Contacts of the helix formed by residues 463 - 485 (chain B) in PDB entry 3ODX
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 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B PHE 3.5 0.2 - - - -
462B PRO* 1.3 85.6 + - - +
464B LEU* 1.3 65.7 + - - +
465B ASP* 3.2 2.4 - - - +
466B GLU* 2.7 21.0 + - - +
467B LEU* 3.1 8.1 + - - -
511B ILE* 4.1 32.5 - - - +
514B ARG* 3.3 31.2 + - - -
515B PHE* 4.1 9.7 - - - +
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU* 4.1 19.1 - - + +
438B LEU* 4.0 16.8 - - + -
439B HIS* 3.7 34.5 - - + +
443B PHE* 4.1 23.5 - - + -
461B PHE* 3.3 26.7 + - + +
463B SER* 1.3 74.4 - - - +
465B ASP* 1.3 65.5 + - - +
466B GLU 3.0 0.2 + - - -
467B LEU* 3.0 7.9 + - + -
468B ILE* 2.8 45.2 + - + +
515B PHE* 4.1 18.6 - - + -
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Residues in contact with ASP 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B HIS* 3.1 33.1 + - - -
443B PHE* 4.2 16.4 - - - -
463B SER 2.8 5.4 + - - +
464B LEU* 1.3 77.0 - - - +
466B GLU* 1.3 59.5 + - - +
468B ILE* 3.5 9.0 - - - +
469B GLU* 3.4 23.0 + - - +
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Residues in contact with GLU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B SER* 2.7 16.2 + - - +
465B ASP* 1.3 74.5 - - + +
467B LEU* 1.3 61.3 + - - +
468B ILE 3.2 1.3 - - - -
469B GLU* 3.2 17.9 + - - +
470B VAL* 3.0 25.8 + - - +
507B TRP* 2.8 46.9 + - + +
511B ILE* 4.1 14.6 - - + -
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Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU* 3.9 16.6 - - + -
463B SER 3.1 10.0 + - - +
464B LEU* 3.0 11.1 + - + +
466B GLU* 1.3 73.6 - - - +
468B ILE* 1.3 66.6 + - - +
469B GLU 3.3 0.3 + - - -
470B VAL* 3.4 7.4 + - + +
471B HIS* 3.4 27.9 + - + +
511B ILE* 3.6 12.8 - - + +
512B SER* 3.7 26.7 - - - +
515B PHE* 3.6 39.3 - - + -
561B GLU* 3.2 42.0 - - - +
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Residues in contact with ILE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 4.8 4.0 - - + +
435B LEU* 3.2 45.8 - - + +
436B ARG* 4.1 28.9 - - + +
439B HIS* 3.6 29.4 - - + -
464B LEU* 2.8 26.6 + - + +
465B ASP* 3.5 11.0 - - - +
467B LEU* 1.3 77.6 - - - +
469B GLU* 1.3 59.9 + - - +
471B HIS* 3.8 2.3 + - - +
472B SER* 2.2 43.3 + - - +
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Residues in contact with GLU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ARG* 5.5 0.7 + - - -
436B ARG* 5.6 2.1 + - - -
465B ASP 3.4 16.7 - - - +
466B GLU* 3.4 26.7 - - - +
467B LEU 3.2 0.4 - - - -
468B ILE* 1.3 82.7 - - - +
470B VAL* 1.3 62.1 + - - +
472B SER* 2.9 11.0 + - - -
473B LEU* 2.7 33.7 + - - +
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B GLU* 3.0 19.1 + - - +
467B LEU* 3.5 19.5 - - + +
469B GLU* 1.3 75.4 - - - +
471B HIS* 1.3 71.1 + - + +
473B LEU* 3.2 13.3 + - - +
474B PHE* 3.3 14.2 + - - +
499B ARG* 4.7 4.1 - - + +
507B TRP* 3.5 35.7 - - + +
508B PHE* 3.3 40.4 - - + +
511B ILE* 4.6 6.7 - - + -
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Residues in contact with HIS 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLU* 2.8 29.7 + - - +
