Contacts of the helix formed by residues 453 - 475 (chain L) in PDB entry 6PSU
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 PRO 453 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46J TYR* 2.9 41.3 - - + +
452L ILE* 1.3 90.4 - - + +
454L VAL* 1.3 54.1 + - - +
455L HIS* 3.4 24.5 - - + -
456L MET* 3.0 17.4 + - + +
457L ILE* 2.6 37.6 + - - +
44O A 3.6 23.1 - - + +
45O A 3.9 10.8 - - - +
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Residues in contact with VAL 454 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440L THR* 5.8 3.8 - - + +
441L ARG* 4.6 29.4 - - - +
444L ALA* 3.9 27.4 - - + +
445L ASP* 5.1 2.7 - - + +
451L ARG* 5.6 7.0 - - - +
452L ILE 3.6 0.9 + - - +
453L PRO* 1.3 73.4 - - - +
455L HIS* 1.3 52.0 + - - +
457L ILE* 3.3 7.6 - - + -
458L GLU* 2.4 38.7 + - + +
44O A 5.8 0.4 - - - +
45O A 4.6 4.3 + - - +
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Residues in contact with HIS 455 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453L PRO* 3.1 25.8 - - + +
454L VAL* 1.3 77.9 - - - +
456L MET* 1.3 64.6 + - + +
458L GLU* 3.1 29.3 - - - +
459L THR* 2.7 25.0 + - - -
43O A 3.8 17.8 - - + +
44O A 2.2 52.1 + + + -
45O A 5.7 4.9 - - - +
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Residues in contact with MET 456 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J TYR* 5.8 4.0 - - + -
452L ILE* 4.9 2.7 - - + -
453L PRO* 3.0 31.1 + - + +
455L HIS* 1.3 92.4 - - + +
457L ILE* 1.3 56.8 + - - +
458L GLU 3.1 1.1 - - - -
459L THR* 2.6 36.1 + - - -
460L ILE* 2.8 15.8 + - + +
493L LYS* 5.9 0.9 - - + +
496L LYS* 4.6 22.0 - - + +
497L VAL* 3.4 33.9 - - + -
500L ILE* 4.8 21.5 - - + -
43O A 6.1 0.9 - - - +
44O A 5.0 7.6 - - - +
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Residues in contact with ILE 457 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444L ALA* 3.1 47.6 - - + +
448L ARG* 5.1 9.4 - - - +
452L ILE* 3.0 47.1 - - + +
453L PRO 2.6 28.3 + - - +
454L VAL* 3.7 5.8 - - + +
456L MET* 1.3 68.5 - - - +
458L GLU* 1.3 64.6 + - - +
460L ILE* 4.3 8.3 - - + +
461L ASN* 3.1 44.7 + - - +
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Residues in contact with GLU 458 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454L VAL* 2.4 31.4 + - + +
455L HIS* 3.1 30.8 - - - +
457L ILE* 1.3 70.7 - - - +
459L THR* 1.3 57.6 + - - -
461L ASN* 4.2 2.7 - - - +
462L LYS* 3.3 30.7 + - - +
38P C 4.6 35.0 + - - +
39P C 5.0 6.4 + - - -
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Residues in contact with THR 459 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455L HIS* 2.7 18.7 + - - -
456L MET* 2.6 36.0 + - - -
458L GLU* 1.3 70.1 - - - +
460L ILE* 1.3 58.1 + - - -
462L LYS* 2.8 13.3 + - + +
463L LEU* 2.8 35.2 + - + +
489L MET* 6.4 2.5 - - + -
493L LYS 6.1 1.1 - - - +
494L ILE* 6.4 2.2 - - + -
497L VAL* 4.4 13.5 - - + -
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Residues in contact with ILE 460 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448L ARG* 4.5 18.8 - - - +
452L ILE* 4.6 7.6 - - + -
456L MET* 2.8 18.1 + - + +
457L ILE* 4.3 5.2 - - + +
459L THR* 1.3 73.0 - - - +
461L ASN* 1.3 65.8 + - - +
463L LEU* 3.3 6.6 + - - +
