Contacts of the helix formed by residues 469 - 485 (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 GLU 469 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C SER* 3.5 20.7 + - - +
468C LYS* 1.3 78.5 - - + +
470C MET* 1.3 64.2 + - - +
471C LYS* 3.3 19.2 + - + +
472C VAL* 3.6 26.7 + - + +
473C ARG* 3.5 11.1 + - - +
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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
----------------------------------------------------------
468C LYS 3.9 3.9 + - - +
469C GLU* 1.3 68.9 - - - +
471C LYS* 1.3 64.0 + - - +
472C VAL 3.1 2.5 - - - -
473C ARG* 3.7 20.2 - - + +
474C GLN* 3.1 49.4 + - - +
553C LEU* 3.9 34.1 - - + +
554C PHE* 3.9 26.2 - - + -
567C ARG* 3.6 29.2 - - - +
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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
----------------------------------------------------------
469C GLU* 3.3 15.6 + - + +
470C MET* 1.3 77.7 - - - +
472C VAL* 1.3 63.4 + - + +
474C GLN* 4.4 3.5 - - - +
475C ARG* 3.5 24.7 + - - +
567C ARG* 4.4 46.9 - - + +
568C LEU* 5.4 3.6 - - - +
572C ILE* 5.7 2.9 - - - +
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Residues in contact with VAL 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ASP* 3.4 21.5 - - + +
467C SER* 3.7 20.6 - - - +
469C GLU* 3.6 31.3 + - + +
470C MET 3.1 0.4 - - - -
471C LYS* 1.3 83.2 - - + +
473C ARG* 1.3 62.0 + - - +
474C GLN 3.4 0.2 - - - -
475C ARG* 3.3 39.6 + - - +
476C ALA* 3.2 23.0 + - - +
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Residues in contact with ARG 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ASP 3.7 19.5 - - - +
465C TRP* 3.2 17.1 + - - +
466C LYS* 3.2 23.8 + - - +
467C SER* 2.7 24.6 + - - +
468C LYS 5.2 0.8 + - - -
469C GLU 3.5 5.9 + - - +
470C MET* 3.2 27.0 + - - +
472C VAL* 1.3 78.3 - - - +
474C GLN* 1.3 57.3 + - - +
476C ALA* 3.5 3.3 + - - +
477C VAL* 3.2 32.7 + - - +
549C LYS* 5.9 1.2 - - - +
550C ASN* 2.8 34.2 + - - +
553C LEU* 4.3 17.2 - - - +
554C PHE* 4.0 11.2 - - + -
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Residues in contact with GLN 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C MET* 3.1 27.8 + - - +
471C LYS* 4.7 3.1 - - - +
473C ARG* 1.3 72.9 - - - +
475C ARG* 1.3 59.6 + - - +
477C VAL* 3.3 1.0 + - - -
478C ALA* 3.0 31.9 + - - +
554C PHE* 3.4 48.3 - - + +
558C LYS* 4.7 0.6 - - - +
564C LEU 4.1 2.8 + - - -
565C PHE* 3.4 19.6 - - + -
566C ASP* 2.3 50.5 + - - +
567C ARG* 4.6 5.0 - - - +
568C LEU* 3.8 10.9 - - + +
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Residues in contact with ARG 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C GLN* 5.6 0.2 + - - -
464C ASP* 3.7 7.5 + - - -
471C LYS 3.5 18.3 + - - +
472C VAL* 3.3 45.7 + - - +
474C GLN* 1.3 77.6 - - - +
476C ALA* 1.3 56.7 + - - +
478C ALA* 3.6 2.6 + - - +
479C LEU* 3.0 29.3 + - + +
568C LEU* 4.0 24.6 - - + +
572C ILE* 4.7 14.6 + - - +
573C LEU* 4.1 15.1 - - + +
576C HIS* 3.5 60.1 + - - +
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Residues in contact with ALA 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C TYR* 3.7 25.3 - - + +
464C ASP* 3.8 14.6 - - + +
465C TRP* 3.3 29.7 + - + -
472C VAL 3.2 14.6 + - - +
473C ARG 3.7 2.2 - - - +
475C ARG* 1.3 79.8 - - - +
477C VAL* 1.3 58.2 + - - +
479C LEU* 3.9 4.4 - - - +
480C TYR* 3.1 22.3 + - - +
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Residues in contact with VAL 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C TRP* 3.9 19.3 - - + +
473C ARG 3.2 17.1 + - - +
474C GLN 3.3 4.7 + - - +
476C ALA* 1.3 73.7 - - - +
478C ALA* 1.3 65.0 + - - +
480C TYR* 3.4 5.7 + - - +
481C PHE* 3.3 32.8 + - + -
547C VAL* 3.9 24.5 - - + -
550C ASN* 4.0 15.7 - - + +
551C LEU* 4.0 10.8 - - + -
554C PHE* 3.9 12.6 - - + -
565C PHE* 3.9 22.7 - - + -
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Residues in contact with ALA 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C GLN 3.0 18.3 + - - +
