Contacts of the helix formed by residues 464 - 486 (chain C) in PDB entry 5U07
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 464 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TRP* 3.9 40.2 - - + -
463C GLY* 1.3 83.1 - - - +
465C TRP* 1.3 66.4 + - + +
466C VAL 3.4 0.2 - - - -
467C GLN* 3.9 12.8 + - + +
468C HIS* 4.0 13.0 + - - +
22D LEU* 4.4 9.6 - - + -
24D SER* 3.8 30.5 - - - +
199D VAL* 4.9 5.8 - - + -
225D GLN* 4.9 4.0 - - - +
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Residues in contact with TRP 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C CYS* 3.9 27.3 - - + +
440C ALA* 4.2 4.5 - - + -
441C TRP* 3.4 58.0 - + + -
463C GLY 3.1 2.1 - - - -
464C PRO* 1.3 85.0 - - + +
466C VAL* 1.3 60.5 + - + +
469C GLY* 2.9 27.9 + - - -
512C TYR* 5.0 3.4 - + - -
515C VAL* 3.7 26.7 + - + +
516C THR* 3.5 18.2 - - - -
519C TYR* 3.3 51.7 - + + -
525C VAL* 4.2 9.2 - - + -
529C VAL* 3.3 35.7 - - + -
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Residues in contact with VAL 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C GLU* 3.0 35.0 - - - +
437C CYS* 3.9 7.0 - - + -
438C LYS* 3.5 49.4 - - + +
463C GLY 3.1 23.3 - - - +
465C TRP* 1.3 75.5 - - + +
467C GLN* 1.3 70.5 + - + +
469C GLY* 4.9 0.2 - - - -
470C MET* 3.0 24.2 + - - +
22D LEU* 6.0 1.8 - - + -
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Residues in contact with GLN 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C GLY 5.4 0.7 - - - +
464C PRO* 3.9 9.6 + - + +
465C TRP 3.4 0.6 - - - -
466C VAL* 1.3 86.3 - - + +
468C HIS* 1.3 72.9 + - - +
470C MET* 3.3 4.1 + - - +
471C SER* 3.0 35.5 + - - -
20D ASP* 6.2 0.2 - - - +
22D LEU* 6.5 0.9 - - + -
69N ARG 4.7 0.2 - - - +
70N LEU* 3.9 18.3 - - - +
71N VAL* 4.1 37.8 + - + +
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Residues in contact with HIS 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C PRO 4.0 9.0 + - - +
465C TRP 3.8 0.8 + - - -
467C GLN* 1.3 86.4 - - - +
469C GLY* 1.3 65.2 + - - +
471C SER* 3.2 5.1 + - - -
472C ARG* 2.9 76.1 + - + +
514C GLU 4.7 0.7 - - - -
515C VAL* 3.8 32.9 - - + +
29D VAL* 4.1 12.2 - - + +
68N VAL* 4.0 6.0 - - + +
70N LEU* 3.4 26.9 - - + -
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Residues in contact with GLY 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LEU* 5.2 2.9 - - - -
434C GLU* 5.0 1.3 - - - -
437C CYS* 5.4 5.2 - - - -
465C TRP 2.9 20.5 + - - -
466C VAL* 3.8 1.1 - - - -
468C HIS* 1.3 77.0 + - - +
470C MET* 1.3 60.4 + - - +
472C ARG* 4.1 1.2 - - - -
473C TYR* 2.9 31.3 + - - +
511C ALA* 4.3 8.9 - - - +
512C TYR* 6.1 0.4 - - - -
515C VAL* 4.2 17.0 - - - +
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Residues in contact with MET 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C GLY 3.6 9.9 - - - +
433C LEU* 3.5 32.3 - - + -
434C GLU* 2.9 50.3 - - + +
466C VAL 3.0 13.7 + - - +
467C GLN* 3.8 3.6 - - - +
469C GLY* 1.3 72.6 - - - +
471C SER* 1.3 71.2 + - - +
473C TYR* 3.9 11.9 - - + -
474C TRP* 2.9 56.8 + - + +
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Residues in contact with SER 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C GLN* 3.0 23.5 + - - -
468C HIS* 3.2 10.7 + - - -
470C MET* 1.3 78.2 - - - +
472C ARG* 1.3 65.1 + - - +
474C TRP* 4.3 1.1 - - - +
475C ALA* 3.0 24.8 + - - +
