Contacts of the helix formed by residues 452 - 480 (chain W) in PDB entry 4BOG
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 452 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315W ARG* 4.9 1.3 - - - +
449W VAL* 2.7 55.5 - - + +
451W GLN* 1.3 78.5 - - - +
453W ILE* 1.3 66.6 + - - +
455W ARG* 2.7 32.6 - - - +
456W LEU* 2.9 39.9 + - + +
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Residues in contact with ILE 453 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247W PHE 5.6 1.3 - - - +
250W PRO* 5.7 2.5 - - + -
251W ALA* 2.8 43.1 - - + +
449W VAL 5.1 0.2 - - - +
450W GLY* 2.9 27.3 + - - +
452W THR* 1.3 84.2 - - - +
454W ASP* 1.3 94.4 + - + +
456W LEU* 2.9 21.5 + - + +
457W SER* 3.1 15.5 + - - +
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Residues in contact with ASP 454 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450W GLY 4.7 0.2 - - - +
451W GLN* 3.8 2.6 - - - +
453W ILE* 1.3 91.9 - - + +
455W ARG* 1.3 94.0 + - - +
456W LEU 3.1 0.2 + - - -
457W SER* 3.1 5.7 + - - +
458W MET* 2.4 45.0 + - + +
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Residues in contact with ARG 455 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451W GLN* 2.3 40.8 + - - +
452W THR* 2.7 30.9 - - - +
454W ASP* 1.3 100.7 + - - +
456W LEU* 1.3 54.6 + - + +
458W MET* 3.8 5.2 - - - -
459W PHE* 2.5 63.8 + - + -
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Residues in contact with LEU 456 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247W PHE* 4.1 14.8 - - + -
250W PRO* 6.3 3.1 - - + -
312W PHE* 2.7 49.8 - - + -
315W ARG* 4.6 8.7 - - - +
452W THR* 2.9 51.1 + - + +
453W ILE* 2.9 12.7 + - + +
455W ARG* 1.3 82.2 - - + +
457W SER* 1.3 63.3 + - - +
459W PHE* 3.0 3.4 + - - +
460W ILE* 2.9 29.5 + - - +
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Residues in contact with SER 457 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247W PHE* 2.4 41.3 + - - +
248W TYR* 4.0 22.8 + - - -
453W ILE* 3.1 10.7 + - - +
454W ASP* 3.3 5.6 - - - -
456W LEU* 1.3 76.7 - - - +
458W MET* 1.3 51.1 + - - +
460W ILE* 3.7 9.6 - - - +
461W ILE* 2.7 41.9 + - - +
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Residues in contact with MET 458 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454W ASP* 2.4 36.5 + - + +
455W ARG* 3.5 8.7 - - - +
457W SER* 1.3 66.1 - - - +
459W PHE* 1.3 73.7 + - + +
460W ILE 3.0 4.5 - - - -
461W ILE* 3.2 14.8 + - + +
462W THR* 2.6 54.2 + - + +
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Residues in contact with PHE 459 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455W ARG* 2.5 55.5 + - + +
456W LEU* 3.3 5.6 - - - +
458W MET* 1.3 89.0 - - + +
460W ILE* 1.3 55.1 + - + +
462W THR* 4.0 10.3 - - + -
463W PRO* 2.7 31.7 - - + +
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Residues in contact with ILE 460 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243W ALA 5.5 1.1 - - - +
244W ALA* 4.8 11.2 - - + +
247W PHE* 3.4 49.6 - - + -
248W TYR* 4.6 14.1 - - + +
305W ASN* 4.8 11.9 - - - +
308W ILE* 6.3 0.4 - - + -
312W PHE* 6.0 1.6 - - + -
456W LEU* 2.9 23.0 + - - +
457W SER* 3.7 11.2 - - - +
459W PHE* 1.3 80.0 - - + +
461W ILE* 1.3 68.6 + - + +
463W PRO* 2.9 20.0 - - + +
464W VAL* 2.9 19.8 + - + +
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Residues in contact with ILE 461 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248W TYR* 2.7 36.8 - - + +