431B HIS* 3.7 21.7 - + + -
432B VAL* 3.7 14.3 - - + +
435B LEU* 3.9 4.5 - - + -
467B LEU* 3.4 25.4 + - + +
468B ILE 4.2 1.6 - - - +
469B GLU 3.3 0.4 - - - -
470B VAL* 1.3 86.3 - - + +
472B SER* 1.3 61.7 + - - +
474B PHE* 3.5 3.8 + - - +
475B LEU* 3.0 21.0 + - - +
508B PHE* 3.6 24.1 - + - -
561B GLU* 2.7 37.9 + - - -
564B ARG* 4.2 2.7 - - + -
565B LEU* 4.8 0.2 - - + -
568B TYR* 3.1 22.7 + + - -
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Residues in contact with SER 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ARG* 3.3 28.9 + - - +
432B VAL* 3.8 17.8 - - - +
436B ARG* 5.5 0.3 + - - -
468B ILE* 2.2 39.3 + - - +
469B GLU* 2.9 21.8 + - - -
471B HIS* 1.3 72.7 - - - +
473B LEU* 1.3 61.5 + - - -
475B LEU* 3.3 4.0 + - - +
476B ASP* 3.0 26.3 + - - -
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B GLU* 2.7 19.5 + - - +
470B VAL* 3.2 6.3 + - - +
472B SER* 1.3 73.5 - - - +
474B PHE* 1.3 62.9 + - - +
476B ASP* 3.1 17.6 + - + +
477B ARG* 3.0 46.8 + - + +
504B GLU* 4.2 18.4 - - - +
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Residues in contact with PHE 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 4.3 16.6 - - + -
428B GLU* 3.5 38.1 - - + -
470B VAL 3.3 6.8 + - - +
471B HIS* 3.6 6.7 - - - +
473B LEU* 1.3 73.2 - - - +
475B LEU* 1.3 64.9 + - - +
476B ASP 3.0 1.3 - - - -
477B ARG* 3.0 10.5 + - + +
478B LEU* 2.9 57.4 + - + +
495B VAL* 4.8 9.4 - - + -
496B LEU* 4.7 11.9 - - + -
499B ARG* 3.0 71.7 - - + +
500B PHE* 4.5 2.0 - + - -
568B TYR* 4.1 5.4 - + - -
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Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A MET* 4.6 5.8 - - - -
716A ARG* 4.0 33.4 - - + +
728A LEU* 4.6 3.8 - - + -
425B LEU* 3.8 13.2 - - + +
428B GLU* 3.9 11.7 - - + -
429B ALA* 3.4 48.0 - - + +
432B VAL* 4.4 13.9 - - + -
471B HIS 3.0 15.4 + - - +
472B SER* 3.6 7.6 - - - +
474B PHE* 1.3 76.1 - - - +
476B ASP* 1.3 58.9 + - - +
478B LEU* 3.8 4.6 - - + +
479B MET* 3.0 48.6 + - + +
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Residues in contact with ASP 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ARG* 2.8 48.9 + - - +
717A GLU 4.9 6.1 - - - +
726A TYR* 5.3 5.2 - - - -
472B SER 3.0 15.3 + - - +
473B LEU* 3.2 19.5 - - + +
474B PHE 3.0 0.4 - - - -
475B LEU* 1.3 77.3 - - - +
477B ARG* 1.3 65.0 + - - +
479B MET* 3.3 5.8 + - - +
480B LYS* 3.0 23.7 + - - +
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Residues in contact with ARG 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B LEU* 3.0 40.3 + - + +
474B PHE* 3.0 14.2 + - - +
476B ASP* 1.3 71.4 - - - +
478B LEU* 1.3 61.3 + - - +
480B LYS* 3.2 9.1 + - - +
481B ARG* 2.9 30.3 + - - +
495B VAL* 3.7 26.5 - - + +
498B ALA* 3.5 43.5 + - - +
499B ARG* 5.3 2.3 - - - +
504B GLU* 5.0 8.1 + - - +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ILE* 6.2 1.6 - - + -
424B LEU* 4.1 17.5 - - + -
425B LEU* 3.6 43.9 - - + +
428B GLU* 4.5 7.0 - - + -
474B PHE* 2.9 53.3 + - + +
475B LEU* 3.8 5.6 - - + +
