Contacts of the helix formed by residues 466 - 487 (chain A) in PDB entry 2XUJ
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 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A SER* 4.0 15.5 - - - +
464A ASN 5.3 0.9 - - - +
465A TYR* 1.3 77.0 - - - +
467A THR* 1.3 65.0 + - - +
468A GLU* 3.3 21.0 + - - +
469A GLU* 2.9 48.6 + - - +
470A ARG* 3.1 12.5 + - - +
515A LEU* 5.7 0.5 - - - +
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Residues in contact with THR 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A TYR 4.0 0.4 + - - -
466A THR* 1.3 72.8 - - - +
468A GLU* 1.3 73.4 + - - +
470A ARG* 3.2 29.8 + - - +
471A ILE* 3.0 34.8 + - + +
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A THR* 3.2 20.7 + - - +
467A THR* 1.3 85.7 + - - +
469A GLU* 1.3 56.9 + - - +
471A ILE* 3.2 13.3 + - + +
472A PHE* 2.9 28.7 + - - +
515A LEU* 4.1 27.2 - - + +
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Residues in contact with GLU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A HIS* 2.8 32.3 + - + +
434A ALA* 3.5 3.8 - - - -
435A SER* 2.7 45.5 + - - -
453A PHE* 3.8 13.7 - - + -
458A PRO* 3.9 4.1 - - - +
465A TYR* 3.5 18.1 - - + +
466A THR* 2.9 45.3 + - - +
468A GLU* 1.3 73.9 - - + +
470A ARG* 1.3 56.0 + - - +
472A PHE* 3.4 7.3 - - - +
473A ALA* 2.7 35.0 + - - +
515A LEU* 4.6 3.1 - - + -
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Residues in contact with ARG 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A PRO* 3.9 27.5 - - - +
459A LEU* 3.9 23.2 - - + +
466A THR 3.1 11.3 + - - +
467A THR* 3.2 43.5 + - - +
469A GLU* 1.3 76.3 - - - +
471A ILE* 1.3 68.2 + - - +
473A ALA* 3.6 2.4 + - - +
474A GLN* 3.1 60.2 + - - +
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Residues in contact with ILE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A THR* 3.0 31.2 + - + +
468A GLU* 3.2 11.2 + - + +
470A ARG* 1.3 87.5 - - - +
472A PHE* 1.3 59.8 + - - +
474A GLN* 3.4 14.7 + - - +
475A ARG* 3.0 34.5 + - + +
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Residues in contact with PHE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A PHE* 3.5 35.9 - + - -
432A HIS* 3.7 18.6 - + + -
453A PHE* 3.8 22.4 - + - -
468A GLU 2.9 16.4 + - - +
469A GLU* 3.4 4.3 - - - +
471A ILE* 1.3 74.6 - - - +
473A ALA* 1.3 64.6 + - - +
475A ARG* 2.9 26.0 + - - +
476A LEU* 2.9 45.1 + - + +
513A LEU* 3.9 16.2 - - + -
514A ASN* 3.1 32.3 - - - -
515A LEU* 3.9 20.2 - - + -
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A PHE* 4.0 18.5 - - + +
456A GLY* 4.4 1.3 - - - -
458A PRO* 3.8 24.5 - - + -
459A LEU* 3.8 16.2 - - + -
469A GLU 2.7 21.7 + - - +
470A ARG 3.7 5.6 - - - +
472A PHE* 1.3 74.1 - - - +
474A GLN* 1.3 60.6 + - - +
476A LEU* 3.3 4.6 + - - +
477A MET* 3.1 30.9 + - - +
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Residues in contact with GLN 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 5.1 12.0 - - + +
142A GLU* 4.5 0.5 - - - +
