Contacts of the helix formed by residues 459 - 476 (chain E) in PDB entry 6O0T
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 SER 459 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D GLN* 2.5 32.9 + - - -
454D ASP* 3.3 13.9 + - - -
429E TYR* 5.4 1.0 + - - -
457E MSE 3.5 0.4 - - - -
458E LYS* 1.3 78.6 - - - +
460E GLY* 1.3 58.1 + - - +
461E ILE 3.2 5.2 + - - -
462E THR* 3.1 29.2 + - - -
463E ARG* 3.0 30.8 + - - +
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Residues in contact with GLY 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D GLU* 4.7 8.9 - - - +
454D ASP* 3.0 17.9 + - - -
448E GLU* 5.0 3.1 - - - +
458E LYS 3.3 4.2 + - - -
459E SER* 1.3 71.3 - - - +
461E ILE* 1.3 58.8 + - - +
463E ARG* 3.4 28.2 + - - +
464E LYS* 3.0 27.4 + - - +
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Residues in contact with ILE 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D GLN* 3.7 28.5 - - + +
438D VAL* 4.2 10.3 - - + -
442D LEU* 4.1 23.3 - - + -
446D MSE 4.5 4.0 - - - -
450D GLU* 4.0 24.9 - - + +
454D ASP* 3.4 18.8 + - + +
455D LEU* 3.8 39.9 - - + -
459E SER* 3.2 6.8 + - - +
460E GLY* 1.3 75.4 - - - +
462E THR* 1.3 63.5 + - - +
464E LYS* 3.2 7.8 + - - +
465E ARG* 3.0 22.7 + - - +
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Residues in contact with THR 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D GLN* 4.0 9.4 + - - -
426E PHE* 3.9 19.7 - - + -
429E TYR* 4.1 14.4 + - + +
457E MSE 3.7 21.3 - - + -
459E SER* 3.1 28.2 + - - -
461E ILE* 1.3 77.6 - - - +
463E ARG* 1.3 60.5 + - - +
465E ARG* 3.3 16.5 + - - +
466E PHE* 3.0 21.0 + - - +
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Residues in contact with ARG 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D GLU* 6.0 0.2 + - - -
448E GLU* 3.3 51.2 + - - +
451E LEU* 4.1 13.7 - - + -
452E GLN* 3.5 29.9 + - - +
457E MSE 3.2 37.6 + - + +
458E LYS 2.7 29.1 + - - -
459E SER 3.0 16.0 + - - +
460E GLY* 3.4 25.3 - - - +
461E ILE 3.2 0.2 - - - -
462E THR* 1.3 76.9 - - - +
464E LYS* 1.3 60.8 + - - +
466E PHE* 3.2 3.2 + - - +
467E PHE* 3.0 33.0 + - + -
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Residues in contact with LYS 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D LEU* 3.6 24.1 + - + +
445D ARG* 3.0 69.2 + - + +
447D THR* 4.5 4.4 - - - +
450D GLU* 2.7 32.1 + - - +
448E GLU* 5.6 0.6 + - - -
460E GLY 3.0 15.4 + - - +
461E ILE* 3.2 7.4 + - - +
463E ARG* 1.3 76.1 - - - +
465E ARG* 1.3 63.1 + - - +
467E PHE* 3.5 8.3 + - + +
468E ARG* 3.1 22.2 + - - +
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Residues in contact with ARG 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D GLN 3.9 11.4 + - - -
437D GLN* 3.2 57.4 + - - +
442D LEU* 3.6 20.4 - - + -
424E ILE 4.8 6.1 + - - -
425E GLY* 5.7 2.6 + - - -
426E PHE* 3.7 34.5 - - + -
461E ILE 3.0 17.8 + - - +
462E THR* 3.3 16.2 + - - +
464E LYS* 1.3 76.6 - - - +
466E PHE* 1.3 62.3 + - - +
468E ARG* 3.2 29.7 + - - +
469E GLU* 3.2 27.5 + - + +
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Residues in contact with PHE 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E TRP* 3.6 26.0 - + - -
421E LEU* 4.1 6.7 - - + -
424E ILE* 4.5 3.1 - - + -
426E PHE* 3.9 19.2 - + + -
433E PHE* 3.8 23.1 - + - -
443E LEU* 3.7 23.6 - - + -
446E MSE 4.3 7.2 - - + -
451E LEU* 3.5 30.7 - - + -
457E MSE 3.8 20.9 - - + -
462E THR 3.0 13.6 + - - +
463E ARG 3.2 8.0 + - - +
465E ARG* 1.3 76.6 - - - +
467E PHE* 1.3 63.0 + + - +
469E GLU* 3.0 7.6 + - - +
470E LEU* 2.8 44.3 + - + +
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Residues in contact with PHE 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446E MSE 4.0 19.3 - - + -
447E THR* 3.9 2.2 - - - -
448E GLU* 3.6 44.4 - - + -
451E LEU* 3.6 28.7 - - + -
463E ARG* 3.0 28.7 + - + +