464L ASN* 2.7 54.7 + - - +
497L VAL* 3.3 26.5 - - + +
498L LEU* 6.6 0.2 - - + -
500L ILE* 3.7 31.4 - - + -
501L ALA* 4.3 20.4 - - + -
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Residues in contact with ASN 461 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397L ARG* 4.8 12.3 + - - +
440L THR* 6.4 0.2 - - - +
448L ARG* 5.4 2.6 + - - -
457L ILE* 3.1 32.8 + - - +
458L GLU* 4.4 2.2 - - - +
460L ILE* 1.3 86.0 - - - +
462L LYS* 1.3 61.0 + - - +
464L ASN* 4.1 5.9 - - - +
465L ARG* 3.3 29.6 + - - +
36P T 3.6 37.8 + - - +
37P G 5.7 0.6 + - - -
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Residues in contact with LYS 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458L GLU* 3.3 22.5 + - - +
459L THR* 2.8 15.9 + - + +
461L ASN* 1.3 76.5 - - - +
463L LEU* 1.3 63.2 + - + +
465L ARG* 3.9 14.4 - - - +
466L ILE* 3.0 55.5 + - + +
487L MET* 4.4 13.2 - - + -
489L MET* 5.5 6.5 - - + -
38P C 5.5 6.7 - - - -
39P C 5.8 1.6 + - - -
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Residues in contact with LEU 463 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459L THR* 2.8 21.4 + - + +
460L ILE* 3.3 7.4 + - - +
462L LYS* 1.3 79.0 - - + +
464L ASN* 1.3 56.5 + - - +
466L ILE* 2.9 3.8 + - + -
467L SER* 2.3 42.1 + - - -
483L LEU* 3.7 23.9 - - + +
487L MET* 4.4 22.4 - - + -
489L MET* 6.1 1.1 - - + -
494L ILE* 4.0 26.2 - - + -
497L VAL* 3.4 32.8 - - + -
498L LEU* 4.0 16.8 - - + -
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Residues in contact with ASN 464 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496I LYS* 4.7 14.0 - - - +
460L ILE* 2.7 46.1 + - - +
461L ASN* 4.5 5.1 - - - +
463L LEU* 1.3 75.0 - - - +
465L ARG* 1.3 57.6 + - - +
467L SER* 2.4 24.4 + - - +
468L ARG* 3.0 23.7 + - - +
498L LEU* 5.4 7.3 - - - +
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Residues in contact with ARG 465 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461L ASN 3.3 21.5 + - - +
462L LYS* 3.9 17.1 + - - +
463L LEU 3.1 0.4 - - - -
464L ASN* 1.3 77.5 - - - +
466L ILE* 1.3 69.6 + - - +
468L ARG* 3.0 42.4 + - - +
469L GLN* 3.4 8.4 + - - +
35P A 5.7 0.9 - - - -
36P T 3.4 61.2 + - - +
38P C 4.4 10.3 + - - -
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Residues in contact with ILE 466 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462L LYS* 3.0 33.0 + - + +
463L LEU* 2.9 6.5 + - + +
465L ARG* 1.3 84.5 - - + +
467L SER* 1.3 64.5 + - - +
469L GLN* 3.3 35.4 + - + +
470L MET* 3.5 14.6 + - + +
483L LEU* 6.0 6.4 - - + +
486L ARG* 3.4 23.6 - - + -
487L MET* 3.5 35.9 - - + -
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Residues in contact with SER 467 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496I LYS* 5.1 7.4 + - - -
463L LEU* 2.3 27.7 + - - -
464L ASN* 2.4 38.6 + - - -
466L ILE* 1.3 69.0 - - - +
468L ARG* 1.3 56.9 + - - +
470L MET* 3.3 0.9 + - - +
471L LEU* 2.9 34.4 + - - +
478L PRO* 4.0 21.6 - - - +
483L LEU* 5.3 8.9 - - - +
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Residues in contact with ARG 468 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494I ASN* 3.6 26.8 + - - +
496I LYS* 6.4 1.8 - - + -
464L ASN* 3.0 21.4 + - - +
465L ARG* 3.0 25.5 + - + +