459A LEU* 3.9 24.0 - - + +
470A ARG* 3.1 58.9 + - - +
471A ILE* 3.5 13.2 - - - +
472A PHE 3.2 0.4 - - - -
473A ALA* 1.3 74.4 - - - +
475A ARG* 1.3 62.3 + - - +
477A MET* 3.5 10.0 + - - +
478A LYS* 3.1 29.1 + - - +
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Residues in contact with ARG 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ILE* 3.0 21.2 + - + +
472A PHE* 2.9 27.2 + - + +
474A GLN* 1.3 74.1 - - - +
476A LEU* 1.3 62.9 + - - +
478A LYS* 3.2 10.9 + - - +
479A TYR* 3.0 60.6 + - + +
512A SER 4.7 3.4 + - - -
513A LEU* 4.8 2.0 - - - +
514A ASN 3.1 25.0 + - - +
515A LEU 4.2 5.5 + - - -
516A LYS 3.2 22.0 + - - -
517A PRO* 4.2 6.2 - - - +
518A LEU* 3.8 22.4 - - - +
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Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A PHE* 3.4 30.3 - - + -
453A PHE* 3.7 24.0 - - + +
454A ILE* 3.9 16.6 - - + -
472A PHE* 2.9 36.6 + - + +
473A ALA 3.6 7.4 - - - +
475A ARG* 1.3 76.5 - - - +
477A MET* 1.3 56.9 + - - +
479A TYR* 3.1 20.3 + - + -
480A TRP* 3.0 39.9 + - + +
513A LEU* 3.6 29.4 - - + -
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Residues in contact with MET 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 3.6 42.2 - - + +
138A LEU* 3.7 19.7 - - + +
141A VAL* 4.0 20.0 - - + -
142A GLU* 4.2 9.6 - - + +
454A ILE 3.3 26.2 - - - +
456A GLY* 3.6 17.3 - - - +
459A LEU* 4.2 9.6 - - + -
473A ALA 3.1 22.6 + - - +
474A GLN* 3.8 7.4 - - - +
476A LEU* 1.3 75.0 - - - +
478A LYS* 1.3 51.3 + - - +
480A TRP* 4.0 2.9 - - - +
481A THR* 2.7 42.2 + - - +
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Residues in contact with LYS 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 3.1 32.3 + - - +
474A GLN 3.1 15.7 + - - +
475A ARG* 3.2 12.1 + - - +
477A MET* 1.3 75.6 - - - +
479A TYR* 1.3 60.6 + - + +
481A THR* 3.8 3.8 - - - -
482A ASN* 2.9 47.9 + - - +
485A ARG* 4.7 6.1 - - - +
491A ASP* 6.3 2.9 - - + -
493A ARG* 5.3 8.4 - - - +
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Residues in contact with TYR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LEU* 5.4 0.4 - - - -
475A ARG* 3.0 54.6 + - + +
476A LEU* 3.1 26.4 + - + +
478A LYS* 1.3 76.4 - - + +
480A TRP* 1.3 64.3 + + + +
482A ASN* 3.6 1.6 - - - +
483A PHE* 2.8 36.4 + - - +
489A PRO* 3.4 27.4 - - + +
490A ASN* 5.6 3.1 - - - -
500A TRP* 3.8 30.5 - + + -
513A LEU* 4.0 17.9 - - + -
518A LEU* 3.3 30.8 - - + +
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Residues in contact with TRP 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.9 10.2 - - + +
138A LEU* 5.4 2.2 - - + -
198A THR* 5.5 1.0 - - - +
200A PHE* 3.8 17.9 - + - -
226A VAL* 3.7 17.1 - - + +
228A GLN* 3.0 26.7 + - + -
327A LEU* 3.9 20.9 - - + -
428A TYR* 3.7 40.4 - + - -
450A GLU* 5.8 0.2 - - + -
454A ILE* 3.2 48.3 - - + +
476A LEU* 3.0 20.6 + - + +
477A MET* 4.0 6.1 - - - +
479A TYR* 1.3 93.1 - - + +
481A THR* 1.3 60.6 + - + +
483A PHE* 3.3 8.6 + - - +
