Contacts of the helix formed by residues 469 - 484 (chain A) in PDB entry 5JQY
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 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A TYR* 2.9 25.3 + - + +
467A ILE* 3.4 19.9 - - + +
468A GLY* 1.3 75.0 - - - +
470A ASN* 1.3 57.1 + - - +
471A ASP* 3.6 8.0 + - - +
472A ASN* 2.7 44.6 + - - +
473A ALA* 3.1 26.0 + - - +
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Residues in contact with ASN 470 (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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465A LEU* 3.3 26.9 - - - +
468A GLY* 3.3 19.3 + - - -
469A ASP* 1.3 70.4 - - - +
471A ASP* 1.3 61.6 + - - +
473A ALA* 3.6 8.0 - - - +
474A LYS* 2.8 31.0 + - - +
496A PHE* 5.6 2.6 - - - -
497A ILE* 4.1 16.9 - - + +
500A ALA* 5.7 9.4 - - + +
501A GLN* 5.1 7.4 - - + +
107B GLU* 5.5 4.4 + - - -
108B TYR* 5.9 0.7 - - - +
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ASP* 3.3 6.9 + - - +
470A ASN* 1.3 78.0 - - - +
472A ASN* 1.3 62.8 + - - +
474A LYS* 3.4 7.5 + - - +
475A LYS* 3.2 36.9 + - - +
501A GLN* 4.4 12.9 + - - +
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Residues in contact with ASN 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A TYR* 3.5 30.1 + - + -
469A ASP* 2.7 33.5 + - - +
471A ASP* 1.3 77.2 - - - +
473A ALA* 1.3 65.5 + - - +
475A LYS* 3.4 26.9 + - - +
476A VAL* 3.2 27.0 + - - +
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Residues in contact with ALA 473 (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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461A GLY 3.8 13.7 - - - +
464A TYR* 3.7 19.0 - - + +
465A LEU* 3.9 9.2 - - + -
469A ASP 3.1 19.7 + - - +
470A ASN* 3.6 8.7 - - - +
471A ASP 3.3 0.2 - - - -
472A ASN* 1.3 77.0 - - - +
474A LYS* 1.3 64.5 + - - +
476A VAL* 3.1 11.7 + - - +
477A TYR* 3.1 20.8 + - + -
497A ILE* 3.8 15.7 - - + -
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Residues in contact with LYS 474 (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 ASN 2.8 21.7 + - - +
471A ASP* 3.6 7.0 - - - +
473A ALA* 1.3 74.2 - - - +
475A LYS* 1.3 56.5 + - - +
477A TYR* 3.4 3.4 + - - +
478A GLU* 3.0 48.7 + - - +
494A TYR* 3.7 18.6 - - + -
497A ILE* 3.7 18.8 - - + +
498A LEU* 3.9 22.9 - - - +
501A GLN* 2.9 37.7 + - - +
503A LYS* 4.6 9.5 - - - +
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Residues in contact with LYS 475 (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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471A ASP* 3.2 22.8 + - - +
472A ASN* 3.6 29.1 + - - +
473A ALA 3.2 0.2 - - - -
474A LYS* 1.3 76.9 - - + +
476A VAL* 1.3 60.3 + - + +
478A GLU* 3.3 14.6 + - - +
479A GLU* 2.9 30.3 + - - +
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS* 3.1 38.8 - - + +
460A LEU* 4.2 11.2 - - + -
461A GLY* 3.9 11.9 - - - +
464A TYR* 3.8 25.8 - - + -
472A ASN 3.2 15.2 + - - +
473A ALA 3.1 8.6 + - - +
475A LYS* 1.3 77.0 - - + +
477A TYR* 1.3 61.9 + - + +
479A GLU* 3.1 14.6 + - - +
480A VAL* 2.9 29.9 + - + +
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Residues in contact with TYR 477 (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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457A LYS 5.0 0.2 - - - -
458A ASN* 2.9 51.6 + - - -
461A GLY* 3.2 24.3 - - - -
462A VAL* 3.1 21.0 + - - +
465A LEU* 4.3 2.9 - - + -
473A ALA 3.1 23.7 + - - +
474A LYS 4.1 3.4 - - - +
476A VAL* 1.3 76.2 - - + +
478A GLU* 1.3 60.8 + - - +
480A VAL* 3.7 3.6 - - + +
481A LEU* 2.9 37.2 + - - +
489A PHE* 3.7 3.3 - + - -
490A ALA* 3.7 27.8 - - + +
493A HIS* 3.7 28.2 - - + -
494A TYR* 4.3 12.3 - - + -
497A ILE* 3.9 18.6 - - + -
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Residues in contact with GLU 478 (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* 3.0 39.7 + - - +
475A LYS* 3.5 18.4 + - - +
477A TYR* 1.3 77.4 - - - +
479A GLU* 1.3 56.5 + - - +
481A LEU* 3.2 6.9 + - + +
482A SER* 2.9 30.9 + - - -
494A TYR* 2.9 35.0 + - + +
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Residues in contact with GLU 479 (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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457A LYS* 4.4 27.6 + - + +
475A LYS 2.9 12.6 + - - +
476A VAL* 3.1 16.9 + - - +
478A GLU* 1.3 77.8 - - - +
480A VAL* 1.3 60.5 + - - +
482A SER* 2.7 25.3 + - - +
483A VAL* 3.6 10.9 + - + +
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Residues in contact with VAL 480 (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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454A THR* 3.7 26.2 - - + +
457A LYS* 3.6 39.7 - - + +
458A ASN* 3.8 12.8 - - - +
476A VAL* 2.9 20.3 + - + +
477A TYR* 3.7 10.1 - - - +
479A GLU* 1.3 75.4 - - - +
481A LEU* 1.3 53.1 + - - +
483A VAL* 3.1 7.5 + - - +
484A THR* 2.7 33.2 + - - +
487A ASP* 4.3 7.9 - - + +
490A ALA* 3.7 21.3 - - + -
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Residues in contact with LEU 481 (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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477A TYR 2.9 24.8 + - - +
478A GLU* 3.2 6.2 + - + +
480A VAL* 1.3 74.2 - - - +
482A SER* 1.3 63.5 + - - +
484A THR 3.8 15.0 - - - +
485A PRO* 3.3 33.9 - - + +
487A ASP 4.0 1.3 - - - +
490A ALA* 3.7 25.4 - - + +
491A LYS* 3.8 22.2 - - + -
494A TYR* 3.9 41.1 - - + -
510A TYR* 4.0 13.7 - - + +
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Residues in contact with SER 482 (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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478A GLU 2.9 14.0 + - - -
479A GLU* 2.7 26.0 + - - +
481A LEU* 1.3 78.0 - - - +
483A VAL* 1.3 65.6 + - - +
485A PRO* 4.5 5.1 - - - +
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Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A THR* 5.6 2.2 - - - +
457A LYS* 6.6 0.4 - - - -
479A GLU* 4.0 13.0 - - + +
480A VAL* 3.1 7.2 + - - +
482A SER* 1.3 85.9 + - - +
484A THR* 1.3 68.5 + - - +
485A PRO* 3.3 9.0 - - - +
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Residues in contact with THR 484 (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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454A THR* 3.9 20.7 + - + +
480A VAL 2.7 20.7 + - - +
481A LEU* 3.7 6.2 - - - +
483A VAL* 1.3 87.6 + - - +
485A PRO* 1.3 63.2 - - - +
486A ASN* 3.1 5.5 + - + +
487A ASP* 3.2 38.9 + - + +
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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