Contacts of the helix formed by residues 461 - 480 (chain C) in PDB entry 1UES
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 GLU 461 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C PHE* 5.3 0.4 - - - -
459C LYS 5.1 1.3 - - - +
460C SER* 1.3 78.1 - - - +
462C GLY* 1.3 73.8 + - - +
463C GLY 3.6 0.2 + - - -
464C ILE* 3.5 11.1 + - - +
465C PHE* 3.3 14.8 + - - -
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Residues in contact with GLY 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C GLU* 1.3 81.5 + - - +
463C GLY* 1.3 59.6 + - - -
465C PHE* 3.1 5.5 + - - +
466C ASN* 2.8 38.0 + - - +
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Residues in contact with GLY 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LEU* 4.0 4.3 - - - -
461C GLU 3.6 0.2 + - - -
462C GLY* 1.3 68.2 - - - -
464C ILE* 1.3 72.4 + - - +
466C ASN* 4.0 11.2 - - - +
467C ASN* 2.8 39.6 + - - -
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Residues in contact with ILE 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 3.8 6.7 - - + +
442C LEU* 3.3 46.9 - - + +
443C ILE* 4.1 20.6 - - + -
446C THR* 5.8 3.8 - - + +
448C PHE* 4.2 11.4 - - + -
456C ILE* 3.4 26.5 - - + -
460C SER* 3.7 8.7 - - - -
461C GLU 3.7 7.9 - - - +
462C GLY 3.2 0.4 - - - -
463C GLY* 1.3 78.7 - - - +
465C PHE* 1.3 58.6 + - - +
468C ALA* 2.8 32.2 + - - +
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Residues in contact with PHE 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C VAL* 3.1 43.5 - - + -
458C GLN 5.0 0.4 - - - -
460C SER* 3.0 26.5 + - - +
461C GLU* 3.3 17.9 + - - -
462C GLY 3.1 8.8 + - - +
464C ILE* 1.3 79.8 - - - +
466C ASN* 1.3 72.2 + - - +
468C ALA* 4.4 1.6 - - - -
469C GLY* 2.8 29.8 + - - -
542C ALA* 4.3 28.5 - - + -
543C GLY* 5.2 4.5 - - - -
544C ASN* 5.8 1.1 - - + -
547C ARG* 5.5 16.2 - - - -
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Residues in contact with ASN 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C GLY* 2.8 27.7 + - - +
463C GLY* 3.2 9.7 + - - +
465C PHE* 1.3 90.4 - - - +
467C ASN* 1.3 60.4 + - - +
470C GLN* 3.0 36.4 + - - +
542C ALA* 3.9 3.5 - - - +
719D PHE* 3.5 55.0 - - + +
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Residues in contact with ASN 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 5.5 2.4 - - - +
435C TYR* 3.3 37.0 - - - +
438C ASN* 3.1 34.0 + - - +
439C LEU* 4.0 13.0 - - + +
442C LEU* 3.6 18.8 - - - +
463C GLY* 2.8 30.0 + - - +
464C ILE* 4.1 1.1 - - - +
466C ASN* 1.3 77.3 - - - +
468C ALA* 1.3 61.5 + - - +
470C GLN* 3.6 1.4 + - - +
471C THR* 2.9 33.8 + - - -
719D PHE* 5.9 0.6 - - - -
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Residues in contact with ALA 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU* 3.9 16.0 - - + +
453C LEU* 4.0 7.2 - - + +
456C ILE* 3.5 28.5 - - + -
457C VAL* 3.7 20.4 - - + +
464C ILE 2.8 19.9 + - - +
465C PHE* 3.9 3.4 - - - +
467C ASN* 1.3 74.9 - - - +
469C GLY* 1.3 66.0 + - - +
471C THR* 3.2 2.8 + - - -
472C LEU* 3.1 19.2 + - - +
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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
----------------------------------------------------------
457C VAL* 3.8 18.5 - - - +
465C PHE* 2.8 23.3 + - - -
466C ASN 4.1 0.4 - - - -
468C ALA* 1.3 72.8 - - - +
470C GLN* 1.3 56.7 + - - +
472C LEU* 3.3 2.6 + - - +
473C ASN* 2.9 41.0 + - - +
542C ALA* 4.1 13.5 - - - -
544C ASN* 6.1 0.9 - - - -
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Residues in contact with GLN 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C TYR* 3.0 53.4 + - + -
466C ASN 3.0 22.1 + - - +
467C ASN 3.9 0.2 - - - +
469C GLY* 1.3 77.1 - - - +
471C THR* 1.3 55.8 + - - +
473C ASN* 3.4 1.7 + - - +
474C HIS* 2.6 51.7 + - - -
523C TRP* 2.9 28.3 + - - -
541C ASN 3.4 3.5 - - - +
542C ALA* 3.4 10.6 - - + +
559C TRP* 3.3 28.2 - - - +
719D PHE* 3.7 10.1 - - + -
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Residues in contact with THR 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C HIS* 5.7 3.6 - - + -
404C GLU 5.6 1.3 - - - +
432C LEU* 3.9 9.4 - - + -
435C TYR* 3.6 14.4 + - - +
436C VAL* 3.8 29.9 + - + +
439C LEU* 4.6 5.5 - - + +
453C LEU* 3.8 24.5 - - + -
467C ASN 2.9 21.5 + - - -
468C ALA 3.2 5.4 + - - -
470C GLN* 1.3 75.8 - - - +
