GLU* 3.2 23.2 + - - +
494C ILE* 1.3 76.5 - - - +
496C ALA* 1.3 57.7 + - - +
498C GLU* 3.2 7.0 + - - +
499C LYS* 2.9 34.2 + - - +
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Residues in contact with ALA 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C LEU* 4.2 6.7 - - - +
443C ILE* 4.3 10.3 - - + -
460C ILE* 3.8 23.1 - - + -
462C ALA* 3.7 26.2 - - + +
470C LEU* 5.1 0.3 - - - +
471C TYR* 4.0 15.3 - - + -
492C GLU 3.0 6.5 + - - -
493C TYR* 3.6 7.4 - - - +
495C LYS* 1.3 75.4 - - - +
497C PHE* 1.3 63.0 + - - +
499C LYS* 3.1 12.6 + - - +
500C TYR* 3.1 12.6 + - - +
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Residues in contact with PHE 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C LEU* 3.9 14.9 - - + +
493C TYR* 2.8 49.7 + + - +
494C ILE* 3.4 14.1 - - - +
496C ALA* 1.3 72.7 - - - +
498C GLU* 1.3 62.3 + - - +
500C TYR* 3.2 14.2 + - - +
501C ILE* 3.2 23.1 + - + +
507C SER* 3.2 27.8 - - - -
508C PRO* 3.5 13.5 - - + -
511C VAL* 4.0 12.3 - - + -
532C TYR* 3.4 38.6 - + + -
533C ASN* 4.2 2.9 - - + -
535C THR* 3.3 23.8 - - + -
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Residues in contact with GLU 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ILE* 2.7 32.0 + - + +
495C LYS* 3.2 6.5 + - - +
497C PHE* 1.3 72.3 - - - +
499C LYS* 1.3 59.6 + - - +
501C ILE* 3.3 24.4 + - - +
502C GLU* 2.8 29.5 + - - +
532C TYR* 2.8 33.6 + - - -
533C ASN* 5.3 0.3 + - - -
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Residues in contact with LYS 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LEU* 3.6 34.3 - - + +
471C TYR* 3.7 28.3 - - + -
495C LYS* 2.9 16.8 + - - +
496C ALA 3.1 9.6 + - - +
498C GLU* 1.3 76.3 - - - +
500C TYR* 1.3 64.6 + - - +
502C GLU* 3.1 37.1 + - - +
503C LYS* 3.1 22.7 + - - +
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Residues in contact with TYR 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438C GLU* 2.5 31.6 + - - +
439C LYS* 3.2 14.1 + - - -
440C ASN 3.8 15.7 - - - -
441C LEU* 4.1 11.9 - - + -
464C ASP* 5.4 0.9 - - + -
470C LEU* 4.0 22.9 - - + +
496C ALA 3.1 10.3 + - - +
497C PHE 3.2 9.2 + - - +
499C LYS* 1.3 77.6 - - - +
501C ILE* 1.3 57.5 + - - +
503C LYS* 3.0 2.9 + - - -
504C PHE* 2.9 63.7 + + + +
506C VAL* 3.1 28.4 - - + +
507C SER 3.9 2.3 + - - -
508C PRO* 3.4 36.8 - - + +
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Residues in contact with ILE 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497C PHE* 3.2 37.6 + - + +
498C GLU* 3.6 30.5 - - - +
500C TYR* 1.3 75.1 - - - +
502C GLU* 1.3 60.2 + - - +
505C ASN* 2.7 42.6 + - - +
506C VAL 3.6 22.2 - - - +
507C SER* 3.9 12.1 - - - +
508C PRO* 4.3 1.3 - - + -
533C ASN* 4.5 10.1 - - - +
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Residues in contact with GLU 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C GLU 2.8 21.2 + - - +
499C LYS* 3.1 38.5 - - - +
500C TYR 3.1 0.4 - - - -
501C ILE* 1.3 75.7 - - - +
503C LYS* 1.3 60.5 + - - +
505C ASN* 4.5 1.2 + - - +
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Residues in contact with LYS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ASP* 2.8 19.6 + - - -
466C THR* 5.0 0.2 + - - -
468C ASP* 2.7 33.7 + - - +
470C LEU* 3.7 20.6 - - + +
499C LYS 3.1 10.8 + - - +
500C TYR 3.0 7.3 + - - +
502C GLU* 1.3 79.8 - - - +
504C PHE* 1.3 86.2 + - + +
505C ASN* 3.6 0.6 - - - +
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Residues in contact with PHE 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C GLU* 3.6 40.6 - - + +
464C ASP* 3.7 26.9 - - + -
465C ASN* 5.0 0.9 - - - -
470C LEU* 4.5 3.4 - - + -
500C TYR* 2.9 71.5 + + + +
503C LYS* 1.3 111.0 - - + +
505C ASN* 1.3 64.6 + - - +
506C VAL* 2.9 23.9 + - + +
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Residues in contact with ASN 505 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C ILE* 2.7 32.0 + - - +
502C GLU 4.5 1.5 + - - +
503C LYS 3.6 1.6 - - - +
504C PHE* 1.3 72.1 - - - +
506C VAL* 1.3 62.8 + - + +
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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