Contacts of the helix formed by residues 458 - 475 (chain N) in PDB entry 6LTJ
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 THR 458 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449N PHE* 3.2 11.1 - - - +
454N ASN 4.6 0.4 - - - +
455N LYS* 3.6 25.8 - - - +
456N SER 4.9 0.2 - - - -
457N LYS* 1.3 77.1 - - - +
459N PRO* 1.3 77.0 - - + +
460N GLU* 3.4 16.9 + - - +
461N ILE* 3.1 27.5 + - + +
462N TYR 3.0 19.1 + - - -
59R LYS* 6.4 0.9 - - + -
62R ARG* 4.6 2.0 - - - +
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Residues in contact with PRO 459 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438N VAL* 4.3 4.6 - - + +
449N PHE 3.1 13.2 - - - +
450N PHE* 3.7 22.7 - - + -
458N THR* 1.3 83.8 - - + +
460N GLU* 1.3 56.5 + - - +
462N TYR* 3.6 6.1 + - + +
463N LEU* 2.9 27.2 + - - +
62R ARG* 3.4 26.0 - - - +
72R TYR* 3.7 33.0 - - + +
74R TYR* 3.5 17.3 + - - +
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Residues in contact with GLU 460 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458N THR* 3.0 14.8 + - - +
459N PRO* 1.3 74.8 - - - +
461N ILE* 1.3 62.3 + - + +
463N LEU* 3.6 7.4 - - - +
464N ALA* 2.9 28.9 + - - +
55R ILE 5.1 1.2 - - - +
56R TRP* 5.0 1.8 - - - -
57R MET* 3.8 21.0 + - + +
58R GLU 3.7 13.7 - - - -
59R LYS* 3.7 19.6 + - - +
62R ARG* 2.6 49.5 + - - +
74R TYR* 2.7 29.1 + - + +
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Residues in contact with ILE 461 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449N PHE* 4.1 7.6 - - + -
455N LYS 5.5 0.7 - - - +
456N SER* 3.4 27.4 - - - +
457N LYS* 5.6 0.2 - - + -
458N THR* 3.1 26.3 + - + +
460N GLU* 1.3 78.9 - - + +
462N TYR* 1.3 57.0 + - - +
464N ALA* 3.2 4.7 + - - +
465N TYR* 2.9 61.0 + - + +
56R TRP* 3.7 25.4 - - + -
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Residues in contact with TYR 462 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438N VAL* 4.1 11.2 - - + -
442N GLU* 2.9 55.3 - - + +
446N LEU* 3.4 23.1 - - + -
449N PHE* 3.4 49.3 - + + -
450N PHE* 4.1 13.9 - + - -
458N THR 3.0 7.6 + - - +
459N PRO* 3.8 2.9 - - + +
461N ILE* 1.3 75.1 - - - +
463N LEU* 1.3 69.1 + - - +
465N TYR* 3.3 3.2 + - - +
466N ARG* 2.9 47.9 + - - +
500N VAL* 4.0 17.9 - - + -
503N PHE* 3.7 8.7 - + - -
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Residues in contact with LEU 463 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435N TYR 3.9 5.6 - - - +
436N ASN* 4.8 1.8 - - - -
437N SER 4.5 3.4 - - - +
438N VAL* 4.5 9.4 - - + -
459N PRO 2.9 18.7 + - - +
460N GLU* 3.3 5.4 + - - +
462N TYR* 1.3 80.5 - - - +
464N ALA* 1.3 57.9 + - - +
466N ARG* 3.1 32.3 - - - +
467N ASN* 2.9 57.6 + - - +
55R ILE 4.5 4.3 - - - +
57R MET* 3.8 23.6 - - + -
74R TYR* 3.5 40.2 - - + -
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Residues in contact with ALA 464 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460N GLU 2.9 14.7 + - - +
