Contacts of the helix formed by residues 464 - 477 (chain f) in PDB entry 5T0J
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 LYS 464 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427f PRO* 2.8 49.1 + - + +
428f PHE* 3.6 18.6 + - - +
430f SER* 5.2 0.9 - - - +
431f PHE* 3.6 39.9 - - + +
462f ASP* 2.8 14.6 + - - +
463f SER* 1.3 82.3 - - - +
465f GLU* 1.3 60.9 + - - +
466f LYS* 3.1 1.5 - - - +
467f GLU* 2.9 31.6 + - - +
468f GLU* 4.0 2.6 + - - +
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Residues in contact with GLU 465 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422f GLU* 5.6 1.8 - - - +
430f SER* 5.5 4.5 - - - +
434f THR* 3.4 37.6 - - + +
438f VAL* 4.5 13.7 - - - +
457f CYS* 3.3 30.3 - - - -
458f SER* 5.9 0.3 - - - -
462f ASP* 3.0 24.4 + - + +
464f LYS* 1.3 79.7 - - - +
466f LYS* 1.3 60.1 + - - +
467f GLU 3.2 0.3 + - - -
468f GLU* 3.2 11.0 + - + +
469f ASP* 2.8 48.1 + - - +
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Residues in contact with LYS 466 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454f LEU* 5.4 8.3 - - + -
458f SER* 6.0 1.6 - - - -
461f PHE* 4.2 23.6 - - + -
462f ASP* 4.4 6.3 - - - +
463f SER* 3.7 40.6 + - - +
464f LYS 3.1 1.8 - - - +
465f GLU* 1.3 77.0 + - - +
467f GLU* 1.3 77.7 + - - +
469f ASP* 3.7 12.4 - - + +
470f LYS* 3.2 20.6 + - - +
491f GLN* 5.6 9.1 - - - +
493f VAL* 6.2 1.6 - - - +
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Residues in contact with GLU 467 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431f PHE* 5.8 3.4 - - + -
463f SER 5.9 0.2 - - - +
464f LYS* 2.9 15.2 + - - +
466f LYS* 1.3 90.8 + - + +
468f GLU* 1.3 67.0 + - + +
469f ASP 3.3 0.2 + - - -
470f LYS 3.4 4.9 + - - -
471f ASP* 3.4 4.0 + - - +
491f GLN* 4.7 4.7 - - - +
493f VAL* 3.3 36.0 - - + +
494f ALA 3.8 1.4 + - - -
495f VAL* 3.1 30.7 + - + -
496f LEU* 3.1 65.9 + - + +
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Residues in contact with GLU 468 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431f PHE* 3.0 65.5 - - + +
434f THR* 3.5 12.4 + - - +
435f LEU* 3.2 47.4 + - + +
438f VAL* 5.3 2.3 - - - +
439f CYS* 4.6 5.5 - - - -
464f LYS 5.2 1.6 - - - +
465f GLU* 3.2 11.1 + - + +
467f GLU* 1.3 78.0 - - + +
469f ASP* 1.3 64.1 + - - +
471f ASP* 3.2 22.9 + - - +
472f LYS* 3.2 12.3 + - - +
495f VAL* 5.2 4.4 - - + +
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Residues in contact with ASP 469 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438f VAL* 4.8 5.9 - - - +
450f VAL* 5.0 6.2 - - - +
453f LEU* 4.9 2.9 - - - +
454f LEU* 3.3 41.6 + - + +
457f CYS* 5.2 3.9 - - - +
465f GLU* 2.8 43.4 + - - +
466f LYS* 3.7 12.1 - - - +
467f GLU 3.2 0.2 - - - -
468f GLU* 1.3 73.9 - - - +
470f LYS* 1.3 61.3 + - - +
472f LYS* 3.2 38.3 + - - +
473f LYS* 3.6 4.0 + - - +
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Residues in contact with LYS 470 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466f LYS 3.2 13.7 + - - +
467f GLU 3.9 2.9 - - - +
469f ASP* 1.3 75.8 - - - +
471f ASP* 1.3 65.8 + - - +
473f LYS* 3.2 31.4 + - - +
474f GLU* 3.1 21.8 + - - +
486f ASP* 3.9 27.6 + - + +
489f ALA* 5.7 5.6 - - - -
496f LEU* 3.6 39.8 - - - +
500f LEU* 5.0 5.5 - - - +
