Contacts of the helix formed by residues 468 - 492 (chain D) in PDB entry 2GZD
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 ARG 468 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D ARG* 1.3 67.3 + - - +
470D LYS 3.2 4.6 - - - +
471D ASP* 3.3 27.8 + - - +
472D THR* 3.3 22.7 + - - -
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Residues in contact with ARG 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ARG* 1.3 80.6 - - - +
470D LYS* 1.3 80.1 + - + +
471D ASP 3.6 0.2 - - - -
472D THR* 3.3 16.4 - - - +
473D HIS* 3.1 20.1 + - - +
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Residues in contact with LYS 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LYS* 5.0 13.8 - - + +
471C ASP* 2.7 34.2 + - - +
474C ILE* 3.9 22.2 - - + +
468D ARG 3.2 1.8 - - - +
469D ARG* 1.3 102.1 - - + +
471D ASP* 1.3 60.5 + - - +
473D HIS* 3.5 15.7 - - + +
474D ILE* 3.2 33.2 + - - +
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Residues in contact with ASP 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LYS* 3.2 29.4 + - - +
468D ARG* 3.3 32.3 + - - +
470D LYS* 1.3 74.5 - - - +
472D THR* 1.3 64.3 + - - +
474D ILE* 3.4 10.0 + - - +
475D ARG* 3.1 22.3 + - - +
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Residues in contact with THR 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ARG 3.3 10.7 + - - -
469D ARG* 3.3 17.9 - - - +
471D ASP* 1.3 80.1 - - - +
473D HIS* 1.3 57.6 + - - +
475D ARG* 3.0 32.1 + - - +
476D GLU* 3.0 41.5 + - - +
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Residues in contact with HIS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 5.1 8.2 - - + +
474C ILE* 4.0 25.2 - - + +
478C GLU* 4.3 8.5 - - - -
469D ARG 3.1 17.3 + - - +
470D LYS* 3.5 18.4 - - + +
471D ASP 3.3 0.6 - - - -
472D THR* 1.3 72.6 - - - +
474D ILE* 1.3 66.0 + - - +
476D GLU* 3.2 22.1 + - + +
477D LEU* 3.1 51.5 + - + +
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Residues in contact with ILE 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LYS* 4.3 37.2 - - + +
473C HIS* 4.1 20.4 - - + +
474C ILE* 3.9 19.9 - - + +
477C LEU* 3.8 12.2 - - + +
470D LYS 3.2 26.2 + - - +
471D ASP* 3.5 7.6 - - - +
473D HIS* 1.3 77.1 + - - +
475D ARG* 1.3 58.3 + - - +
477D LEU* 3.4 4.5 + - - +
478D GLU* 2.9 56.3 + - - +
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Residues in contact with ARG 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 4.9 9.9 - - - +
471D ASP 3.1 15.6 + - - +
472D THR* 3.0 50.6 + - - +
473D HIS 3.2 0.4 - - - -
474D ILE* 1.3 74.1 - - + +
476D GLU* 1.3 79.3 + - - +
478D GLU* 4.0 15.0 - - + +
479D ASP* 2.7 66.4 + - - +
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Residues in contact with GLU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.6 22.7 + - - +
44A ILE* 4.1 18.4 - - + +
472D THR* 3.0 28.5 + - - +
473D HIS* 3.2 27.6 + - + +
475D ARG* 1.3 95.3 + - - +
477D LEU* 1.3 58.7 + - - +
479D ASP* 3.3 5.4 + - - +
480D TYR* 2.9 28.6 + - - +
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Residues in contact with LEU 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.6 33.6 - - + +
474C ILE* 3.9 31.4 - - + +
477C LEU* 4.1 17.0 - - + -
478C GLU* 4.0 14.4 - - + -
481C ILE* 3.7 14.0 - - + +
