Contacts of the helix formed by residues 458 - 475 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449O PHE* 3.6 7.0 - - - -
454O ASN 4.9 1.0 + - - -
455O LYS* 3.4 21.0 + - - -
456O SER 3.5 3.4 + - - -
457O LYS* 1.3 76.3 - - - +
459O PRO* 1.3 77.2 - - + +
460O GLU* 3.2 26.9 - - + +
461O ILE* 3.3 15.4 + - - +
462O TYR 3.1 21.3 + - - -
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Residues in contact with PRO 459 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438O VAL* 5.2 6.2 - - + +
443O ARG* 5.1 8.1 - - - +
449O PHE 3.3 14.1 - - - +
450O PHE* 3.6 34.3 - - + -
452O GLY* 6.4 0.9 - - - -
458O THR* 1.3 88.4 - - + +
460O GLU* 1.3 74.1 + - - +
462O TYR* 3.8 5.1 - - + +
463O LEU* 2.9 28.2 + - - +
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Residues in contact with GLU 460 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458O THR* 3.2 17.0 - - + +
459O PRO* 1.3 88.9 - - - +
461O ILE* 1.3 63.8 + - + +
463O LEU* 3.3 19.0 - - + +
464O ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 461 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336M VAL* 3.2 36.6 - - + +
337M GLU 4.7 6.1 - - - +
338M ILE* 5.1 0.2 - - - -
339M ALA* 4.0 17.0 - - + +
449O PHE* 4.5 4.7 - - + -
456O SER 3.4 27.1 - - - +
457O LYS* 5.8 0.2 - - + -
458O THR* 3.3 22.7 + - - +
460O GLU* 1.3 79.5 - - + +
462O TYR* 1.3 56.3 + - - +
464O ALA* 3.3 1.2 + - - +
465O TYR* 2.9 63.4 + - + +
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Residues in contact with TYR 462 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438O VAL* 3.9 11.9 - - + -
442O GLU* 3.0 47.3 + - + +
446O LEU* 3.5 24.0 - - + -
449O PHE* 3.6 32.5 - + + -
450O PHE* 3.7 19.3 - + - -
458O THR 3.1 8.6 + - - +
459O PRO* 3.8 7.9 - - + +
460O GLU 3.3 0.2 - - - -
461O ILE* 1.3 74.5 - - - +
463O LEU* 1.3 70.6 + - + +
465O TYR* 3.3 2.8 + - - +
466O ARG* 3.0 48.6 + - + +
500O VAL* 4.0 26.9 - - + -
503O PHE* 3.8 9.4 - + - -
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Residues in contact with LEU 463 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435O TYR 4.4 4.0 - - - +
436O ASN* 4.7 6.7 - - - +
437O SER* 4.5 11.7 - - - +
438O VAL* 5.0 4.3 - - + +
459O PRO 2.9 15.4 + - - +
460O GLU* 3.3 24.9 - - - +
462O TYR* 1.3 81.5 - - + +
464O ALA* 1.3 57.7 + - - +
466O ARG* 3.2 34.4 - - - +
467O ASN* 2.9 49.0 + - - +
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Residues in contact with ALA 464 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M ALA* 3.6 24.9 - - + +
340M ILE* 4.4 13.0 - - + +
460O GLU 2.9 16.0 + - - +
461O ILE* 3.9 0.4 - - + +
463O LEU* 1.3 73.5 - - - +
465O TYR* 1.3 67.5 + - - +
467O ASN* 3.9 6.0 - - - +
468O PHE* 2.9 26.7 + - - +
490O LEU* 5.3 0.4 - - - -
17R TYR* 4.2 2.9 + - - -
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Residues in contact with TYR 465 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336M VAL* 4.2 2.6 - - - +
339M ALA* 3.6 22.4 - - + -
449O PHE* 4.1 26.0 - + - -
456O SER 5.1 0.9 + - - -
457O LYS* 6.3 0.4 - - + -
461O ILE* 2.9 37.6 + - + +
462O TYR* 3.7 4.9 - - - +
464O ALA* 1.3 77.8 - - - +
466O ARG* 1.3 57.2 + - - +
468O PHE* 3.3 2.8 + - - +
469O MET* 3.0 36.1 + - + +
490O LEU* 3.8 28.1 - - + +
491O ALA 2.4 32.2 + - - -
492O GLY* 3.3 14.4 - - - -
493O ASP 4.4 0.7 + - - -
496O ALA* 5.0 4.3 - - + -
497O ILE* 3.8 23.3 - - + -
500O VAL* 4.4 14.6 - - + -
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Residues in contact with ARG 466 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433O PHE* 3.2 34.7 - - - -
434O ASP 3.5 4.2 + - - -
435O TYR 3.4 7.3 + - - -
437O SER 2.9 29.9 + - - -
438O VAL* 4.1 1.6 - - - +
442O GLU* 3.8 6.4 + - - -
462O TYR* 3.0 52.3 + - + +
463O LEU* 3.2 28.7 - - - +
465O TYR* 1.3 74.3 - - - +
467O ASN* 1.3 89.2 + - - +
469O MET* 3.8 1.1 - - - +
470O ILE* 2.9 35.4 + - - +
500O VAL* 4.0 11.2 - - + -
504O LEU* 3.6 28.7 - - + -
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Residues in contact with ASN 467 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433O PHE* 4.9 0.2 - - - -
435O TYR* 3.1 45.6 + - + +
463O LEU* 2.9 40.3 + - - +
464O ALA* 3.9 5.2 - - - +
466O ARG* 1.3 100.4 + - - +
468O PHE* 1.3 57.4 - - - +
470O ILE* 3.4 3.9 + - - +
471O ASP* 2.9 35.5 + - - +
17R TYR* 3.7 9.2 - - - +