464E LYS* 4.1 7.0 - - + +
466E PHE* 1.3 76.9 - + - +
468E ARG* 1.3 57.4 + - - +
470E LEU* 4.1 22.4 - - + -
471E THR* 2.8 39.2 + - - +
474E LYS* 5.9 3.4 - - - -
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Residues in contact with ARG 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D ASP* 3.2 38.3 + - - -
441D ASP* 2.9 37.6 + - - +
442D LEU* 3.8 11.3 - - - +
445D ARG* 4.5 7.6 - - - +
464E LYS 3.1 13.6 + - - +
465E ARG* 3.3 39.0 + - - +
466E PHE 3.1 0.4 - - - -
467E PHE* 1.3 78.1 - - - +
469E GLU* 1.3 67.4 + - + +
471E THR* 3.9 4.4 - - - -
472E GLU* 3.3 21.0 + - - +
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Residues in contact with GLU 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E TRP* 4.0 7.9 + - + -
424E ILE* 3.7 50.0 - - + +
426E PHE* 4.9 6.3 - - + -
465E ARG* 3.2 15.3 + - + +
466E PHE 3.0 8.1 + - - +
468E ARG* 1.3 80.4 + - + +
470E LEU* 1.3 60.7 + - - +
472E GLU* 3.2 13.0 + - - +
473E LEU* 3.0 27.2 + - - +
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Residues in contact with LEU 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E TRP* 4.0 11.8 - - + -
443E LEU* 3.5 49.6 - - + +
444E LEU* 5.0 1.6 - - + +
446E MSE 4.3 9.2 - - + +
466E PHE* 2.8 28.7 + - + +
467E PHE* 4.0 26.0 - - + +
469E GLU* 1.3 76.6 - - - +
471E THR* 1.3 57.9 + - - +
473E LEU* 3.2 16.5 + - + +
474E LYS* 2.8 57.8 + - + +
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Residues in contact with THR 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467E PHE* 2.8 27.3 + - - +
468E ARG* 3.9 5.4 - - - -
470E LEU* 1.3 76.4 - - - +
472E GLU* 1.3 58.2 + - - +
474E LYS* 3.8 12.3 + - - +
475E THR* 2.8 39.3 + - - +
500E GLN* 3.3 36.8 + - - +
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Residues in contact with GLU 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E ARG 3.3 12.0 + - - +
469E GLU* 3.2 16.9 + - - +
471E THR* 1.3 80.0 - - - +
473E LEU* 1.3 61.2 + - - +
475E THR* 3.4 10.3 + - - -
476E PHE* 3.4 44.4 + - + +
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Residues in contact with LEU 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407E ASN* 4.6 8.1 - - - +
409E VAL* 3.7 26.2 - - + -
412E TRP* 3.7 41.3 - - + -
420E TRP* 4.0 28.0 - - + +
443E LEU* 4.1 9.6 - - + -
444E LEU* 5.1 1.8 - - + -
469E GLU 3.0 13.5 + - - +
470E LEU* 3.2 17.5 + - + +
472E GLU* 1.3 78.7 - - - +
474E LYS* 1.3 63.2 + - - +
476E PHE* 3.5 2.0 + - - -
477E ALA* 3.2 26.0 + - - +
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Residues in contact with LYS 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444E LEU* 3.8 42.5 + - + +
446E MSE 6.0 0.2 + - - -
467E PHE* 5.9 2.8 - - - -
470E LEU* 2.8 51.5 + - + +
471E THR* 3.9 7.1 + - - +
473E LEU* 1.3 73.5 - - - +
475E THR* 1.3 62.6 + - - +
477E ALA* 4.4 1.6 - - - -
479E TYR* 2.7 30.2 + - - +
499E ARG 3.6 7.4 - - - +
500E GLN* 3.6 45.7 + - + +
501E TYR* 5.8 3.6 - - - -
503E TYR* 5.8 2.5 - - + -
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Residues in contact with THR 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471E THR* 2.8 28.4 + - - +
472E GLU* 3.7 6.9 - - - -
473E LEU 3.2 0.6 - - - -
474E LYS* 1.3 77.9 - - - +
476E PHE* 1.3 87.0 + - + +
477E ALA 3.5 0.2 - - - -
496E PRO* 3.7 26.1 + - + +
497E ARG* 4.6 6.1 + - - -
499E ARG* 3.1 29.4 + - + -
500E GLN* 3.9 19.4 + - - +
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Residues in contact with PHE 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407E ASN* 2.7 32.0 + - - +
472E GLU* 3.4 46.3 + - + +
473E LEU* 3.8 2.9 - - - -
474E LYS 3.4 0.2 - - - -
475E THR* 1.3 99.8 - - + +
477E ALA* 1.3 53.4 + - - +
496E PRO* 6.4 2.2 - - + -
499E ARG* 3.9 3.1 - - - +
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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