473D HIS* 3.1 43.2 + - + +
474D ILE 3.5 8.1 - - - +
476D GLU* 1.3 76.9 - - - +
478D GLU* 1.3 55.6 + - - +
480D TYR* 3.2 6.0 + - - +
481D ILE* 3.0 35.2 + - - +
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Residues in contact with GLU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 3.4 27.5 + - - +
473C HIS* 3.4 24.3 - - - -
477C LEU* 3.8 16.5 - - + +
474D ILE* 2.9 37.2 + - - +
475D ARG* 3.0 12.2 + - - +
477D LEU* 1.3 73.0 - - - +
479D ASP* 1.3 64.8 + - - +
481D ILE* 3.5 8.4 + - + +
482D ASP* 3.2 30.8 + - - +
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Residues in contact with ASP 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 4.8 9.0 + - - -
475D ARG* 2.7 53.0 + - - +
476D GLU* 3.6 5.6 - - - +
478D GLU* 1.3 72.3 - - - +
480D TYR* 1.3 66.4 + - - +
482D ASP* 3.4 8.3 + - - +
483D ASN* 3.1 36.1 + - - +
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Residues in contact with TYR 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.3 45.3 - - + -
45A GLY* 3.6 10.5 - - - -
46A VAL 3.8 8.8 + - - -
481C ILE* 3.7 37.9 - - + -
485C LEU* 3.6 22.0 - - - +
496C LEU* 5.1 0.9 - - - +
476D GLU 2.9 13.7 + - - +
477D LEU 3.2 8.0 + - - +
479D ASP* 1.3 75.4 - - - +
481D ILE* 1.3 66.7 + - - +
483D ASN* 3.2 7.7 + - + +
484D LEU* 2.9 46.6 + - + +
487D ARG* 5.1 11.0 + - - -
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Residues in contact with ILE 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 4.4 1.8 - - + -
45B GLY* 4.2 9.2 - - - +
74B ARG* 5.9 0.2 - - - +
477C LEU* 4.1 31.0 - - + +
480C TYR* 3.6 25.8 - - + -
481C ILE* 3.5 33.0 - - + -
484C LEU* 5.4 1.8 - - + -
477D LEU 3.0 28.3 + - - +
478D GLU* 3.8 7.0 - - - +
480D TYR* 1.3 77.4 - - - +
482D ASP* 1.3 56.7 + - - +
484D LEU* 3.2 5.2 + - + +
485D LEU* 2.8 60.9 + - + +
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Residues in contact with ASP 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 5.1 5.0 + - - -
74B ARG* 3.4 53.3 + - - +
75B ALA* 4.1 16.6 + - + +
76B ILE* 3.1 18.0 - - + +
478D GLU* 3.2 19.4 + - - +
479D ASP* 3.9 8.9 - - - +
480D TYR 3.3 0.2 - - - -
481D ILE* 1.3 79.7 - - - +
483D ASN* 1.3 56.0 + - - +
485D LEU* 4.4 0.3 - - - +
486D VAL* 2.8 40.4 + - - +
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Residues in contact with ASN 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA* 3.6 21.8 - - - +
479D ASP* 3.1 25.2 + - - +
480D TYR* 3.7 6.5 - - + +
482D ASP* 1.3 72.8 - - - +
484D LEU* 1.3 68.8 + - - +
486D VAL* 3.5 7.4 + - - +
487D ARG* 3.4 29.1 + - - +
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Residues in contact with LEU 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C ILE* 5.5 2.7 - - + +
484C LEU* 3.8 29.8 - - + -
485C LEU* 3.6 26.2 - - + -
488C VAL* 4.8 2.0 - - + -
495C ILE* 3.3 32.3 - - + -
496C LEU* 4.1 11.2 - - + -
480D TYR* 2.9 34.8 + - + +
481D ILE* 3.5 4.9 - - - +
483D ASN* 1.3 77.1 - - - +
485D LEU* 1.3 62.2 + - - +
487D ARG* 3.1 30.8 + - - +
488D VAL* 3.0 22.6 + - + +
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Residues in contact with LEU 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY* 3.6 21.8 - - - -
46B VAL* 3.6 14.8 - - + +
76B ILE* 3.3 20.9 - - + -
480C TYR* 3.7 10.1 - - - +
