Contacts of the helix formed by residues 473 - 494 (chain A) in PDB entry 3EE6
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 GLY 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 6.1 0.2 - - - -
360A ASP* 3.7 14.8 - - - -
407A ILE* 4.0 9.5 - - - +
456A SER* 2.7 30.4 + - - -
472A SER* 1.3 76.4 - - - +
474A THR* 1.3 61.3 + - - -
475A SER* 3.2 5.6 - - - -
476A ALA* 3.1 23.3 - - - +
477A SER 3.7 0.3 + - - -
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Residues in contact with THR 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ALA* 3.1 25.4 - - + -
358A SER* 3.3 5.8 + - - +
359A GLY* 3.2 32.9 + - - +
360A ASP* 3.0 17.8 + - - +
388A VAL 3.2 16.5 + - - +
389A GLY 3.4 17.5 - - - -
390A GLY* 3.8 3.2 + - - -
407A ILE* 5.8 1.1 - - - -
408A SER* 4.8 2.0 + - - -
409A GLY 4.9 0.2 + - - -
456A SER* 4.3 2.7 - - - -
473A GLY* 1.3 70.4 - - - -
475A SER* 1.3 57.0 + - - +
476A ALA 3.1 4.5 - - - -
477A SER* 3.0 17.2 + - - -
478A THR* 3.1 23.6 + - - -
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Residues in contact with SER 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLU* 3.7 24.3 + - - -
275A LEU* 3.9 9.7 - - - +
276A ASP* 2.8 24.0 - - - +
324A SER* 2.8 28.3 + - - -
357A ALA* 4.3 8.8 - - - +
360A ASP* 4.9 4.8 + - - -
473A GLY* 4.9 2.9 - - - -
474A THR* 1.3 78.2 - - - +
476A ALA* 1.3 58.7 + - - +
478A THR* 4.7 1.6 - - - -
479A PRO* 3.0 16.2 - - - +
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Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.9 20.4 - - + +
279A TYR* 5.0 0.9 - - - +
455A LEU 4.0 1.3 - - - +
456A SER* 4.3 1.6 - - - +
459A TYR* 3.7 40.6 + - + -
471A VAL 5.2 1.1 - - - +
473A GLY 3.1 18.6 + - - +
474A THR 3.1 0.2 - - - -
475A SER* 1.3 79.9 - - - +
477A SER* 1.3 63.1 + - - +
479A PRO* 3.2 14.7 - - - +
480A VAL* 3.6 14.9 - - - +
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL* 3.9 4.0 - - - +
389A GLY 3.0 19.2 + - - -
454A ALA* 3.1 39.1 + - - +
455A LEU 3.3 10.3 - - - -
456A SER* 4.1 1.2 - - - -
473A GLY 3.7 0.5 + - - -
474A THR* 3.0 24.7 + - - -
476A ALA* 1.3 78.5 - - - +
478A THR* 1.3 57.3 + - - +
480A VAL* 3.2 5.0 + - - +
481A PHE* 2.9 30.7 + - - +
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Residues in contact with THR 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A THR* 3.7 12.9 - - - +
323A VAL 4.0 7.2 - - - +
324A SER* 6.1 0.7 - - - -
355A LEU* 3.7 40.1 - - + +
356A PHE 3.7 2.1 - - - -
357A ALA* 3.1 26.4 + - - +
388A VAL* 3.7 14.8 - - + +
474A THR 3.1 16.0 + - - -
475A SER* 4.8 2.2 - - - -
477A SER* 1.3 76.5 - - - +
479A PRO* 1.3 64.9 - - + +
481A PHE* 3.2 3.5 + - - +
482A GLY* 2.8 26.0 + - - -
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Residues in contact with PRO 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU 4.8 2.7 - - - +
276A ASP* 3.6 36.8 - - + +
279A TYR* 4.4 2.7 - - + -
280A LEU* 3.6 24.6 - - + +
283A ALA* 4.1 0.3 - - - +
322A THR* 3.9 19.1 - - + +
475A SER 3.0 28.5 - - - +
476A ALA* 3.2 12.8 - - - +
478A THR* 1.3 90.5 - - + +
480A VAL* 1.3 58.0 + - - +
483A GLY* 2.9 24.9 + - - -
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 3.6 28.9 - - + -
209A TYR* 3.7 32.8 - - + -
279A TYR* 4.2 14.8 - - + +
283A ALA* 3.3 20.9 - - + +
454A ALA* 4.3 5.4 - - + -
