Contacts of the helix formed by residues 487 - 501 (chain A) in PDB entry 5JZU
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 487 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A THR* 3.9 13.2 - - - +
458A ASN* 3.1 23.4 + - - -
480A VAL* 4.5 1.6 - - + -
481A LEU* 4.1 0.9 - - - +
484A THR* 3.2 31.8 + - + +
485A PRO 3.5 0.2 - - - -
486A ASN* 1.3 74.8 - - - +
488A GLY* 1.3 63.0 + - - +
489A PHE* 3.2 6.5 + - - +
490A ALA* 2.7 37.6 + - + +
491A LYS* 3.2 22.9 + - - +
519A ASP* 4.1 4.6 - - - +
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASN 2.9 5.4 + - - -
487A ASP* 1.3 69.8 - - - +
489A PHE* 1.3 63.3 + - - +
491A LYS* 3.0 10.2 + - - +
492A VAL* 3.0 24.4 + - - +
514A GLY* 3.7 4.8 - - - -
517A SER* 3.3 27.6 - - - -
519A ASP* 2.8 14.8 + - - -
522A THR* 3.6 8.2 - - - +
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Residues in contact with PHE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ASN* 3.4 40.6 - - + +
459A ASP* 5.0 6.5 - - - -
462A VAL* 3.8 13.7 - - + -
477A TYR* 3.6 15.0 - + - -
487A ASP* 3.2 9.5 + - - +
488A GLY* 1.3 74.9 - - - +
490A ALA* 1.3 62.6 + - - +
492A VAL* 3.1 8.1 - - - +
493A HIS* 2.9 57.7 + + - -
519A ASP* 4.1 4.8 + - + +
520A PRO 3.6 23.8 - - - +
521A GLY* 4.1 16.8 - - - -
522A THR* 3.6 11.0 - - - +
108B TYR* 5.3 0.4 - - - -
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Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ASN* 3.7 5.2 - - - +
477A TYR* 3.6 22.2 - - + +
480A VAL* 3.7 26.9 - - + -
481A LEU* 3.8 16.4 - - + +
487A ASP* 2.7 24.6 + - - +
489A PHE* 1.3 73.9 - - - +
491A LYS* 1.3 57.9 + - - +
493A HIS 3.9 0.4 - - - -
494A TYR* 2.9 30.1 + - - +
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Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 3.9 12.8 - - + -
485A PRO 3.3 22.6 + - - +
486A ASN* 4.2 20.6 + - - +
487A ASP 3.2 11.7 - - - +
488A GLY* 3.0 10.2 + - - +
490A ALA* 1.3 76.0 - - - +
492A VAL* 1.3 61.0 + - - +
494A TYR* 3.2 1.1 + - - +
495A GLY 2.8 26.2 + - - -
510A TYR* 3.4 43.4 - - + +
513A GLU* 3.0 44.5 + - + +
514A GLY* 4.0 4.5 - - - -
517A SER* 5.9 1.1 - - - -
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Residues in contact with VAL 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A GLY 3.0 8.2 + - - +
489A PHE* 3.1 25.4 - - - +
491A LYS* 1.3 75.0 - - - +
493A HIS* 1.3 69.6 + - + +
495A GLY 3.3 0.5 + - - -
496A PHE* 2.8 29.8 + - - +
510A TYR 4.0 3.8 - - - -
511A LEU* 3.5 15.5 - - - +
514A GLY* 3.4 34.3 - - - +
515A ILE* 3.5 7.6 - - + +
522A THR* 4.1 10.3 - - + -
527A PHE* 3.6 36.2 - - + -
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Residues in contact with HIS 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A VAL* 4.0 1.6 - - + +
465A LEU* 3.6 22.2 - - + +
477A TYR* 3.5 36.8 - - + -
489A PHE* 2.9 56.7 + + - +
490A ALA 4.1 0.4 - - - +
491A LYS 3.1 0.6 - - - -
492A VAL* 1.3 83.4 - - + +
494A TYR* 1.3 66.1 + - - +
496A PHE* 3.4 6.6 + - + +
497A ILE* 3.1 32.0 + - - +
521A GLY 4.5 1.1 - - - -
527A PHE* 3.6 19.7 - + - -
108B TYR* 3.1 30.8 + + - -
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Residues in contact with TYR 494 (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 LYS* 3.6 31.1 - - + -
477A TYR* 4.4 14.7 - - + -
478A GLU* 2.9 46.5 + - + +
481A LEU* 4.0 13.7 - - + -
490A ALA 2.9 19.7 + - - +
491A LYS* 3.2 4.7 + - - +