472C LEU* 1.3 63.9 + - - +
474C HIS* 3.4 0.9 + - - +
475C ASN* 3.0 40.5 + - - +
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C LEU* 4.2 18.5 - - + +
454C ASN* 3.7 34.3 - - - +
457C VAL* 3.7 27.6 - - + -
468C ALA 3.1 14.5 + - - +
469C GLY* 3.7 4.3 - - - +
471C THR* 1.3 75.6 - - - +
473C ASN* 1.3 65.4 + - - +
475C ASN* 3.3 6.7 + - - +
476C LEU* 3.1 43.0 + - + +
544C ASN* 3.9 14.1 - - - +
546C VAL* 5.7 8.7 - - + -
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Residues in contact with ASN 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C GLY* 2.9 21.2 + - - +
470C GLN* 3.6 5.2 + - - +
472C LEU* 1.3 77.8 - - - +
474C HIS* 1.3 58.0 + - - +
476C LEU* 3.2 4.3 + - - +
477C TYR* 2.9 28.4 + - - +
523C TRP* 3.2 43.9 - - + +
525C TRP* 3.8 15.9 - - + -
542C ALA 3.2 23.2 + - - -
543C GLY 3.2 8.3 + - - -
544C ASN* 2.8 29.3 - - - +
555C THR* 4.4 1.9 - - - +
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Residues in contact with HIS 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C HIS* 3.0 19.0 + + - -
431C HIS* 5.3 0.2 - - - +
432C LEU* 3.7 29.8 - - + -
435C TYR* 3.5 26.6 - + - -
470C GLN* 2.6 36.0 + - - +
473C ASN* 1.3 73.3 - - - +
475C ASN* 1.3 67.3 + - - +
477C TYR* 4.0 6.3 - + - -
478C PHE* 2.9 43.1 + + + -
523C TRP* 3.4 20.6 - + - -
557C ASP* 3.6 0.2 + - - -
561C HIS* 3.9 0.4 + - - -
592C MN 2.2 36.0 + - - -
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Residues in contact with ASN 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C GLU 5.5 1.0 + - - +
406C ILE* 3.1 47.4 + - + +
432C LEU* 3.9 7.8 - - - +
453C LEU* 4.1 13.3 - - - +
471C THR* 3.0 36.2 + - - +
472C LEU* 3.6 6.3 - - - +
473C ASN 3.2 0.2 - - - -
474C HIS* 1.3 75.5 - - - +
476C LEU* 1.3 55.4 + - + +
478C PHE* 4.2 0.3 - - - +
479C THR* 2.7 41.5 + - + +
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Residues in contact with LEU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LEU* 3.1 35.3 + - + +
473C ASN 3.6 6.1 - - - +
475C ASN* 1.3 77.0 - - + +
477C TYR* 1.3 63.3 + - - +
479C THR* 3.0 8.3 + - - +
480C GLN* 3.3 7.6 + - - +
525C TRP* 3.6 33.0 - - + -
544C ASN* 4.1 1.6 - - - +
552C PRO* 4.2 17.5 - - + +
555C THR* 4.8 0.7 - - + -
590C ARG* 3.0 48.3 + - - +
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Residues in contact with TYR 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C ILE* 3.6 17.1 - - + +
427C HIS* 3.7 21.5 + + - -
473C ASN 2.9 16.5 + - - +
474C HIS* 3.3 5.4 + + - +
476C LEU* 1.3 75.8 - - - +
478C PHE* 1.3 91.1 + + - +
480C GLN* 3.2 28.0 - - - +
481C PHE* 3.2 38.6 - + - -
523C TRP* 3.9 14.1 - + + -
555C THR* 3.4 22.3 - - + +
556C PHE* 4.4 0.9 - - - -
557C ASP* 3.5 31.4 - - + +
562C ALA* 4.0 17.8 + - - +
574C HIS* 4.5 9.2 + - - -
578C LEU* 4.6 3.0 - - + +
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Residues in contact with PHE 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ILE* 4.3 9.0 - - + -
408C LEU* 3.9 19.5 - - + -
409C PRO* 4.4 1.6 - - + +
410C TYR* 2.7 45.3 + + - +
415C LEU* 5.4 2.2 - - + -
419C ILE* 5.4 10.3 - - + -
424C VAL* 5.4 6.3 - - + -
427C HIS* 3.7 33.2 - + + -
428C HIS* 3.7 32.3 - + + -
432C LEU* 4.0 14.4 - - + -
474C HIS* 2.9 50.9 + + - +
477C TYR* 1.3 94.4 - + - +
479C THR* 1.3 61.0 + - - +
480C GLN 3.4 0.7 + - - -
481C PHE* 3.8 5.6 + + - -
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Residues in contact with THR 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ILE* 5.0 12.3 - - + -
407C SER 5.6 1.6 - - - +
409C PRO* 4.5 14.8 - - + -
475C ASN* 2.7 25.7 + - + +
476C LEU* 3.0 12.1 + - - +
478C PHE* 1.3 78.0 - - - +
480C GLN* 1.3 58.0 + - - +
481C PHE 3.4 0.4 - - - -
482C ARG* 3.1 23.1 + - - +
586C ILE* 3.7 13.3 - - - +
590C ARG* 3.2 11.2 + - - -
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Residues in contact with GLN 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C LEU 3.3 5.0 + - - +
477C TYR* 3.2 19.5 + - - +
478C PHE 3.3 0.4 - - - -
479C THR* 1.3 77.8 - - - +
481C PHE* 1.3 86.4 + - + +
554C LEU* 3.6 16.3 - - + +
555C THR* 2.6 45.8 + - - +
582C VAL* 4.1 1.9 - - - +
583C ASP* 3.1 32.4 + - - +
586C ILE* 4.3 7.4 - - + -
587C VAL* 4.8 7.4 - - + -
590C ARG* 3.1 34.9 + - - +
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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