484A ALA* 2.9 26.0 + - - +
500A TRP* 4.6 4.9 - + - -
513A LEU* 4.2 18.8 - - + -
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Residues in contact with THR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PRO* 5.6 0.2 - - - +
115A LEU* 4.4 11.0 - - + -
138A LEU* 3.8 20.2 - - + -
142A GLU* 3.2 29.2 + - + -
144A ALA* 4.7 9.9 - - + -
477A MET 2.7 21.9 + - - +
478A LYS 3.6 1.6 + - - -
480A TRP* 1.3 72.7 - - - +
482A ASN* 1.3 62.2 + - - +
483A PHE 3.2 0.2 - - - -
484A ALA* 3.6 9.2 - - - +
485A ARG* 2.9 54.3 + - - +
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Residues in contact with ASN 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A LYS* 2.9 35.7 + - - +
479A TYR* 3.6 4.0 - - - +
481A THR* 1.3 73.8 + - - +
483A PHE* 1.3 62.1 + - - +
485A ARG* 3.2 25.9 + - - +
486A THR* 2.8 39.1 + - + +
488A ASP 3.2 12.6 - - - +
489A PRO 3.2 18.4 + - - +
490A ASN 3.3 17.9 + - - +
491A ASP* 3.7 17.3 + - - +
492A PRO* 5.5 2.1 - - - +
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Residues in contact with PHE 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR* 4.6 2.2 - - + -
224A ARG* 3.3 18.6 - - + -
225A ALA 3.6 18.2 - - - -
226A VAL* 3.7 22.2 - - + -
325A GLN* 3.1 38.1 - - + -
326A VAL 3.7 4.5 - - - -
327A LEU* 3.7 15.7 - - + -
426A TYR* 4.1 18.2 - + - -
479A TYR 2.8 13.9 + - - +
480A TRP* 3.3 11.7 - - - +
482A ASN* 1.3 74.6 - - - +
484A ALA* 1.3 65.6 + - - +
487A GLY* 2.7 58.4 + - - -
488A ASP* 3.4 9.8 + - - +
489A PRO* 4.3 7.9 - - + -
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PRO* 4.7 10.1 - - + -
114A VAL 5.4 0.2 - - - +
115A LEU* 3.1 35.9 - - + -
196A SER* 3.8 5.9 + - - +
198A THR* 3.3 21.7 + - + +
224A ARG* 2.9 27.7 + - - -
480A TRP 2.9 11.7 + - - +
481A THR* 3.6 9.4 - - - +
483A PHE* 1.3 75.3 - - - +
485A ARG* 1.3 58.6 + - - +
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Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PRO* 3.7 31.3 - - + +
142A GLU* 3.3 31.7 + - - -
144A ALA* 6.1 0.8 - - - +
196A SER* 4.7 1.9 + - - -
224A ARG* 4.2 8.6 + - - -
478A LYS* 4.7 4.6 - - - +
481A THR* 2.9 47.7 + - - +
482A ASN* 3.2 27.3 + - - +
484A ALA* 1.3 76.0 - - - +
486A THR* 1.3 72.1 + - + +
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Residues in contact with THR 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 4.7 5.5 + - - -
325A GLN* 5.1 1.7 - - - +
482A ASN* 2.8 23.7 + - + +
485A ARG* 1.3 94.1 - - + +
487A GLY* 1.3 60.2 + - - +
488A ASP* 2.9 27.4 + - - +
490A ASN 4.9 1.7 + - - -
492A PRO* 5.4 13.0 - - + +
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Residues in contact with GLY 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 3.6 17.4 - - - +
325A GLN* 4.0 17.9 - - - +
424A ARG* 5.3 2.3 - - - +
426A TYR* 3.2 21.7 + - - -
483A PHE* 2.7 36.0 + - - -
486A THR* 1.3 72.7 - - - +
488A ASP* 1.3 57.5 + - - +
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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