68N VAL* 4.1 8.4 - - - +
69N ARG* 2.6 37.8 + - - +
70N LEU* 5.3 0.9 - - - -
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Residues in contact with ARG 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C HIS* 2.9 40.2 + - + +
469C GLY* 4.3 1.8 - - - +
471C SER* 1.3 76.5 - - - +
473C TYR* 1.3 63.9 + - - +
475C ALA* 4.3 4.5 - - - -
476C LYS* 2.9 35.1 + - + +
511C ALA* 4.6 9.9 - - + +
514C GLU* 3.1 55.5 + - - +
29D VAL* 3.2 33.3 - - - +
32D GLY* 5.3 3.8 + - - -
68N VAL* 3.4 29.8 - - + +
110N ASP* 4.6 2.4 + - - -
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Residues in contact with TYR 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ALA 3.1 14.0 + - - -
429C LEU* 3.1 21.1 - - - +
430C GLY* 3.5 21.1 - - - -
433C LEU* 4.3 2.9 - - + -
469C GLY 2.9 21.2 + - - +
470C MET* 3.1 21.0 + - + +
472C ARG* 1.3 78.2 - - - +
474C TRP* 1.3 94.4 + + - +
476C LYS* 3.1 3.5 + - - +
477C ALA* 2.8 34.4 + - + +
504C PHE* 4.1 8.7 - - - +
507C VAL* 3.5 26.2 - - + -
508C ALA* 3.7 28.5 - - + -
511C ALA* 4.1 10.5 - - + +
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Residues in contact with TRP 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C GLU 5.3 8.3 - - - +
333C ALA* 5.0 9.6 - - + +
335C TRP* 3.6 25.6 + + - -
336C ARG* 3.1 46.1 - - - +
426C ALA* 4.9 0.7 - - + -
427C GLU* 3.7 37.0 - - + -
430C GLY* 5.0 4.7 - - - -
431C ARG 5.5 0.2 - - - -
470C MET* 2.9 54.0 + - + +
471C SER 4.6 0.4 - - - +
473C TYR* 1.3 101.5 - + - +
475C ALA* 1.3 63.5 + - - +
477C ALA* 2.9 13.9 + - + -
478C GLU* 3.0 18.2 + - - +
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Residues in contact with ALA 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C SER* 3.0 22.1 + - - +
472C ARG* 3.9 5.4 - - - +
474C TRP* 1.3 77.5 - - - +
476C LYS* 1.3 62.4 + - + +
478C GLU* 4.0 10.3 - - - +
479C PRO* 3.6 15.6 - - - +
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Residues in contact with LYS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ARG* 2.9 32.8 + - + +
473C TYR* 3.7 3.1 - - - +
475C ALA* 1.3 78.4 - - + +
477C ALA* 1.3 59.9 + - - +
478C GLU 3.6 0.4 - - - -
479C PRO* 3.6 8.2 - - - +
480C VAL* 3.5 20.6 - - - +
507C VAL* 3.8 19.3 - - + +
510C ALA* 6.1 4.0 - - - -
511C ALA* 5.8 3.4 - - + -
514C GLU* 4.9 16.0 + - - +
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Residues in contact with ALA 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TRP* 4.6 2.7 - - + -
473C TYR* 2.8 26.9 + - + +
474C TRP* 2.9 22.8 + - + +
476C LYS* 1.3 78.8 - - - +
478C GLU* 1.3 67.0 + - - +
479C PRO 3.4 0.2 - - - -
480C VAL* 3.4 2.3 + - - +
481C PHE* 3.1 23.0 + - - +
504C PHE* 3.7 25.7 - - + -
507C VAL* 4.5 5.2 - - + -
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Residues in contact with GLU 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ALA* 4.7 7.2 - - + +
334C ILE* 6.0 1.6 - - - +
335C TRP* 3.5 36.9 - - + +
474C TRP 3.0 14.9 + - - +
475C ALA* 4.0 9.4 - - - +
477C ALA* 1.3 77.1 - - - +
479C PRO* 1.3 82.2 - - + +
481C PHE* 3.1 4.9 + - - +
482C TRP* 2.9 37.3 + - + -
28N PRO* 6.2 0.3 - - - +
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Residues in contact with PRO 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C ALA 3.6 10.8 - - - +
476C LYS* 3.6 16.6 - - - +
478C GLU* 1.3 102.0 - - + +