467L SER* 1.3 82.0 + - - +
469L GLN* 1.3 58.5 + - + +
470L MET 2.9 1.7 + - - -
471L LEU* 3.7 5.7 - - - +
472L GLN* 2.8 44.9 + - - +
34P T 3.3 32.3 + - - -
35P A 2.3 42.6 + - - -
36P T 3.4 9.1 + - - +
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Residues in contact with GLN 469 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490I GLN* 5.9 1.1 - - - -
491I ASP* 5.2 9.0 - - - +
465L ARG 3.9 9.4 - - - +
466L ILE* 3.3 40.9 + - + +
468L ARG* 1.3 77.1 - - + +
470L MET* 1.3 59.9 + - - +
472L GLN* 4.7 7.2 - - - -
473L GLU* 3.0 49.5 - - - +
486L ARG* 3.5 33.2 + - - +
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Residues in contact with MET 470 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466L ILE* 3.5 16.1 + - - +
467L SER 3.3 2.8 + - - +
468L ARG 3.0 0.6 - - - -
469L GLN* 1.3 81.2 - - - +
471L LEU* 1.3 59.7 + - - +
472L GLN 3.3 0.9 - - - -
473L GLU* 3.6 3.1 - - - +
474L MET* 2.8 39.6 + - + +
478L PRO* 3.9 18.6 - - + -
482L GLU* 3.3 52.5 - - + +
483L LEU* 4.5 3.6 - - - -
486L ARG* 3.3 48.9 - - + +
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Residues in contact with LEU 471 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I TYR* 4.3 13.3 - - + +
495I ALA* 4.0 27.4 - - + -
496I LYS* 5.6 7.4 - - + +
467L SER 2.9 19.0 + - - +
468L ARG* 3.8 4.3 - - - +
470L MET* 1.3 78.8 - - - +
472L GLN* 1.3 67.8 + - + +
473L GLU 3.4 0.5 + - - -
475L GLY 2.7 27.6 - - - +
476L ARG 3.5 19.1 - - - +
477L GLU* 4.3 13.7 - - + +
478L PRO* 3.6 18.7 - - + +
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Residues in contact with GLN 472 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ARG* 4.6 3.6 + - - -
123I TYR* 3.8 18.8 + - + +
490I GLN* 2.5 59.8 + - + +
491I ASP* 4.9 0.2 - - - -
493I ILE 2.1 33.2 + - - +
494I ASN* 3.1 10.0 + - - +
495I ALA* 2.9 26.3 - - + +
468L ARG* 2.8 29.4 + - - +
469L GLN* 4.7 4.3 - - - -
471L LEU* 1.3 87.6 - - + +
473L GLU* 1.3 60.9 + - - +
475L GLY 4.6 0.9 + - - -
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Residues in contact with GLU 473 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ARG* 5.1 4.0 + - - -
120I GLN* 5.7 1.6 - - - +
488I MET* 4.7 15.4 - - + +
490I GLN* 4.3 19.9 - - + +
491I ASP* 5.4 3.3 - - - +
469L GLN* 3.0 42.5 + - - +
470L MET* 3.2 4.2 + - - +
471L LEU 3.2 0.4 - - - -
472L GLN* 1.3 79.6 - - - +
474L MET* 1.3 67.3 + - + +
475L GLY* 3.1 3.5 + - - -
486L ARG* 4.6 8.0 + - - -
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Residues in contact with MET 474 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470L MET* 2.8 32.6 + - + +
473L GLU* 1.3 75.1 - - - +
475L GLY* 1.3 57.1 + - - +
476L ARG* 3.4 21.5 - - + +
477L GLU 3.3 34.3 - - - +
482L GLU* 3.0 43.1 - - - +
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Residues in contact with GLY 475 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I ARG* 3.3 25.8 - - - -
123I TYR* 3.1 19.6 - - - -
471L LEU 2.7 22.2 + - - +
472L GLN 4.6 0.2 + - - -
473L GLU 3.1 4.9 + - - -
474L MET* 1.3 81.9 - - - +
476L ARG* 1.3 61.1 + - - +
477L GLU 3.6 0.7 - - - -
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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