459A TYR* 3.6 21.1 - - + +
476A ALA 3.6 15.0 + - - +
477A SER* 3.2 9.3 + - - +
479A PRO* 1.3 77.8 - - - +
481A PHE* 1.3 65.7 + - - +
484A ILE* 3.4 15.2 + - + +
551A PRO* 5.4 0.4 - - + -
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Residues in contact with PHE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 4.0 7.6 - - + -
386A THR* 5.4 0.4 - - + -
388A VAL* 4.1 12.1 - - + -
452A VAL* 3.5 43.3 - - + -
453A ALA 3.5 24.2 - - - -
454A ALA* 4.6 1.5 - - + +
477A SER 2.9 16.2 + - - +
478A THR 3.7 3.6 - - - +
480A VAL* 1.3 78.9 - - - +
482A GLY* 1.3 61.7 + - - +
484A ILE* 3.2 8.9 + - + +
485A LEU* 3.1 51.3 + - + +
503A LEU* 5.0 5.4 - - + -
507A LEU* 6.2 0.7 - - + -
515A LEU* 4.0 15.3 - - + -
549A GLY 4.0 5.8 - - - -
551A PRO* 4.0 21.3 - - + -
556A LEU* 4.6 6.5 - - + -
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Residues in contact with GLY 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 4.3 2.9 - - - -
320A VAL* 3.5 15.1 - - - +
322A THR* 3.6 17.3 - - - -
355A LEU* 4.0 8.9 - - - +
478A THR 2.8 16.3 + - - -
480A VAL 3.3 0.2 - - - -
481A PHE* 1.3 77.6 - - - +
483A GLY* 1.3 56.0 + - - +
485A LEU* 3.1 5.6 + - - +
486A SER* 2.9 28.9 + - - -
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Residues in contact with GLY 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLN* 3.8 11.2 - - - -
280A LEU* 3.7 4.8 - - - +
283A ALA 4.0 0.9 - - - -
284A GLY* 3.2 38.3 - - - -
479A PRO 2.9 16.8 + - - -
481A PHE 3.3 0.2 - - - -
482A GLY* 1.3 76.0 - - - +
484A ILE* 1.3 61.2 + - - +
486A SER* 3.2 2.6 + - - -
487A LEU* 3.2 17.5 + - - +
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 5.4 1.1 - - + -
209A TYR* 4.0 14.6 - - + -
211A LEU* 4.0 28.9 - - + -
283A ALA* 4.0 16.8 - - + +
480A VAL* 3.4 19.1 + - + +
481A PHE* 3.2 8.9 + - + +
482A GLY 3.2 0.4 - - - -
483A GLY* 1.3 73.6 - - - +
485A LEU* 1.3 67.4 + - + +
487A LEU* 3.4 8.6 + - - +
488A ILE* 3.3 22.0 + - + +
551A PRO* 3.9 27.6 - - + -
553A PHE* 4.0 20.5 - - + -
556A LEU* 4.2 22.4 - - + -
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 4.4 8.1 - - + -
353A THR* 4.1 18.8 - - + -
355A LEU* 3.9 19.7 - - + -
386A THR* 5.4 0.4 - - + -
481A PHE* 3.1 41.1 + - + +
482A GLY* 3.3 9.6 - - - +
484A ILE* 1.3 80.8 - - + +
486A SER* 1.3 56.7 + - - +
488A ILE* 3.1 12.8 + - + +
489A ASN* 3.0 27.0 + - - +
500A LEU* 4.2 21.3 - - + +
503A LEU* 4.0 25.6 - - + -
556A LEU* 5.2 4.5 - - + -
560A LEU* 4.5 11.7 - - + -
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASN* 2.8 37.3 + - - -
224A SER 4.1 5.7 + - - -
225A GLN* 3.0 43.1 + - - +
287A ILE* 4.0 6.7 - - - +
320A VAL* 3.9 16.8 - - - +
482A GLY 2.9 12.9 + - - -
483A GLY 3.5 2.5 - - - -
484A ILE 3.2 0.2 - - - -
485A LEU* 1.3 79.2 - - - +
487A LEU* 1.3 59.5 + - - +
489A ASN* 3.3 4.0 + - - +
490A GLU 3.2 5.5 + - - -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 5.5 0.2 - - - +
211A LEU* 3.9 11.7 - - + -
215A ASP 3.3 26.7 - - - +
216A VAL* 3.6 31.9 - - - +
217A GLY* 3.9 7.2 - - - +
283A ALA 4.5 8.3 - - - +
284A GLY* 5.5 0.9 - - - -
285A ALA 5.2 0.9 - - - +
287A ILE* 4.1 12.3 - - + +
483A GLY 3.2 10.8 + - - +
484A ILE* 3.5 10.5 - - - +
486A SER* 1.3 74.2 - - - +
488A ILE* 1.3 66.1 + - - +
490A GLU* 3.1 17.7 + - + +
491A HIS* 3.2 29.4 + - + -