461N ILE 3.5 2.5 - - - +
463N LEU* 1.3 74.0 - - - +
465N TYR* 1.3 66.9 + - - +
468N PHE* 2.9 25.0 + - - +
490N LEU* 5.0 1.1 - - - -
55R ILE* 3.3 24.2 + - + +
56R TRP* 3.4 50.7 - - + -
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Residues in contact with TYR 465 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449N PHE* 4.1 23.6 - + - -
456N SER 5.2 1.0 + - - -
461N ILE* 2.9 41.6 + - + +
462N TYR* 3.8 4.0 - - - +
464N ALA* 1.3 75.8 - - - +
466N ARG* 1.3 63.8 + - - +
468N PHE* 3.3 1.7 + - - +
469N MET* 3.0 32.1 + - + +
490N LEU* 3.7 37.4 - - + +
491N ALA 2.4 32.3 + - - -
492N GLY* 3.6 7.8 - - - -
493N ASP 5.4 0.2 - - - -
496N ALA* 5.1 3.8 - - + -
497N ILE* 3.7 26.0 - - + -
500N VAL* 4.4 16.6 - - + -
56R TRP* 4.1 12.6 - + - -
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Residues in contact with ARG 466 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N PHE* 3.1 32.0 - - - -
435N TYR 3.4 5.3 + - - -
437N SER 2.8 28.5 + - - -
438N VAL* 4.1 2.6 - - - +
442N GLU* 3.2 24.0 + - - -
462N TYR* 2.9 44.3 + - + +
463N LEU* 3.1 26.3 - - - +
465N TYR* 1.3 77.6 - - - +
467N ASN* 1.3 84.4 + - - +
469N MET* 3.3 2.9 + - - +
470N ILE* 2.9 40.3 + - + +
500N VAL* 4.2 11.4 - - + +
504N LEU* 3.9 14.8 - - + +
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Residues in contact with ASN 467 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N PHE* 4.7 0.5 - - - -
435N TYR* 3.4 39.3 + - - +
436N ASN* 5.3 0.6 - - - +
463N LEU* 2.9 44.2 + - - +
466N ARG* 1.3 101.1 + - - +
468N PHE* 1.3 60.7 + - - +
470N ILE* 4.0 4.0 - - - +
471N ASP* 2.9 36.9 + - - +
55R ILE* 3.6 24.6 + - + +
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Residues in contact with PHE 468 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464N ALA 2.9 19.4 + - - +
465N TYR 3.6 3.4 - - - +
467N ASN* 1.3 77.6 - - - +
469N MET* 1.3 64.0 + - + +
471N ASP* 3.8 3.7 - - - +
472N THR* 2.6 52.8 + - + -
486N CYS* 4.6 9.4 - - - -
489N ASN* 3.3 45.5 - - + -
490N LEU* 4.0 28.9 - - + -
523O MET 4.6 4.3 - - - -
524O GLY* 4.1 8.5 - - - -
525O PRO* 3.4 26.9 - - + +
46R THR* 5.5 0.4 - - + -
50R GLN* 3.9 15.3 - - - -
55R ILE* 4.0 11.1 - - + +
56R TRP* 6.0 3.4 - - - -
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Residues in contact with MET 469 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465N TYR* 3.0 19.2 + - + +
466N ARG 3.8 3.8 - - - +
468N PHE* 1.3 79.0 - - + +
470N ILE* 1.3 58.0 + - - +
472N THR* 3.3 0.8 + - - -
473N TYR* 2.9 26.3 + - - +
481N LEU* 3.3 13.7 - - + +
486N CYS* 3.5 26.7 - - + -
490N LEU* 4.0 12.1 - - + -
497N ILE* 3.3 45.1 - - + +
500N VAL* 4.0 13.0 - - + -
501N HIS* 3.6 37.2 - - + +
504N LEU* 3.9 16.8 - - + -
510N ILE* 3.9 3.1 - - + -
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Residues in contact with ILE 470 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N PHE* 3.4 32.5 - - + -