484C LEU* 4.0 11.9 - - + -
481D ILE* 2.8 44.0 + - + +
482D ASP* 4.4 1.3 - - - +
483D ASN 3.3 0.2 - - - -
484D LEU* 1.3 73.7 - - - +
486D VAL* 1.3 53.0 + - - +
488D VAL* 4.2 4.3 - - + -
489D MSE 2.8 41.5 + - - +
496D LEU* 3.5 39.0 - - + -
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Residues in contact with VAL 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA* 3.3 39.7 - - + +
76B ILE* 3.6 6.9 - - + +
79B ALA* 5.4 8.4 - - + +
482D ASP 2.8 26.1 + - - +
483D ASN* 3.7 8.5 - - - +
484D LEU 3.3 0.2 - - - -
485D LEU* 1.3 74.7 - - - +
487D ARG* 1.3 63.1 + - + +
489D MSE 3.7 6.6 + - - +
490D GLU* 3.2 44.9 + - + +
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Residues in contact with ARG 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C ILE* 2.5 43.9 + - + +
496C LEU* 4.3 9.1 - - - +
497C ARG 4.6 3.2 + - - -
498C VAL* 6.4 0.2 - - - +
500C TYR* 3.6 54.3 - - + +
480D TYR* 5.1 11.1 + - - -
483D ASN* 3.4 17.9 + - - +
484D LEU* 3.1 37.2 + - - +
486D VAL* 1.3 76.8 - - + +
488D VAL* 1.3 59.6 + - - +
490D GLU* 3.4 4.8 + - - +
491D GLU* 3.1 35.0 + - - +
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Residues in contact with VAL 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C LEU* 4.7 3.6 - - + -
488C VAL* 3.8 20.4 - - + -
495C ILE* 3.7 21.1 - - + -
484D LEU* 3.0 22.7 + - + +
485D LEU* 3.2 10.1 + - + +
487D ARG* 1.3 71.0 - - - +
489D MSE 1.3 62.7 + - - +
491D GLU* 5.2 0.4 - - - -
492D THR* 2.8 49.4 + - - +
495D ILE* 3.3 30.1 - - + -
496D LEU* 3.7 16.4 - - + -
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Residues in contact with MSE 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS* 5.0 0.9 - - - +
46B VAL* 4.3 15.5 - - + -
65B TRP* 4.0 24.9 - - + -
76B ILE* 3.7 27.6 - - - -
79B ALA* 3.4 48.2 - - + +
80B TYR* 3.5 12.6 - - + +
485D LEU* 2.8 26.2 + - - +
486D VAL 3.9 4.9 - - - +
488D VAL* 1.3 72.8 - - - +
490D GLU* 1.3 59.3 + - + +
493D PRO* 3.7 26.2 - - - +
496D LEU* 3.6 19.5 - - + -
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Residues in contact with GLU 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA* 5.6 2.6 - - + +
82B ARG* 4.7 21.4 + - - +
500C TYR* 4.1 16.1 + - - -
502C PRO* 6.1 0.9 - - - +
486D VAL* 3.2 37.3 + - + +
487D ARG* 3.7 7.2 - - - +
488D VAL 3.1 0.8 - - - -
489D MSE 1.3 81.7 - - + +
491D GLU* 1.3 61.4 + - + +
493D PRO* 4.9 1.3 - - - +
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Residues in contact with GLU 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C THR* 4.3 5.6 - - + +
494C SER* 4.2 10.0 + - - -
495C ILE* 3.4 24.2 - - + +
500C TYR* 3.5 27.0 + - - +
501C GLU 5.2 0.2 - - - +
502C PRO* 3.1 29.8 - - + +
487D ARG 3.1 16.8 + - - +
490D GLU* 1.3 82.3 - - + +
492D THR* 1.3 70.3 + - - +
493D PRO* 3.7 5.4 - - - +
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Residues in contact with THR 492 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C GLU* 4.7 12.3 - - + +
492C THR* 2.6 37.1 + - - +
495C ILE* 5.3 0.2 - - - +
488D VAL* 2.8 17.6 + - - +
491D GLU* 1.3 81.3 + - - +
493D PRO* 1.3 61.6 - - - +
494D SER* 3.1 17.0 - - - +
495D ILE* 2.5 49.0 - - + +
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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