Contacts of the helix formed by residues 493 - 512 (chain A) in PDB entry 5J3V
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 493 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LYS 5.8 1.8 + - - -
452A ALA* 3.3 31.0 - - + +
453A LEU* 6.0 1.2 - - - +
455A ARG* 4.8 2.9 - - - +
491A ASP* 2.7 20.8 + - - +
492A SER* 1.3 74.8 + - - +
494A LYS* 1.3 71.1 + - - +
495A ARG* 3.3 21.9 + - - +
496A VAL* 3.3 21.5 + - + +
497A GLN* 3.2 17.4 + - - +
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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
----------------------------------------------------------
492A SER* 3.6 16.8 + - - +
493A ASN* 1.3 78.2 + - - +
495A ARG* 1.3 60.6 + - - +
497A GLN* 3.5 26.6 + - - +
498A GLU* 3.7 3.8 + - - +
532A LYS* 4.8 14.4 + - - +
534A GLN* 5.6 17.3 - - + +
536A LYS* 4.7 8.7 + - - +
537A ASN* 3.0 28.7 + - - +
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 3.4 35.2 - - - +
319A LYS 5.6 0.8 - - - +
368A ASP* 3.0 33.9 - - - +
369A THR* 4.4 7.9 + - - +
453A LEU* 4.2 24.2 - - - +
456A SER* 4.4 11.8 - - - -
493A ASN* 3.2 17.4 + - - +
494A LYS* 1.3 78.3 - - - +
496A VAL* 1.3 63.8 + - + +
498A GLU* 3.2 35.5 + - - +
499A ALA* 3.5 9.0 + - - +
536A LYS* 5.8 0.2 - - - +
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ALA* 3.7 19.1 - - + +
455A ARG* 3.6 36.1 - - + +
456A SER* 4.2 13.7 - - - +
459A CYS* 4.9 0.9 - - - -
488A ARG* 4.0 15.3 - - + +
491A ASP* 3.8 28.9 - - + +
493A ASN* 3.3 24.2 + - + +
495A ARG* 1.3 74.7 - - - +
497A GLN* 1.3 65.5 + - - +
499A ALA* 3.4 1.6 + - - +
500A ALA* 3.0 21.8 + - - +
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Residues in contact with GLN 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ARG 3.7 7.8 - - - +
489A ILE* 3.6 10.4 + - - +
491A ASP 2.6 29.8 + - - +
492A SER 4.0 7.5 + - - -
493A ASN 3.2 14.0 + - - +
494A LYS* 3.5 20.8 - - - +
495A ARG 3.2 0.2 - - - -
496A VAL* 1.3 78.7 - - - +
498A GLU* 1.3 56.8 + - - +
500A ALA* 3.2 3.1 + - - +
501A CYS* 2.8 31.5 + - - +
532A LYS* 4.1 20.9 + - - +
533A TYR* 3.5 35.1 + - - +
534A GLN 5.6 0.5 + - - -
537A ASN* 3.3 21.7 + - - +
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Residues in contact with GLU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASP* 5.7 1.6 + - - +
494A LYS 4.0 5.4 - - - +
495A ARG* 3.2 35.3 + - - +
497A GLN* 1.3 78.6 - - - +
499A ALA* 1.3 58.4 + - + +
501A CYS* 4.4 5.6 - - - -
502A SER* 3.0 32.4 + - - -
536A LYS* 3.5 20.8 + - - +
537A ASN* 3.6 19.6 - - - +
540A ILE* 3.9 21.8 - - + +
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Residues in contact with ALA 499 (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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456A SER* 3.5 35.7 - - - +
459A CYS* 3.6 5.3 - - + +
460A TRP* 4.8 4.6 + - + +
495A ARG 3.7 9.9 - - - +
496A VAL 3.4 8.2 + - - +
497A GLN 3.2 0.4 - - - -
498A GLU* 1.3 84.7 - - + +
500A ALA* 1.3 57.3 + - - +
502A SER* 4.0 3.1 - - - -
503A ALA* 3.1 27.7 + - - +
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Residues in contact with ALA 500 (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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459A CYS* 3.7 15.5 - - - -
485A LEU* 3.9 11.0 - - + +
488A ARG* 3.6 38.6 - - + +
489A ILE* 3.9 4.5 - - - +
496A VAL 3.0 17.3 + - - +
497A GLN 3.8 0.7 - - - +
499A ALA* 1.3 75.2 - - - +
501A CYS* 1.3 55.1 + - - +
502A SER 3.2 0.2 - - - -
503A ALA* 3.2 2.1 + - - +
504A PHE* 2.7 36.9 + - - +
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Residues in contact with CYS 501 (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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489A ILE* 4.2 18.6 - - + +
497A GLN 2.8 18.0 + - - +
498A GLU* 4.4 0.2 - - - -
500A ALA* 1.3 77.5 - - - +
502A SER* 1.3 59.8 + - - +
504A PHE* 4.0 0.9 - - - +
505A ALA* 3.2 21.5 + - - +
533A TYR* 4.1 15.5 - - + +
540A ILE* 3.7 17.5 - - + +
541A LEU* 3.7 42.6 - - - -
544A ALA* 3.9 13.4 - - - +
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Residues in contact with SER 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLU 3.0 20.1 + - - -
499A ALA* 4.0 4.3 - - - -
501A CYS* 1.3 77.3 - - - +
503A ALA* 1.3 63.2 + - - +
504A PHE 3.2 0.2 - - - -
505A ALA* 3.3 7.7 + - - +
506A THR* 3.1 25.9 + - - -
540A ILE* 3.6 15.8 - - - +
543A ASP* 5.7 0.2 - - - -
22C THR* 5.5 2.3 + - - +
26C ARG* 3.7 26.7 - - - +
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Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A CYS* 3.3 34.3 - - + +
460A TRP* 4.8 1.1 - - - -
463A SER* 3.9 18.7 - - - +
485A LEU* 3.9 11.8 - - + +
499A ALA 3.1 20.2 + - - +
500A ALA 3.2 4.2 + - - +