457W SER 2.7 24.5 - - - +
458W MET* 3.4 15.5 - - + +
460W ILE* 1.3 76.5 - - - +
462W THR* 1.3 67.1 + - - +
464W VAL* 2.7 32.9 - - + +
465W MET* 2.8 10.1 + - + +
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Residues in contact with THR 462 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458W MET* 2.6 39.3 + - + +
459W PHE* 4.0 11.2 - - + -
461W ILE* 1.3 78.2 - - - +
463W PRO* 1.4 56.6 - - + +
465W MET* 3.0 18.7 - - - +
466W VAL* 2.6 43.0 + - + +
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Residues in contact with PRO 463 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459W PHE* 2.7 41.1 - - + +
460W ILE* 2.9 20.0 - - + +
462W THR* 1.4 80.8 - - + +
464W VAL* 1.3 52.2 + - - +
465W MET 2.9 1.8 - - - -
466W VAL* 2.6 16.3 + - + -
467W LEU* 2.5 52.8 + - + +
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Residues in contact with VAL 464 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W SER* 5.8 9.0 - - - -
244W ALA* 6.2 4.0 - - + -
460W ILE* 2.9 21.9 + - + +
461W ILE* 2.7 28.3 - - + +
463W PRO* 1.3 71.3 - - - +
465W MET* 1.3 71.0 + - + +
467W LEU* 3.7 12.0 - - + +
468W GLY* 2.6 36.6 + - - +
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Residues in contact with MET 465 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461W ILE* 2.8 12.3 + - + +
462W THR* 3.0 23.1 - - - +
464W VAL* 1.3 84.4 - - + +
466W VAL* 1.3 68.5 + - + +
469W THR* 2.5 57.6 + - + +
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Residues in contact with VAL 466 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462W THR* 2.6 40.6 + - + +
463W PRO* 2.6 23.8 + - + +
465W MET* 1.3 87.7 - - + +
467W LEU* 1.3 53.3 + - + +
469W THR* 3.5 1.7 - - - -
470W ILE* 2.5 49.3 + - + +
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Residues in contact with LEU 467 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298W LEU* 3.2 34.7 - - + +
301W GLY* 5.2 13.0 - - - -
463W PRO* 2.5 53.2 + - + +
464W VAL* 3.7 9.2 - - + +
466W VAL* 1.3 70.8 - - + +
468W GLY* 1.3 70.2 + - - +
469W THR 3.0 1.1 - - - -
470W ILE* 2.7 22.6 + - + +
471W PHE* 2.8 15.4 + - - +
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Residues in contact with GLY 468 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298W LEU* 5.3 5.6 - - - -
464W VAL* 2.6 27.7 + - - -
467W LEU* 1.3 77.9 - - - +
469W THR* 1.3 60.4 + - - +
471W PHE* 3.6 6.6 + - - +
472W ILE* 3.5 23.4 + - - +
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Residues in contact with THR 469 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464W VAL 3.9 0.2 + - - -
465W MET* 2.5 43.2 + - + +
466W VAL* 3.5 2.9 - - - +
468W GLY* 1.3 75.0 - - - +
470W ILE* 1.3 53.5 + - + +
471W PHE 3.0 0.3 + - - -
472W ILE* 3.3 8.9 + - + -
473W PHE* 2.4 66.8 + - + +
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Residues in contact with ILE 470 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466W VAL* 2.5 39.7 + - + +
467W LEU* 2.7 18.2 + - - +
469W THR* 1.3 70.3 - - + +
471W PHE* 1.3 49.4 + - - +
473W PHE* 3.1 16.1 - - + +
474W VAL* 2.6 54.0 + - + +
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Residues in contact with PHE 471 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233W ILE* 5.3 17.7 - - + -
294W PHE* 4.9 29.6 - + + -
295W ILE* 6.5 0.2 - - - -
298W LEU* 3.5 31.9 - - + -
467W LEU 2.8 12.4 + - - +
468W GLY* 3.8 8.7 - - - +
469W THR 3.0 0.4 + - - -