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Residues in contact with PHE 468 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340M ILE* 3.9 15.5 - - + -
464O ALA 2.9 18.6 + - - +
465O TYR 3.5 4.0 - - - +
467O ASN* 1.3 77.8 - - - +
469O MET* 1.3 63.6 + - + +
471O ASP* 3.9 1.5 - - - +
472O THR* 2.6 46.4 + - - -
486O CYS* 5.1 3.4 - - + -
489O ASN* 4.0 20.9 - - + -
490O LEU* 4.0 25.8 - - + -
17R TYR* 3.2 34.0 + + + +
20R ALA* 4.0 27.1 - - + -
21R MET* 3.9 22.9 - - + -
24R CYS* 3.9 18.6 - - + -
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Residues in contact with MET 469 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465O TYR* 3.0 17.5 + - + +
466O ARG* 3.8 4.0 - - - +
467O ASN 3.3 0.2 - - - -
468O PHE* 1.3 78.2 - - - +
470O ILE* 1.3 62.8 + - - +
472O THR* 4.6 0.4 - - - -
473O TYR 2.9 19.8 + - - -
481O LEU* 3.6 7.8 - - + +
486O CYS* 4.0 17.7 - - + -
490O LEU* 4.0 13.9 - - + -
497O ILE* 3.3 44.4 - - + +
500O VAL* 3.7 20.9 - - + -
501O HIS* 3.5 30.7 - - + -
504O LEU* 3.8 6.7 - - + -
510O ILE* 3.4 23.4 - - + +
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Residues in contact with ILE 470 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433O PHE* 4.1 25.4 - - + -
435O TYR* 4.7 10.8 - - + -
466O ARG* 2.9 26.0 + - + +
467O ASN* 3.6 6.5 - - - +
469O MET* 1.3 77.4 - - - +
471O ASP* 1.3 68.5 + - - +
473O TYR* 3.3 5.2 + - - +
474O ARG* 2.9 63.1 + - + +
504O LEU* 4.3 12.6 - - + -
509O LEU* 3.1 43.3 - - + +
510O ILE* 4.3 1.8 - - - +
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Residues in contact with ASP 471 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1807L SER* 3.4 22.2 + - - -
1808L LYS 4.4 0.7 - - - +
1809L PHE* 4.2 16.6 - - + +
435O TYR* 3.7 18.0 + - - -
467O ASN 2.9 22.2 + - - +
470O ILE* 1.3 83.1 - - - +
472O THR* 1.3 58.3 + - - +
474O ARG* 3.1 9.7 + - - +
475O LEU* 3.0 32.6 + - - +
17R TYR* 3.6 18.9 + - - -
21R MET* 3.4 23.8 - - + -
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Residues in contact with THR 472 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468O PHE* 2.6 34.4 + - - -
469O MET 4.0 2.2 - - - -
471O ASP* 1.3 73.1 - - - +
473O TYR* 1.3 68.2 + - - +
475O LEU* 3.4 19.1 - - - +
476O ASN 4.2 0.9 + - - -
479O GLU* 5.4 0.3 - - - +
481O LEU* 4.3 14.6 - - + +
21R MET* 3.3 39.7 - - - +
24R CYS* 3.7 23.1 - - + -
25R HIS* 3.9 15.9 + - + +
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Residues in contact with TYR 473 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424O ILE* 5.7 5.8 - - + -
469O MET 2.9 10.4 + - - +
470O ILE 3.5 4.0 - - - +
472O THR* 1.3 76.9 - - - +
474O ARG* 1.3 64.9 + - + +
476O ASN 2.9 33.0 + - - +
477O PRO* 2.9 37.1 + - + -
479O GLU* 3.6 17.9 - - + -
481O LEU* 3.9 11.9 - - + +
508O GLY 5.8 0.2 - - - -
509O LEU 4.4 4.7 - - - -
510O ILE* 3.4 31.6 - - + -
511O ASN* 3.2 38.6 - - - -
512O TYR* 3.0 7.2 + - + -
513O GLN* 2.9 34.3 + - + +
514O VAL* 3.8 1.1 + - + -
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Residues in contact with ARG 474 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805L LEU 2.6 25.8 + - - -
1806L ILE* 3.6 4.9 - - - +
1807L SER* 3.4 28.0 + - - +
1809L PHE 5.6 3.4 - - - +
1810L ASP* 3.3 31.3 + - - +
1811L LYS* 5.6 4.2 + - - +
1812L LEU* 4.5 9.0 - - - +
1814L VAL* 4.8 1.0 - - - +
424O ILE* 3.6 35.3 - - + +
426O ILE* 4.1 13.1 - - - +
433O PHE* 4.3 9.9 - - - -
470O ILE* 2.9 46.0 + - - +
471O ASP* 3.1 13.0 + - - +
473O TYR* 1.3 83.0 - - + +
475O LEU* 1.3 63.5 + - - +
476O ASN 3.0 1.2 + - - -
477O PRO* 3.5 16.0 - - - +
509O LEU* 5.9 0.4 - - - +
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Residues in contact with LEU 475 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809L PHE 4.4 17.0 - - - +
1811L LYS* 5.2 20.5 - - + +
471O ASP 3.0 20.0 + - - +
472O THR* 3.4 11.7 - - - +
473O TYR 3.1 0.2 + - - -
474O ARG* 1.3 75.8 - - - +
476O ASN* 1.3 61.5 + - - +
477O PRO* 4.6 0.5 - - - +
18R LYS* 5.9 3.4 - - + -
21R MET* 3.6 45.8 - - + +
22R GLU* 3.8 24.5 - - + +
25R HIS* 4.2 16.6 + - + +
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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
------------------------------------------------------------
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