502A SER* 1.3 76.5 - - - +
504A PHE* 1.3 58.4 + - - +
506A THR* 3.3 4.7 + - - -
507A LEU* 3.0 26.2 + - - +
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Residues in contact with PHE 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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482A MET* 3.6 26.2 - - + -
485A LEU* 3.7 25.3 - - + +
486A LEU* 3.8 19.7 - - + -
489A ILE* 4.2 18.8 - - + -
500A ALA 2.7 19.6 + - - +
501A CYS 4.0 4.5 - - - +
503A ALA* 1.3 72.4 - - - +
505A ALA* 1.3 59.0 + - - +
507A LEU* 3.1 12.5 + - + +
508A GLU* 2.9 64.2 + - + +
515A LEU* 5.2 1.6 - - + -
522A ILE* 3.6 39.3 - - + -
526A LEU* 4.6 8.5 - - + -
544A ALA* 4.9 4.3 - - + -
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Residues in contact with ALA 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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501A CYS 3.2 16.0 + - - +
502A SER* 3.3 6.9 + - - +
504A PHE* 1.3 80.5 - - - +
506A THR* 1.3 61.4 + - - +
508A GLU* 3.5 15.5 + - - +
509A GLU* 3.6 5.7 + - - +
540A ILE* 5.4 0.4 - - + +
543A ASP* 3.8 21.5 - - - +
544A ALA* 3.9 17.3 - - - +
547A THR* 3.4 22.7 - - - +
26C ARG* 3.9 10.0 + - - +
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Residues in contact with THR 506 (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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463A SER* 3.7 32.2 - - - +
466A ALA* 4.9 2.9 - - + -
502A SER 3.1 15.0 + - - -
503A ALA* 3.5 9.2 - - - -
505A ALA* 1.3 75.2 - - - +
507A LEU* 1.3 63.5 + - - +
509A GLU* 3.3 15.4 + - + +
510A GLU* 3.6 14.8 + - + +
26C ARG* 3.7 28.8 + - - +
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Residues in contact with LEU 507 (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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463A SER* 6.2 0.9 - - - -
466A ALA* 4.1 24.7 - - + +
469A VAL* 5.1 1.1 - - + -
470A VAL* 4.6 6.3 - - + -
478A LEU* 4.1 21.5 - - + -
481A LEU* 3.9 25.4 - - + -
482A MET* 4.3 22.9 - - + -
485A LEU* 4.3 12.3 - - + -
503A ALA 3.0 13.9 + - - +
504A PHE* 3.1 30.5 + - + +
506A THR* 1.3 78.1 - - - +
508A GLU* 1.3 61.2 + - - +
510A GLU* 3.4 2.3 + - - +
511A ALA* 3.1 24.0 + - + +
515A LEU* 5.3 4.3 - - + -
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Residues in contact with GLU 508 (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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504A PHE* 2.9 44.0 + - + +
505A ALA* 3.5 18.6 - - - +
506A THR 3.2 0.2 - - - -
507A LEU* 1.3 77.7 - - + +
509A GLU* 1.3 56.6 + - - +
512A CYS 2.9 22.9 + - - -
515A LEU* 3.7 25.7 - - + +
526A LEU* 4.4 0.7 - - - +
544A ALA 2.8 24.2 - - - +
547A THR* 3.6 9.2 - - + -
548A LEU* 3.3 34.2 + - + +
551A SER* 2.9 19.9 + - - +
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Residues in contact with GLU 509 (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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505A ALA 3.6 3.8 + - - +
506A THR* 3.3 9.5 + - - +
507A LEU 3.3 0.8 - - - -
508A GLU* 1.3 79.8 - - - +
510A GLU* 1.3 60.5 + - + +
512A CYS* 3.2 21.8 - - - -
547A THR* 3.6 20.6 + - + +
551A SER* 4.0 4.7 - - - +
23C LYS* 4.3 7.1 - - - -
26C ARG* 3.3 32.2 + - - -
27C LYS* 2.9 32.3 + - - +
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Residues in contact with GLU 510 (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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466A ALA* 4.0 26.0 - - + +
467A HIS* 2.9 51.1 + - - +
470A VAL* 3.4 18.4 - - + +
506A THR* 3.6 9.8 + - + +
507A LEU 3.4 6.8 + - - +
508A GLU 3.4 0.4 - - - -
509A GLU* 1.3 79.0 - - + +
511A ALA* 1.3 60.4 + - - +
512A CYS* 4.8 1.9 - - - -
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Residues in contact with ALA 511 (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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470A VAL* 3.7 19.3 - - + -
478A LEU* 4.6 5.2 - - + -
507A LEU 3.1 17.5 + - - +
510A GLU* 1.3 80.5 - - - +
512A CYS* 1.3 71.6 + - - +
513A THR* 3.2 2.8 + - - -
514A GLU* 3.2 26.5 + - + +
515A LEU* 3.7 29.2 - - + -
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Residues in contact with CYS 512 (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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508A GLU 2.9 16.8 + - - -
509A GLU* 3.2 26.2 - - - -
510A GLU 4.8 1.6 - - - -
511A ALA* 1.3 76.8 - - - +
513A THR* 1.3 66.9 + - + +
514A GLU 3.0 6.2 + - - -
515A LEU* 3.2 19.6 + - - +
551A SER* 3.7 29.8 - - - +
552A VAL* 4.1 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
------------------------------------------------------------
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