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Residues in contact with ASP 471 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435f LEU* 5.4 5.4 - - + +
439f CYS* 4.9 3.4 - - - -
467f GLU 3.4 14.5 + - - +
468f GLU* 3.2 20.1 + - + +
470f LYS* 1.3 75.9 + - - +
472f LYS* 1.3 56.1 + - - +
474f GLU* 3.2 14.0 + - - +
475f LYS* 2.7 35.2 + - - +
495f VAL* 3.9 19.4 - - - +
496f LEU* 3.3 30.5 - - - +
499f ALA* 4.1 21.5 - - + +
500f LEU* 5.3 0.5 + - - +
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Residues in contact with LYS 472 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438f VAL* 3.3 44.9 - - + +
439f CYS* 3.6 28.7 - - - +
444f SER* 5.7 2.8 + - - -
449f LYS* 4.6 10.4 - - + +
450f VAL* 3.5 40.6 - - - +
453f LEU* 4.3 10.6 - - + +
468f GLU 3.2 8.6 + - - +
469f ASP* 3.3 26.0 - - - +
470f LYS 3.2 0.4 - - - -
471f ASP* 1.3 74.5 - - - +
473f LYS* 1.3 55.3 + - - +
475f LYS* 3.4 6.5 - - - +
476f LYS* 2.5 41.5 + - + +
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Residues in contact with LYS 473 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447f VAL* 6.5 0.7 - - + -
450f VAL* 3.6 34.8 - - + -
469f ASP 3.6 2.2 + - - -
470f LYS* 3.2 36.1 + - - +
472f LYS* 1.3 79.2 - - - +
474f GLU* 1.3 62.9 + - - +
476f LYS* 3.3 36.4 + - - +
477f ASP* 3.4 12.5 + - - +
482f GLU* 4.9 10.2 + - - +
486f ASP* 3.1 32.7 + - - +
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Residues in contact with GLU 474 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470f LYS* 3.1 15.2 + - - +
471f ASP* 3.2 16.9 + - - +
473f LYS* 1.3 80.5 - - - +
475f LYS* 1.3 67.4 + - - +
477f ASP* 2.9 21.5 - - - +
483f ALA* 4.2 18.7 - - + +
486f ASP* 5.4 6.5 - - + +
499f ALA* 2.9 31.2 - - - +
500f LEU* 3.2 22.6 - - + +
503f MET* 3.3 9.2 - - - +
504f GLY* 2.7 34.7 + - - -
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Residues in contact with LYS 475 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439f CYS* 3.6 49.2 + - + +
442f ALA 4.8 5.3 + - - -
443f GLY* 5.2 6.9 + - - -
471f ASP 2.7 19.9 + - - +
472f LYS* 3.8 6.9 + - - +
474f GLU* 1.3 73.8 + - - +
476f LYS* 1.3 70.9 + - - +
477f ASP 3.9 1.1 - - - +
478f LYS* 4.2 5.8 + - - +
503f MET* 3.6 45.9 - - + +
671f LEU* 5.8 9.0 - - + +
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Residues in contact with LYS 476 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443f GLY 4.1 8.6 - - - +
444f SER* 3.2 26.2 - - - +
445f GLY* 3.6 23.3 + - - +
447f VAL* 3.8 28.6 - - - +
450f VAL* 3.8 31.4 - - + +
472f LYS* 2.5 25.7 + - + +
473f LYS* 3.4 16.7 + - - +
474f GLU 3.3 0.2 - - - -
475f LYS* 1.3 80.3 - - - +
477f ASP* 1.3 98.9 + - - +
478f LYS* 3.3 17.5 + - - +
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Residues in contact with ASP 477 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445f GLY* 5.2 3.8 - - - +
447f VAL* 4.5 7.9 - - - +
473f LYS* 3.4 10.3 + - - +
474f GLU* 2.9 20.9 - - - +
475f LYS* 3.9 1.4 - - - +
476f LYS* 1.3 111.3 + - - +
478f LYS* 1.3 61.4 + - - +
479f ASP 3.7 2.6 + - - -
480f LYS* 3.7 25.7 + - + +
482f GLU* 2.9 28.9 - - + +
503f MET* 5.0 2.6 - - - +
504f GLY* 5.2 1.6 - - - -
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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