480C VAL* 1.3 56.7 + - + +
482C TRP* 3.3 10.9 + - + +
483C ASN* 2.9 38.3 + - - +
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Residues in contact with VAL 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C LYS 3.5 17.0 - - - +
477C ALA* 3.4 8.5 + - - +
478C GLU 3.2 0.8 - - - -
479C PRO* 1.3 77.3 - - + +
481C PHE* 1.3 63.9 + - - +
483C ASN* 3.2 11.3 + - - +
484C ILE* 3.0 25.1 + - + +
490C ALA* 4.7 12.6 - - + -
491C GLN* 5.9 1.8 - - - +
503C ALA* 4.4 24.2 - - + +
504C PHE* 4.4 14.8 - - + -
507C VAL* 4.8 12.8 - - + -
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Residues in contact with PHE 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TRP* 3.4 60.1 - + + -
338C LEU* 5.5 6.1 - - + -
339C ASP* 5.1 1.3 - - + -
419C ILE* 3.9 26.9 - - + -
422C ALA* 3.8 29.6 - - + -
423C ARG* 3.9 10.3 - - + -
477C ALA 3.1 14.0 + - - +
478C GLU 3.5 8.1 - - - +
480C VAL* 1.3 76.9 - - - +
482C TRP* 1.3 70.7 + + - +
484C ILE* 2.7 27.8 + - + +
485C VAL* 2.9 25.4 + - + -
504C PHE* 3.8 16.3 - + + -
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Residues in contact with TRP 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ILE* 6.1 2.7 - - + -
335C TRP* 4.3 23.1 - - + +
338C LEU* 4.5 20.9 - - + -
395C THR* 5.3 3.8 - - + -
396C PRO* 3.5 39.5 - - + -
398C VAL* 5.4 4.3 - - + -
478C GLU* 2.9 46.1 + - + +
479C PRO* 3.3 9.8 + - + +
481C PHE* 1.3 84.6 - + - +
483C ASN* 1.3 59.5 + - - +
484C ILE 3.3 0.2 - - - -
485C VAL* 3.1 38.6 - - + +
486C TYR* 3.4 30.8 + + + -
488C ARG* 4.3 9.0 - - - +
196N THR* 5.3 17.4 - - + +
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Residues in contact with ASN 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C PRO* 2.9 22.7 + - - +
480C VAL* 3.5 11.4 - - - +
481C PHE 3.0 0.2 - - - -
482C TRP* 1.3 75.8 - - - +
484C ILE* 1.3 64.2 + - - +
486C TYR 3.6 0.5 + - - -
487C ASP 3.3 2.1 + - - -
488C ARG* 2.7 81.1 + - + +
489C PRO 4.9 5.3 + - - +
490C ALA* 4.3 19.5 - - + +
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Residues in contact with ILE 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 3.0 30.3 + - + -
419C ILE* 6.3 0.4 - - - -
422C ALA* 4.2 21.1 - - + -
480C VAL* 3.0 19.6 + - + +
481C PHE* 2.7 16.5 + - + +
483C ASN* 1.3 71.2 - - - +
485C VAL* 1.3 65.0 + - - +
487C ASP* 3.2 8.7 + - - -
490C ALA* 5.0 2.2 - - + -
493C TYR* 3.6 52.4 + - + +
500C PRO 4.7 3.6 - - - +
503C ALA* 4.3 11.4 - - + -
504C PHE* 3.8 30.3 - - + -
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Residues in contact with VAL 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C LEU* 6.5 0.2 - - + -
398C VAL* 5.6 5.6 - - + -
415C ILE* 4.7 9.6 - - + +
418C ARG* 2.6 28.6 + - - +
419C ILE* 3.5 36.3 - - + +
481C PHE* 2.9 18.3 + - + +
482C TRP* 3.1 50.0 - - + +
484C ILE* 1.3 79.1 - - - +
486C TYR* 1.3 69.1 + - + +
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Residues in contact with TYR 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C PRO* 4.3 22.2 - - - +
397C ALA 5.1 7.4 + - - -
482C TRP* 3.4 31.7 + + + +
483C ASN 3.6 0.2 + - - -
484C ILE 3.3 0.6 - - - -
485C VAL* 1.3 90.9 - - + +
487C ASP* 1.3 67.4 + - - +
488C ARG* 3.1 44.6 + - + +
196N THR* 5.6 8.2 - - + +
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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