Contacts of the helix formed by residues 477 - 490 (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 TYR 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A PRO* 3.7 24.7 + - + +
440A ILE* 3.5 24.9 - - + -
441A PRO* 4.0 27.4 - - + -
444A ILE* 3.9 4.2 - - + +
468A TRP* 3.6 26.4 - + - -
469A VAL* 3.7 19.5 - - + +
472A GLN* 3.7 27.6 - - + -
473A PRO* 4.2 1.3 + - + -
476A THR* 1.3 114.2 + - - +
478A LEU* 1.3 60.7 + - - +
479A LYS 3.4 1.1 - - - -
480A PRO* 3.2 5.4 - - - +
481A LEU* 2.9 33.9 + - + +
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Residues in contact with LEU 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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469A VAL* 3.7 16.7 - - + +
470A VAL* 4.2 20.9 - - + -
473A PRO 4.7 1.0 + - - -
474A PRO* 3.3 30.0 + - + +
477A TYR* 1.3 80.0 - - - +
479A LYS* 1.3 57.6 + - - +
481A LEU* 3.8 1.9 - - + +
482A MET* 2.8 36.2 + - + +
507A LEU* 4.1 32.3 - - + -
511A ALA* 4.6 5.8 - - + -
514A GLU* 4.1 35.7 - - + +
515A LEU* 4.6 11.7 - - + -
518A TYR* 4.9 5.8 - - + -
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Residues in contact with LYS 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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474A PRO 2.9 11.0 + - - +
475A ASP* 3.1 35.2 - - + +
478A LEU* 1.3 74.9 - - - +
480A PRO* 1.3 62.6 - - + +
482A MET* 4.1 8.1 - - + +
483A THR* 2.6 41.0 + - - +
518A TYR* 4.2 30.0 + - + +
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Residues in contact with PRO 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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444A ILE* 4.2 16.8 - - + -
475A ASP 5.1 0.4 - - - -
476A THR 3.6 22.7 - - - +
477A TYR* 3.2 23.8 - - - +
479A LYS* 1.3 92.7 - - + +
481A LEU* 1.3 56.3 + - - +
483A THR* 3.3 5.5 + - - +
484A GLU* 2.9 37.5 + - + +
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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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440A ILE* 6.0 0.7 - - + -
444A ILE* 3.8 16.5 - - + +
447A LEU* 4.3 7.4 - - + -
462A LEU* 3.6 48.9 - - + +
469A VAL* 4.1 26.2 - - + -
477A TYR 2.9 19.1 + - - +
478A LEU 3.8 2.2 - - - +
480A PRO* 1.3 77.5 - - - +
482A MET* 1.3 57.9 + - - +
484A GLU* 3.3 1.6 + - - +
485A LEU* 2.8 44.1 + - + +
507A LEU* 3.9 31.6 - - + -
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Residues in contact with MET 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 LEU* 2.8 24.2 + - + +
479A LYS* 4.1 6.5 - - + +
481A LEU* 1.3 74.7 - - - +
483A THR* 1.3 67.0 + - - +
485A LEU* 3.9 3.1 - - - +
486A LEU* 3.0 39.2 + - + +
504A PHE* 3.6 22.2 - - + -
507A LEU* 4.3 15.3 - - + -
515A LEU* 4.0 10.1 - - + -
518A TYR* 3.6 53.4 - - + -
521A TYR* 4.3 15.9 - - + -
522A ILE* 3.9 17.7 - - + -
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Residues in contact with THR 483 (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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479A LYS* 2.6 31.4 + - - +
480A PRO* 3.6 7.0 - - - -
482A MET* 1.3 83.9 - - - +
484A GLU* 1.3 67.6 + - - +
486A LEU* 3.4 5.1 + - - +
487A LYS* 3.2 45.1 + - - +
521A TYR* 3.7 30.5 + - + +
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Residues in contact with GLU 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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444A ILE* 3.6 21.3 - - + +