470W ILE* 1.3 70.2 - - + +
472W ILE* 1.3 64.9 + - + +
473W PHE 2.8 3.1 - - - -
474W VAL* 2.5 13.4 + - + +
475W MET* 2.3 55.5 + - + -
478W PHE* 5.6 2.9 - + - -
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Residues in contact with ILE 472 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468W GLY 3.5 13.4 + - - +
469W THR* 3.3 12.9 + - + +
471W PHE* 1.3 93.1 - - + +
473W PHE* 1.3 58.0 + - - +
475W MET* 2.9 54.3 - - + +
476W GLY* 3.1 10.9 + - - -
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Residues in contact with PHE 473 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469W THR* 2.4 55.9 + - + +
470W ILE* 3.1 19.1 - - + +
472W ILE* 1.3 71.5 - - - +
474W VAL* 1.3 52.1 + - + +
476W GLY* 3.2 3.1 + - - -
477W ASN* 2.7 51.0 + - + +
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Residues in contact with VAL 474 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294W PHE* 4.1 31.0 - - + -
470W ILE* 2.6 39.7 + - + +
471W PHE* 2.5 15.2 + - + +
473W PHE* 1.3 67.7 - - + +
475W MET* 1.3 67.3 + - - +
476W GLY 3.0 0.2 - - - -
477W ASN* 2.5 40.5 + - - +
478W PHE* 3.1 21.0 + - + -
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Residues in contact with MET 475 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471W PHE* 2.3 36.0 + - + +
472W ILE* 2.9 55.6 - - + +
474W VAL* 1.3 66.2 - - - +
476W GLY* 1.3 60.2 + - - +
478W PHE* 2.3 57.5 - - + -
479W ASN* 2.9 9.0 + - + +
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Residues in contact with GLY 476 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472W ILE 3.1 7.5 + - - -
473W PHE 3.5 3.4 - - - -
474W VAL 3.0 0.2 - - - -
475W MET* 1.3 83.7 - - - +
477W ASN* 1.3 50.3 + - - +
478W PHE 2.7 6.9 + - - -
479W ASN* 2.6 33.3 + - - -
480W ARG* 2.6 36.0 - - - +
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Residues in contact with ASN 477 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473W PHE* 2.7 36.3 + - + +
474W VAL* 2.5 57.1 - - - +
476W GLY* 1.3 70.5 - - - +
478W PHE* 1.3 56.5 + - - +
480W ARG* 4.2 6.2 - - - +
481W PRO* 3.0 18.0 - - - +
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Residues in contact with PHE 478 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139W PHE* 3.8 36.0 - + + -
291W TYR* 5.0 14.4 - + - -
294W PHE* 4.7 17.0 - + - -
471W PHE* 5.6 3.8 - + - -
474W VAL* 3.1 22.3 + - + +
475W MET* 2.3 48.7 - - + -
476W GLY 2.7 0.8 + - - -
477W ASN* 1.3 77.3 - - - +
479W ASN* 1.3 63.7 + - + +
480W ARG 3.3 2.2 - - - -
481W PRO* 3.3 9.4 - - - +
482W PRO* 2.5 30.0 - - - +
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Residues in contact with ASN 479 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139W PHE* 5.8 0.4 - - - -
475W MET* 3.0 22.1 - - + +
476W GLY* 2.6 9.9 + - - +
478W PHE* 1.3 86.5 - - + +
480W ARG* 1.3 79.0 + - - +
482W PRO* 3.1 21.5 - - - +
483W ALA* 3.4 13.0 - - - +
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Residues in contact with ARG 480 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476W GLY* 2.6 36.3 + - - +
477W ASN* 4.2 4.3 - - - +
479W ASN* 1.3 89.0 - - - +
481W PRO* 1.4 61.3 - - + +
482W PRO* 3.1 4.9 - - - -
483W ALA* 3.3 9.1 + - - +
484W LYS* 3.0 27.5 + - - +
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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
------------------------------------------------------------
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