Contacts of the helix formed by residues 463 - 476 (chain C) in PDB entry 1RC5
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 ARG 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B GLU* 4.3 16.6 + - - -
278B GLU* 3.8 24.8 + - - +
302B GLU* 5.0 3.6 + - - -
461C ASN* 2.5 44.4 + - - +
462C LYS* 1.3 78.0 - - - +
464C GLU* 1.3 56.0 + - - +
465C GLY* 5.0 2.7 - - - +
466C PHE* 3.1 17.9 + - + +
467C LEU* 2.5 37.6 + - - +
548C HIS* 5.1 7.3 - - - -
637D GLU* 5.1 9.6 - - - +
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Residues in contact with GLU 464 (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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462C LYS 3.8 3.0 + - - -
463C ARG* 1.3 71.8 - - - +
465C GLY* 1.3 65.6 + - - +
467C LEU* 3.0 12.8 + - - +
468C SER* 2.9 38.9 + - - +
637D GLU* 3.5 31.5 + - + +
640D GLU* 5.5 4.6 - - - +
641D PHE* 2.8 39.4 - - - +
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Residues in contact with GLY 465 (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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463C ARG* 3.3 4.5 - - - +
464C GLU* 1.3 79.4 - - - +
466C PHE* 1.3 56.2 + - - +
468C SER* 4.3 2.2 - - - -
469C PRO* 3.0 22.7 - - - +
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Residues in contact with PHE 466 (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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459C SER* 3.6 14.6 - - - -
460C PRO* 3.9 8.5 - - + -
461C ASN* 3.0 39.3 - - - +
463C ARG* 3.1 16.7 + - + +
465C GLY* 1.3 72.9 - - - +
467C LEU* 1.3 68.1 + - - +
468C SER 3.2 2.2 - - - -
469C PRO* 3.0 19.7 - - + +
470C LEU* 3.5 32.0 + - + +
546C GLY 5.0 0.4 - - - -
547C ARG* 3.3 23.3 - - + -
548C HIS* 3.0 50.5 - + + +
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Residues in contact with LEU 467 (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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455C LEU* 4.5 13.3 - - + +
456C VAL* 4.6 7.4 - - - -
459C SER* 4.1 25.4 - - - +
461C ASN 4.1 3.8 - - - +
462C LYS* 3.3 29.2 - - + +
463C ARG 2.5 31.9 + - - +
464C GLU* 3.0 8.0 + - - +
466C PHE* 1.3 74.8 - - - +
468C SER* 1.3 52.1 + - - +
470C LEU* 3.7 4.3 - - - +
471C LYS* 2.7 35.5 + - - +
637D GLU* 6.1 0.4 - - + -
638D THR* 5.0 4.7 - - + +
641D PHE* 3.3 52.2 - - + -
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Residues in contact with SER 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C GLU* 2.9 32.0 + - - -
465C GLY* 4.3 2.2 - - - -
467C LEU* 1.3 75.1 - - - +
469C PRO* 1.3 63.2 - - - +
471C LYS* 2.9 8.0 + - - +
472C ALA* 2.7 37.5 + - - +
641D PHE* 4.7 2.8 - - - -
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Residues in contact with PRO 469 (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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465C GLY 3.0 28.3 - - - +
466C PHE* 3.0 25.1 - - + +
468C SER* 1.3 81.3 - - - +
470C LEU* 1.3 61.4 + - - +
472C ALA* 3.2 8.2 - - + +
473C TYR* 3.2 23.4 + - - +
546C GLY 5.8 2.7 - - - +
548C HIS 6.2 0.4 - - - +
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Residues in contact with LEU 470 (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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455C LEU* 3.6 18.4 - - + -
459C SER* 4.8 0.2 - - - +
466C PHE* 3.5 36.2 + - + +
467C LEU* 3.5 7.1 + - - +
468C SER 3.2 0.6 - - - -
469C PRO* 1.3 78.9 - - - +
471C LYS* 1.3 65.5 + - - +
473C TYR* 4.1 7.5 - - + +
474C LEU* 2.9 36.7 + - + +
542C ALA 4.2 4.5 - - - +
543C ILE* 3.3 59.5 - - + +
546C GLY* 3.9 21.9 + - - +
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Residues in contact with LYS 471 (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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448C ASN* 2.8 32.2 + - - +
451C ILE* 5.6 0.7 - - + -
452C VAL* 3.5 23.6 - - + +
455C LEU* 3.8 13.0 - - + +
467C LEU 2.7 23.2 + - - +
468C SER* 3.3 8.1 - - - +
470C LEU* 1.3 74.4 - - - +
472C ALA* 1.3 63.2 - - - +
474C LEU* 3.0 15.3 + - - +
475C ILE* 3.1 42.3 + - + +
641D PHE* 4.0 23.8 - - + -
644D ASP* 5.5 6.2 + - - -
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Residues in contact with ALA 472 (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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468C SER 2.7 20.4 + - - +
469C PRO* 3.2 12.1 - - + +
471C LYS* 1.3 72.7 - - - +
473C TYR* 1.3 61.7 + - - +
475C ILE* 3.6 7.9 + - - +
476C SER* 3.2 22.6 + - - -
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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
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469C PRO 3.2 13.1 + - - +
470C LEU* 4.1 9.2 - - + +
472C ALA* 1.3 73.5 - - - +
474C LEU* 1.3 73.1 + - + +
475C ILE 2.9 11.1 + - - -
476C SER* 2.9 28.8 + - - -
478C GLU* 3.9 30.0 + - + -
479C PHE* 3.1 49.6 - + + +
482C LEU* 4.7 7.8 - - - +
542C ALA* 4.2 12.1 - - + +
546C GLY* 6.2 3.1 - - - -
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Residues in contact with LEU 474 (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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451C ILE* 3.4 22.7 - - + +
455C LEU* 3.2 32.1 - - + -
470C LEU* 2.9 20.2 - - + +
471C LYS 3.0 6.0 + - - +
473C TYR* 1.3 88.8 - - + +
475C ILE* 1.3 58.0 + - - +
479C PHE* 2.9 50.8 - - + -
480C PHE* 3.2 9.0 - - - -
539C ILE* 3.7 24.2 - - + -
542C ALA* 4.0 11.2 - - + -
543C ILE* 4.1 13.5 - - + -
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Residues in contact with ILE 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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448C ASN* 3.4 21.5 - - + +
451C ILE* 3.9 26.5 - - + -
471C LYS* 3.1 52.0 + - - +
472C ALA* 3.8 7.2 - - - +
473C TYR 3.0 0.4 - - - -
474C LEU* 1.3 82.2 - - - +
476C SER* 1.3 68.4 + - - +
480C PHE* 3.3 27.8 - - + -
510C GLU* 5.3 0.2 - - - +
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Residues in contact with SER 476 (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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472C ALA 3.2 14.3 + - - -
473C TYR* 2.9 25.8 + - - -
475C ILE* 1.3 83.9 - - - +
477C GLU* 1.3 64.3 + - - +
478C GLU* 3.4 10.2 + - - +
479C PHE* 3.3 12.5 + - - +
480C PHE* 3.3 19.1 + - - -
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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
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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