493A HIS* 1.3 76.7 - - - +
495A GLY* 1.3 56.3 + - - +
497A ILE* 3.3 7.2 + - + +
498A LEU* 2.9 53.7 + - + +
510A TYR* 3.6 37.9 - + - -
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Residues in contact with GLY 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LYS 2.8 14.7 + - - -
492A VAL 3.6 4.0 - - - -
494A TYR* 1.3 76.8 - - - +
496A PHE* 1.3 54.7 + - - +
498A LEU* 3.3 3.2 + - - -
499A LYS* 3.0 27.5 + - - +
507A SER* 3.3 21.2 - - - -
510A TYR* 3.7 17.6 - - - +
511A LEU* 3.8 10.0 - - - +
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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
----------------------------------------------------------
465A LEU* 4.9 6.7 - - + -
470A ASN* 5.2 3.8 - - - -
492A VAL 2.8 19.1 + - - +
493A HIS* 3.6 7.4 - - + +
494A TYR 3.2 0.2 - - - -
495A GLY* 1.3 73.9 - - - +
497A ILE* 1.3 67.0 + - + +
499A LYS* 3.5 4.5 + - - +
500A ALA* 3.0 29.5 + - + +
511A LEU* 3.6 5.6 - - - +
526A ARG* 4.4 12.6 - - + -
527A PHE* 4.0 26.5 - + + -
530A HIS* 3.3 36.9 - + + -
106B GLY 3.7 18.4 - - - -
107B GLU 3.8 3.8 - - - -
108B TYR* 3.5 52.3 - + + -
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Residues in contact with ILE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 3.9 20.6 - - + -
470A ASN* 4.0 22.2 - - + +
473A ALA* 3.8 17.5 - - + -
474A LYS* 3.8 37.5 - - + +
477A TYR* 4.0 11.7 - - + -
493A HIS 3.1 18.9 + - - +
494A TYR* 3.3 6.9 + - - +
496A PHE* 1.3 76.9 - - + +
498A LEU* 1.3 65.9 + - - +
500A ALA* 3.3 6.9 + - - +
501A GLN* 3.0 43.3 + - + +
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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
----------------------------------------------------------
474A LYS* 3.8 31.9 - - - +
494A TYR* 2.9 50.0 + - + +
495A GLY 3.6 4.0 - - - +
496A PHE 3.3 0.2 - - - -
497A ILE* 1.3 77.2 - - - +
499A LYS* 1.3 57.3 + - - +
501A GLN* 2.8 24.3 + - - +
503A LYS* 2.9 36.3 + - + +
506A GLU* 3.8 31.0 - - + +
507A SER* 3.8 9.9 - - - -
510A TYR* 4.0 8.1 - - + -
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Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A GLY 3.0 16.7 + - - +
496A PHE* 4.0 4.7 - - - +
498A LEU* 1.3 77.2 - - - +
500A ALA* 1.3 58.0 + - - +
501A GLN 3.0 0.2 - - - -
502A ASN* 2.8 21.1 + - - +
503A LYS 4.4 4.3 - - - +
504A ILE* 3.9 15.8 - - + +
507A SER* 3.6 15.2 - - - +
511A LEU* 4.7 2.9 - - + -
530A HIS* 3.3 63.0 + - + +
533A ASP* 2.8 30.1 + - - -
534A ALA* 3.7 12.3 - - + +
537A ARG* 4.2 11.5 - - - +
618A ASN* 4.3 7.2 + - - +
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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
----------------------------------------------------------
470A ASN* 4.9 10.8 - - - +
496A PHE* 3.0 23.9 + - + +
497A ILE* 3.6 8.5 - - - +
498A LEU 3.2 0.4 - - - -
499A LYS* 1.3 76.2 - - - +
501A GLN* 1.3 59.1 + - + +
502A ASN* 3.2 1.3 + - - +
618A ASN* 5.2 5.4 + - - +
106B GLY* 4.4 17.3 - - - +
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Residues in contact with GLN 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ASN* 5.1 6.6 + - + +
471A ASP* 4.5 13.9 + - - -
474A LYS* 2.8 45.0 + - - +
497A ILE* 3.0 27.4 + - + +
498A LEU* 2.8 16.8 + - - +
500A ALA* 1.3 79.2 - - + +
502A ASN* 1.3 69.4 + - - +
503A LYS* 3.2 19.1 + - + +
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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