477B ARG* 1.3 77.8 - - - +
479B MET* 1.3 62.9 + - - +
481B ARG* 3.5 3.6 + - - +
482B ARG* 3.0 18.4 + - - +
492B ILE* 4.1 20.7 - - + +
495B VAL* 4.0 18.4 - - + -
496B LEU* 4.8 1.8 - - + -
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Residues in contact with MET 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ARG* 4.3 13.2 - - + -
726A TYR* 3.5 47.3 - - + -
728A LEU* 3.6 36.6 - - + -
737A ILE* 3.2 29.2 - - + +
425B LEU* 3.9 13.5 - - + -
475B LEU* 3.0 38.2 + - + +
476B ASP* 3.8 6.5 - - - +
477B ARG 3.2 0.4 - - - -
478B LEU* 1.3 73.9 - - - +
480B LYS* 1.3 59.6 + - - +
483B GLN* 2.8 29.2 + - - +
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Residues in contact with LYS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A THR* 4.1 24.2 - - - +
726A TYR* 4.3 17.9 + - + +
476B ASP 3.0 17.1 + - - +
477B ARG* 3.6 7.6 - - - +
479B MET* 1.3 75.1 - - - +
481B ARG* 1.3 65.5 + - - +
483B GLN* 3.2 1.6 + - - +
484B GLU* 3.0 43.0 + - + +
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Residues in contact with ARG 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ARG 2.9 17.2 + - - +
478B LEU* 3.8 5.6 - - - +
480B LYS* 1.3 77.0 - - - +
482B ARG* 1.3 64.1 + - - +
484B GLU* 2.7 46.9 + - - +
485B SER* 3.0 17.0 + - - -
489B ILE* 4.6 11.9 - - + -
490B GLU 5.6 0.4 - - - -
491B GLU* 2.9 42.8 + - - +
492B ILE* 3.6 13.2 - - + +
494B ASP* 3.1 40.3 + - - -
495B VAL* 3.7 18.1 - - + +
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Residues in contact with ARG 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU* 6.4 0.2 - - - +
734A GLU 4.5 3.1 + - - -
735A ALA* 2.7 31.3 + - - +
736A GLN 4.4 2.0 - - - +
737A ILE* 3.8 23.3 - - + -
418B GLN* 3.6 26.4 - - - +
421B ILE* 6.2 2.5 - - - -
422B SER* 5.4 3.8 + - - +
425B LEU* 4.2 10.3 - - + -
478B LEU 3.0 18.0 + - - +
481B ARG* 1.3 76.1 - - - +
483B GLN* 1.3 64.0 + - - +
484B GLU 3.3 0.2 + - - -
485B SER* 3.4 22.1 + - - -
489B ILE* 4.0 33.4 - - + +
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Residues in contact with GLN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A TRP* 5.7 0.4 - - - -
657A ARG 3.5 23.0 + - - -
658A VAL* 4.2 10.9 + - - +
659A THR* 5.2 10.0 - - - +
660A LYS 5.9 0.5 + - - -
704A LEU* 5.8 1.3 - - - +
726A TYR* 4.2 17.9 - - + +
737A ILE* 3.2 38.5 + - + +
739A GLU* 3.6 31.1 + - - +
479B MET 2.8 18.0 + - - +
480B LYS 3.7 4.0 - - - +
482B ARG* 1.3 78.1 - - - +
484B GLU* 1.3 61.9 + - - +
485B SER 3.4 2.6 + - - -
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Residues in contact with GLU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A LYS* 5.8 12.8 - - + +
480B LYS* 3.0 35.2 + - + +
481B ARG* 2.7 55.9 + - - +
483B GLN* 1.3 79.5 - - - +
485B SER* 1.3 57.0 + - - +
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ARG* 3.0 23.0 + - - -
482B ARG* 3.4 18.3 + - - -
483B GLN 3.3 4.1 - - - -
484B GLU* 1.3 79.4 - - - +
489B ILE* 3.6 23.4 + - - +
490B GLU* 3.5 25.3 - - - +
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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