553A PHE* 3.9 28.0 - - + -
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Residues in contact with ILE 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE 3.3 12.1 + - - +
485A LEU* 3.1 14.3 + - + +
487A LEU* 1.3 76.9 - - - +
489A ASN* 1.3 63.5 + - - +
491A HIS* 3.3 8.7 + - - +
492A ARG* 3.2 27.3 + - + +
500A LEU* 3.8 21.3 - - + -
553A PHE* 4.0 16.4 - - + -
556A LEU* 3.9 24.5 - - + +
557A LEU* 3.9 36.8 - - + +
560A LEU* 4.1 23.8 - - + +
561A LEU* 5.6 0.2 - - + -
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Residues in contact with ASN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASN* 3.9 10.1 + - - +
319A HIS* 3.3 30.5 - - - +
320A VAL* 3.8 15.9 - - - +
353A THR* 4.7 4.4 + - - -
485A LEU 3.0 12.2 + - - +
486A SER 3.4 11.2 - - - +
487A LEU 3.2 0.4 - - - -
488A ILE* 1.3 77.6 - - - +
490A GLU* 1.3 56.2 + - - +
492A ARG* 3.1 5.3 + - - +
493A ILE* 2.8 38.2 + - + +
499A PRO* 3.6 14.1 - - - +
500A LEU* 3.0 37.1 + - - +
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Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLY* 3.7 10.5 - - - -
218A SER* 3.6 33.8 + - - +
219A GLY* 4.2 5.4 + - - -
221A SER* 4.6 8.1 - - - -
223A ASN* 2.8 38.8 - - + +
287A ILE* 4.0 13.1 - - + +
486A SER 3.2 4.5 + - - +
487A LEU* 3.1 16.4 + - + +
489A ASN* 1.3 80.3 - - - +
491A HIS* 1.3 58.9 + - - +
493A ILE* 4.7 2.9 - - - -
494A LEU* 3.0 61.0 + - + +
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Residues in contact with HIS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ASP* 5.5 6.6 + - - -
216A VAL 5.7 2.0 - - - -
487A LEU* 3.2 34.0 + - + +
488A ILE 3.7 7.9 - - - +
489A ASN 3.3 0.6 - - - -
490A GLU* 1.3 80.6 - - + +
492A ARG* 1.3 54.8 + - - +
494A LEU* 2.4 23.0 - - - +
495A SER* 3.1 9.4 + - - -
553A PHE* 4.5 18.8 - + - -
557A LEU* 4.2 20.0 - - + +
561A LEU* 3.6 34.0 - - + +
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Residues in contact with ARG 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 4.2 16.4 + - - -
488A ILE* 3.2 16.6 + - + +
489A ASN* 3.1 11.5 + - - +
491A HIS* 1.3 75.7 - - - +
493A ILE* 1.3 51.1 - - - +
494A LEU 2.8 16.0 - - - +
495A SER* 3.2 4.8 + - - -
497A ARG* 2.7 41.7 + - + +
498A PRO* 2.8 51.2 + - - +
499A PRO 4.5 2.0 + - - -
500A LEU* 3.7 30.6 - - - +
506A ARG* 3.8 11.9 - - - +
560A LEU 2.9 27.2 + - - +
561A LEU* 3.6 19.4 - - + +
562A ASN 4.2 2.2 + - - -
580A CL 3.8 19.2 - - - +
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Residues in contact with ILE 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A SER* 4.0 18.8 - - - +
223A ASN* 3.7 19.1 - - + +
319A HIS* 3.7 34.8 - - + +
489A ASN* 2.8 26.9 + - + +
490A GLU* 4.2 2.0 - - - +
492A ARG* 1.3 70.7 - - - +
494A LEU* 1.3 58.9 + - + +
496A GLY* 2.8 24.8 + - - -
497A ARG 3.5 16.8 - - - +
498A PRO 5.0 0.7 - - - -
499A PRO* 4.7 14.4 - - + -
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Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 3.8 15.0 - - - +
220A THR 6.0 1.3 - - - +
221A SER* 4.5 19.1 - - - -
490A GLU* 3.0 44.5 + - + +
491A HIS* 2.4 32.6 - - - +
492A ARG 2.8 2.3 - - - +
493A ILE* 1.3 74.8 - - + +
495A SER* 1.3 62.1 + - - +
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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