475C ARG 3.8 3.1 - - - +
477C VAL* 1.3 79.3 - - - +
479C LEU* 1.3 55.7 + - - +
481C PHE 3.4 1.0 + - - -
482C ILE* 3.2 26.2 + - - +
504C CYS* 3.2 29.2 - - - -
505C CYS* 4.7 8.1 - - - -
565C PHE* 4.0 15.0 - - + -
568C LEU* 3.8 20.4 - - + -
573C LEU* 5.2 2.9 - - + -
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Residues in contact with LEU 479 (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* 4.3 10.8 - - + -
461C TYR* 3.8 31.0 - - + -
475C ARG* 3.0 18.8 + - + +
476C ALA* 3.9 6.7 - - - +
477C VAL 3.3 0.2 - - - -
478C ALA* 1.3 73.4 - - - +
480C TYR* 1.3 59.9 + - - +
482C ILE* 3.8 10.9 - - + +
483C ASP* 3.0 28.9 + - - +
573C LEU* 4.2 16.8 - - + +
576C HIS* 5.1 11.9 - - + +
577C LEU* 3.9 35.7 - - + -
580C LEU* 5.1 2.0 - - + -
589C PHE* 3.9 21.5 - - + -
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Residues in contact with TYR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C TYR* 3.8 22.9 - + + -
465C TRP* 3.7 29.2 - + + -
476C ALA 3.1 18.8 + - - +
477C VAL* 3.4 6.5 - - - +
478C ALA 3.2 0.2 - - - -
479C LEU* 1.3 77.0 - - - +
481C PHE* 1.3 71.4 + + - +
483C ASP* 3.4 1.6 + - - +
484C LYS* 2.9 72.0 + - + +
542C PRO 4.5 0.2 + - - -
543C VAL* 3.7 32.8 - - + -
544C GLU* 3.7 25.5 + - + +
547C VAL* 3.9 18.8 - - + -
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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
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477C VAL* 3.3 17.4 + - + -
478C ALA 3.6 7.2 - - - +
480C TYR* 1.3 100.5 - + - +
482C ILE* 1.3 56.8 + - - +
484C LYS* 5.0 0.2 - - - -
485C LEU* 2.9 44.7 + - + +
486C ALA 3.4 1.2 + - - -
487C LEU* 3.8 12.8 + - + +
504C CYS* 3.8 15.9 - - - -
507C LEU* 4.5 4.7 - - + -
512C ILE* 5.7 0.9 - - + -
525C VAL* 5.0 0.7 - - + -
527C PHE* 3.7 39.0 - + - -
543C VAL* 4.7 7.0 - - + -
547C VAL* 4.4 7.2 - - + -
551C LEU* 3.9 29.6 - - + -
564C LEU* 5.1 1.1 - - + -
565C PHE* 3.7 29.6 - + - -
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Residues in contact with ILE 482 (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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478C ALA 3.2 18.5 + - - +
479C LEU* 3.8 11.0 - - + +
480C TYR 3.4 0.2 - - - -
481C PHE* 1.3 76.2 - - - +
483C ASP* 1.3 58.2 + - - +
486C ALA* 3.3 20.0 - - - -
487C LEU 3.9 22.0 - - - +
489C ALA* 4.5 7.4 - - - -
504C CYS* 3.7 25.1 - - + -
573C LEU* 3.6 30.3 - - + -
586C ALA* 3.5 33.2 - - + +
589C PHE* 3.8 23.7 - - + +
590C ARG 5.1 0.4 + - - +
593C ASN* 4.1 0.7 - - - +
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Residues in contact with ASP 483 (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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454C VAL* 4.5 1.4 - - - +
458C ARG* 2.7 45.5 + - - +
461C TYR* 2.7 24.1 + - + +
479C LEU 3.0 17.0 + - - +
480C TYR 3.8 0.4 - - - +
482C ILE* 1.3 77.6 - - - +
484C LYS* 1.3 65.3 + - - +
486C ALA 4.0 0.7 + - - -
589C PHE* 3.7 28.9 - - + -
592C TYR* 4.6 1.6 - - - -
593C ASN* 2.7 33.1 + - - +
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Residues in contact with LYS 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C TYR* 5.8 0.4 - - - +
480C TYR* 2.9 60.8 + - + +
481C PHE* 5.0 0.2 - - - -
483C ASP* 1.3 77.6 - - - +
485C LEU* 1.3 75.1 + - + +
486C ALA 3.8 0.3 + - - -
541C VAL* 3.7 20.0 - - + +
542C PRO* 4.2 13.5 + - - +
543C VAL* 5.6 0.7 - - + -
593C ASN* 5.6 0.2 - - - -
629C LEU* 4.9 10.6 - - - +
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Residues in contact with LEU 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C PHE* 2.9 28.4 + - + +
484C LYS* 1.3 89.0 - - + +
486C ALA* 1.3 68.4 + - - +
487C LEU* 3.2 12.4 + - + +
527C PHE* 3.5 38.4 - - + -
537C TYR* 3.4 25.2 + - + +
539C ASN* 3.7 23.6 - - - +
541C VAL* 3.9 24.5 - - + -
629C LEU* 3.9 11.3 - - - +
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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