435N TYR* 4.6 11.2 - - + -
466N ARG* 2.9 34.2 + - + +
467N ASN* 4.0 4.5 - - - +
469N MET* 1.3 74.3 - - - +
471N ASP* 1.3 61.3 + - - +
473N TYR* 3.8 0.5 - - - +
474N ARG* 2.9 71.0 + - + +
504N LEU* 3.8 13.7 - - + -
509N LEU* 4.5 9.9 - - + +
510N ILE* 3.6 20.9 - - + -
528O THR* 4.6 3.1 - - - +
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Residues in contact with ASP 471 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435N TYR* 2.2 33.6 + - - -
467N ASN 2.9 19.2 + - - +
470N ILE* 1.3 75.9 - - - +
472N THR* 1.3 61.4 + - - +
475N LEU* 3.1 29.8 + - - +
525O PRO* 3.6 20.3 - - + +
526O PRO 3.8 9.0 - - - +
527O PRO* 4.0 2.6 - - - +
528O THR* 2.2 51.0 + - - +
55R ILE* 3.2 12.0 - - - +
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Residues in contact with THR 472 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468N PHE* 2.6 42.7 + - + -
469N MET* 3.7 5.6 - - - -
470N ILE 3.2 0.2 - - - -
471N ASP* 1.3 78.3 - - - +
473N TYR* 1.3 65.5 + - - +
475N LEU* 3.7 10.7 + - - +
476N ASN* 4.3 4.2 + - - +
481N LEU* 3.6 25.2 - - + +
486N CYS* 5.4 0.2 - - - -
525O PRO* 3.5 14.1 - - - +
46R THR* 3.6 21.8 - - + -
48R VAL* 4.0 19.3 - - + +
50R GLN* 6.3 0.4 - - - +
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Residues in contact with TYR 473 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424N ILE* 5.8 1.6 - - + -
469N MET 2.9 8.4 + - - +
470N ILE 3.9 0.2 - - - +
472N THR* 1.3 78.6 - - - +
474N ARG* 1.3 68.5 + - + +
475N LEU 3.1 0.4 - - - -
476N ASN 2.8 33.7 + - - +
477N PRO* 2.6 43.3 + - + -
479N GLU 3.5 14.8 - - - -
481N LEU* 3.9 13.2 - - + +
509N LEU 3.9 16.6 - - - -
510N ILE* 3.5 20.9 - - + -
511N ASN* 3.2 46.9 - - - -
512N TYR* 3.3 4.1 + - + -
513N GLN* 3.0 35.9 + - - +
514N VAL* 3.9 0.8 + - + -
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Residues in contact with ARG 474 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424N ILE* 3.4 32.0 - - + +
426N ILE* 4.3 18.0 - - - +
433N PHE* 3.9 28.1 - - - -
435N TYR* 5.0 6.5 - - - +
470N ILE* 2.9 40.7 + - + +
471N ASP 3.8 0.2 + - - -
472N THR 3.4 0.4 - - - -
473N TYR* 1.3 88.6 - - + +
475N LEU* 1.3 60.4 + - - +
476N ASN 3.2 1.0 + - - -
477N PRO* 3.8 16.1 - - - +
509N LEU* 4.5 12.3 + - - +
528O THR* 3.9 34.1 + - + +
529O SER* 5.6 0.8 - - - +
531O PHE* 3.6 16.8 - - - -
533O VAL* 3.9 30.0 - - - +
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Residues in contact with LEU 475 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471N ASP 3.1 18.8 + - - +
472N THR 4.0 5.6 - - - +
473N TYR 3.0 1.4 + - - -
474N ARG* 1.3 78.0 - - - +
476N ASN* 1.3 64.1 + - + +
477N PRO* 3.9 2.3 - - - +
525O PRO* 3.7 3.8 - - + -
526O PRO* 3.6 41.7 - - + +
528O THR* 3.9 17.9 - - + -
531O PHE* 4.7 9.2 - - + -
48R VAL* 3.7 29.4 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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