445A GLN* 6.3 0.7 - - - -
447A LEU* 3.8 22.6 - - + +
448A SER* 3.4 21.4 + - - -
480A PRO* 2.9 22.1 + - + +
481A LEU 4.0 0.4 - - - +
483A THR* 1.3 79.9 - - - +
485A LEU* 1.3 62.2 + - - +
487A LYS* 3.3 31.6 + - - +
488A ARG* 3.3 28.2 + - - +
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Residues in contact with LEU 485 (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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447A LEU* 4.3 13.6 - - + +
459A CYS* 3.9 37.7 - - + +
462A LEU* 6.0 1.3 - - + -
481A LEU* 2.8 29.9 + - + +
482A MET* 3.9 4.3 - - - +
484A GLU* 1.3 76.7 - - - +
486A LEU* 1.3 64.4 + - - +
488A ARG* 3.2 12.4 + - + +
489A ILE* 3.2 18.2 + - - +
500A ALA* 3.9 11.7 - - + +
503A ALA* 3.9 9.4 - - + +
504A PHE* 3.7 38.8 - - + +
507A LEU* 4.3 13.7 - - + -
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Residues in contact with LEU 486 (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* 3.0 28.9 + - + +
483A THR 3.6 5.4 - - - +
485A LEU* 1.3 76.7 - - - +
487A LYS* 1.3 62.5 + - + +
489A ILE* 3.4 29.9 + - + +
490A LEU* 3.7 4.7 + - - +
504A PHE* 3.8 22.9 - - + -
521A TYR* 3.9 43.1 - - + +
522A ILE* 3.9 22.0 - - + +
525A THR* 3.4 40.5 - - - +
526A LEU* 5.0 1.1 - - + -
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Residues in contact with LYS 487 (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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483A THR* 3.2 35.9 + - - +
484A GLU* 3.4 34.2 + - - +
485A LEU 3.1 0.6 - - - -
486A LEU* 1.3 79.1 - - + +
488A ARG* 1.3 89.4 + - - +
490A LEU* 3.4 16.3 + - - +
491A ASP 3.6 3.1 + - - -
521A TYR* 3.8 11.8 + - - +
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Residues in contact with ARG 488 (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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447A LEU* 3.1 45.0 + - + +
448A SER* 4.9 6.4 + - - +
455A ARG* 3.9 12.1 - - - +
459A CYS* 4.4 3.8 - - - -
484A GLU* 3.3 15.6 + - - +
485A LEU* 3.2 5.6 + - - +
487A LYS* 1.3 114.5 + - - +
489A ILE* 1.3 64.6 + - - +
490A LEU 3.3 0.4 - - - -
491A ASP* 2.7 55.2 + - - +
496A VAL* 3.8 9.5 - - + +
497A GLN* 3.7 11.4 - - - -
500A ALA* 3.6 21.5 - - + +
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Residues in contact with ILE 489 (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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485A LEU 3.2 13.2 + - - +
486A LEU* 3.4 35.2 - - + +
487A LYS 3.2 0.2 - - - -
488A ARG* 1.3 80.1 - - - +
490A LEU* 1.3 57.2 + - + +
491A ASP 3.2 2.8 + - - -
497A GLN* 3.6 8.3 - - - +
500A ALA* 4.2 3.1 - - + -
501A CYS* 4.2 26.9 - - - +
504A PHE* 4.2 20.0 - - + -
525A THR* 4.2 11.7 - - + -
526A LEU* 4.0 18.8 - - + -
529A ALA* 4.3 12.8 - - + -
533A TYR* 2.7 43.3 + - + +
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Residues in contact with LEU 490 (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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486A LEU 3.7 3.3 + - - +
487A LYS* 3.4 12.3 + - - +
488A ARG 3.3 0.4 - - - -
489A ILE* 1.3 75.8 - - - +
491A ASP* 1.3 64.1 + - - +
492A SER 3.8 0.2 + - - -
525A THR* 3.6 44.0 - - + +
528A PHE* 3.6 41.1 - - + -
529A ALA* 3.7 19.5 - - + -
532A LYS* 3.4 22.9 + - + +
533A TYR* 5.2 0.2 - - + -
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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