Contacts of the helix formed by residues 453 - 464 (chain C) in PDB entry 1RR8
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 CYS 453 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449C ARG 3.7 17.0 - - - +
450C LEU* 3.8 6.1 - - - +
451C LYS 3.2 0.6 + - - -
452C LYS* 1.3 79.8 - - - +
454C VAL* 1.3 62.1 + - - +
455C ASP 3.4 2.4 - - - +
456C LYS* 3.3 24.6 + - + +
457C ILE* 3.1 42.5 + - + +
580C LEU 5.5 2.9 - - - -
581C MET* 4.3 20.4 - - - -
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Residues in contact with VAL 454 (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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450C LEU* 2.8 17.4 + - + +
451C LYS 3.5 16.4 + - - +
453C CYS* 1.3 74.7 - - - +
455C ASP* 1.3 62.5 + - - +
457C ILE* 3.2 7.6 + - + -
458C ARG* 2.7 77.7 + - + +
483C ASP* 4.5 4.9 - - - +
589C PHE* 4.5 16.2 - - + -
592C TYR* 3.5 30.7 - - + +
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Residues in contact with ASP 455 (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 LYS 5.0 0.6 + - - -
453C CYS 3.4 0.8 - - - +
454C VAL* 1.3 85.1 - - - +
456C LYS* 1.3 57.4 + - - +
458C ARG* 3.9 19.4 + - - +
459C ASN* 3.0 40.1 + - - +
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Residues in contact with LYS 456 (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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453C CYS* 3.3 25.5 + - - +
454C VAL 3.3 0.4 - - - -
455C ASP* 1.3 78.7 - - - +
457C ILE* 1.3 65.1 + - - +
459C ASN* 3.7 6.6 + - - +
460C GLN* 3.3 37.2 + - - +
580C LEU* 5.1 14.8 + - - +
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Residues in contact with ILE 457 (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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450C LEU* 3.8 28.7 - - + -
453C CYS* 3.1 25.2 + - + +
454C VAL* 3.2 6.0 + - + +
456C LYS* 1.3 81.2 - - + +
458C ARG* 1.3 58.1 - - + +
460C GLN* 3.4 7.3 + - - +
461C TYR* 3.1 32.1 + - + +
479C LEU* 4.3 18.4 - - + -
580C LEU* 3.9 35.4 - - + -
581C MET* 5.0 2.5 - - + -
584C LEU* 4.0 17.0 - - + -
589C PHE* 4.3 12.6 - - + -
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Residues in contact with ARG 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C VAL* 2.7 46.5 + - + +
455C ASP* 3.9 16.8 + - - +
457C ILE* 1.3 70.9 - - + +
459C ASN* 1.3 65.1 + - - +
461C TYR* 3.6 19.9 + - + +
462C ARG* 3.1 33.5 + - + +
483C ASP* 2.7 41.3 + - - +
592C TYR* 3.8 22.8 + - - -
593C ASN* 4.6 5.3 - - - +
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Residues in contact with ASN 459 (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 ASP* 3.0 22.8 + - - +
456C LYS* 4.0 6.7 - - - +
458C ARG* 1.3 77.6 - - - +
460C GLN* 1.3 62.5 + - - +
462C ARG* 3.5 14.8 + - - +
463C GLU* 3.1 36.7 + - - +
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Residues in contact with GLN 460 (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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456C LYS* 3.3 30.4 + - - +
457C ILE* 3.7 7.8 - - + +
458C ARG 3.3 0.2 - - - -
459C ASN* 1.3 78.7 - - - +
461C TYR* 1.3 57.0 + - - +
463C GLU* 3.4 11.7 + - + +
464C ASP* 2.8 43.2 + - - +
475C ARG* 5.6 0.2 + - - -
576C HIS* 3.8 15.2 + - - -
580C LEU* 3.3 35.7 - - + +
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Residues in contact with TYR 461 (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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457C ILE* 3.1 26.4 + - + +
458C ARG* 3.6 28.5 + - + +
460C GLN* 1.3 74.6 - - - +
462C ARG* 1.3 70.7 + - + +
463C GLU 3.3 0.2 - - - -
464C ASP* 3.4 13.0 + - - +
465C TRP* 3.2 38.9 + + - -
476C ALA* 3.7 23.8 - - + +
479C LEU* 3.8 37.2 - - + -
480C TYR* 3.8 35.3 - + + -
483C ASP* 2.7 31.6 + - + +
484C LYS* 5.1 0.5 + - - +
576C HIS* 6.3 2.0 - - + -
589C PHE* 5.5 1.3 - + - -
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Residues in contact with ARG 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C ARG* 3.1 26.6 + - + +
459C ASN* 3.7 16.8 - - - +
460C GLN 3.3 0.2 - - - -
461C TYR* 1.3 81.6 - - + +
463C GLU* 1.3 61.9 + - + +
465C TRP* 3.5 48.2 + - + +
466C LYS* 4.9 9.2 + - - +
544C GLU* 3.3 28.0 + - - +
546C ARG* 5.9 1.1 - - - +
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Residues in contact with GLU 463 (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 ASN* 3.1 25.9 + - - +
460C GLN* 3.7 11.0 - - - +
462C ARG* 1.3 76.5 - - + +
464C ASP* 1.3 62.2 + - - +
465C TRP 3.2 6.0 + - - -
466C LYS* 3.3 25.9 + - + +
467C SER* 4.0 3.3 + - - -
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Residues in contact with ASP 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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460C GLN* 2.8 40.2 + - - +
461C TYR* 3.4 10.5 + - - +
463C GLU* 1.3 76.6 - - - +
465C TRP* 1.3 60.5 + - - +
466C LYS 3.2 2.9 - - - -
467C SER* 2.9 28.0 + - - -
472C VAL* 3.4 25.9 - - + +
473C ARG* 3.7 11.4 - - - +
475C ARG* 3.7 10.9 + - - -
476C ALA* 3.8 14.7 - - + +
576C HIS* 4.8 5.0 - - - -
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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