Contacts of the helix formed by residues 523 - 546 (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 ASP 523 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C TYR* 3.5 6.3 + - - -
520C SER* 3.1 26.0 + - - +
521C GLY 4.2 2.2 - - - +
522C ARG* 1.3 73.4 - - - +
524C ALA* 1.3 57.6 + - - +
525C ASN* 3.3 2.3 + - - +
526C PHE* 3.0 34.9 + - + +
527C THR* 2.9 31.2 + - - -
725D ASN* 3.0 22.5 + - - +
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Residues in contact with ALA 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 5.0 5.2 - - + -
449C PHE* 5.2 4.7 - - + -
450C PHE* 4.0 3.3 - - - -
517C TYR* 3.5 21.7 - - + -
522C ARG 3.5 1.6 + - - -
523C ASP* 1.3 71.6 - - - +
525C ASN* 1.3 63.9 + - - +
527C THR* 4.6 2.0 - - - +
528C ARG* 3.0 26.2 + - - +
649D PHE* 4.2 15.9 - - + -
724D ALA* 3.7 19.0 - - + +
725D ASN* 2.7 21.4 + - - +
728D ARG* 4.3 1.1 - - - +
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Residues in contact with ASN 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C ASP* 3.3 5.2 + - - +
524C ALA* 1.3 75.0 - - - +
526C PHE* 1.3 65.3 + - - +
528C ARG* 3.3 16.4 + - - +
529C GLU* 2.9 29.3 + - + +
722D ARG 3.4 10.9 - - - +
723D ASP* 3.0 29.9 + - - +
724D ALA* 2.7 33.1 + - - +
725D ASN* 3.4 16.3 - - - +
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Residues in contact with PHE 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C GLY 5.5 1.3 - - - -
413C TYR* 3.3 42.6 - + - -
516C VAL* 4.1 2.7 - - + -
520C SER* 3.7 20.2 - - - -
523C ASP* 3.0 30.8 + - - +
525C ASN* 1.3 76.9 - - - +
527C THR* 1.3 60.4 + - - +
529C GLU* 3.2 6.4 + - + +
530C LEU* 2.8 57.3 + - + +
533C LYS* 6.4 0.2 - - - -
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Residues in contact with THR 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 4.0 2.5 - - + -
450C PHE* 3.7 17.5 - - + -
513C TRP* 3.3 43.6 - - + +
516C VAL* 4.0 4.9 - - + +
517C TYR* 3.4 23.2 + - - +
520C SER* 3.8 5.5 + - - -
523C ASP 2.9 20.0 + - - -
524C ALA* 4.1 2.0 - - - -
526C PHE* 1.3 79.4 - - - +
528C ARG* 1.3 53.6 + - - +
530C LEU* 3.5 5.8 - - - +
531C PHE* 2.7 35.3 + - - +
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Residues in contact with ARG 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C PHE* 4.5 7.7 - - - -
450C PHE* 3.3 33.8 - - + -
453C ASP* 4.1 2.7 - - - -
524C ALA 3.0 19.3 + - - +
525C ASN* 3.6 19.4 + - - +
527C THR* 1.3 77.9 - - - +
529C GLU* 1.3 88.0 + - - +
531C PHE* 3.1 1.9 + - - +
532C TYR* 2.8 65.6 + - + +
717D TYR* 2.5 39.6 + - - -
721D GLY 5.5 0.6 + - - -
722D ARG* 3.0 32.3 + - - +
724D ALA* 4.8 1.0 - - - +
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Residues in contact with GLU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C ASN* 2.9 21.1 + - + +
526C PHE* 3.7 6.3 - - + +
528C ARG* 1.3 113.2 + - - +
530C LEU* 1.3 51.9 + - - +
532C TYR* 3.5 19.8 - - - +
533C LYS* 2.8 38.0 + - - +
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Residues in contact with LEU 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C LEU* 3.8 18.8 - - + +
412C GLY* 4.1 13.7 - - - +
413C TYR* 3.6 25.8 - - + -
513C TRP* 4.0 15.0 - - + -
516C VAL* 3.9 13.9 - - + -
526C PHE* 2.8 45.6 + - + +
527C THR* 3.5 5.2 - - - +
529C GLU* 1.3 74.5 - - - +
531C PHE* 1.3 63.9 + - - +
533C LYS* 3.2 37.2 + - + +
534C LEU* 3.2 18.8 + - + +
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Residues in contact with PHE 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C VAL* 3.8 25.1 - - + -
450C PHE* 3.4 39.0 - + + -
451C ILE* 4.4 6.7 - - + -
483C LEU* 4.1 17.7 - - + -
509C PHE* 3.9 11.7 - + - -
513C TRP* 3.4 49.9 - + + -
527C THR 2.7 21.2 + - - +
528C ARG 3.1 4.7 + - - +
530C LEU* 1.3 72.4 - - - +
532C TYR* 1.3 67.0 + + - +
534C LEU 3.4 1.4 + - - -
535C PHE* 3.0 41.1 + + + +
539C ILE* 4.1 22.9 - - + -
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Residues in contact with TYR 532 (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 PHE* 3.0 34.2 + - + -
453C ASP* 3.6 13.9 + - - +
454C LEU* 3.5 43.1 + - + -
457C GLN* 4.4 6.6 + - - -
528C ARG* 2.8 48.7 + - + +
529C GLU* 3.5 24.0 - - - +
531C PHE* 1.3 80.8 - + - +
533C LYS* 1.3 65.1 + - - +
534C LEU 3.0 2.0 - - - -
536C LYS* 2.7 50.2 + - + +
539C ILE* 5.7 0.7 - - + -
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Residues in contact with LYS 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C GLY* 6.0 3.8 - - - -
526C PHE* 6.4 0.2 - - - -
529C GLU 2.8 22.9 + - - +
530C LEU* 3.3 28.7 - - + +
532C TYR* 1.3 73.6 - - - +
534C LEU* 1.3 66.0 + - + +
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Residues in contact with LEU 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LYS 3.3 24.9 - - - +
411C LEU* 3.4 27.6 - - + +
412C GLY* 5.8 0.2 - - - -
486C LYS* 3.0 33.0 + - - +
487C LEU* 4.2 12.6 - - + -
513C TRP* 3.8 26.0 - - + -
530C LEU* 3.2 15.5 + - + +
531C PHE 3.7 1.1 - - - +
532C TYR 3.0 0.6 - - - -
533C LYS* 1.3 87.7 - - + +
535C PHE* 1.3 77.8 + - + +
536C LYS 3.9 0.2 - - - -
537C GLU* 6.1 0.9 - - - +
538C ASP* 5.5 0.7 - - - +
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Residues in contact with PHE 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C LEU* 3.4 61.0 - - + -
486C LYS* 3.6 17.0 - - - +
487C LEU* 3.5 29.2 - - + -
509C PHE* 4.0 16.4 - + - -
513C TRP* 3.7 21.8 - + - -
531C PHE* 3.0 32.1 + + + +
534C LEU* 1.3 96.8 - - + +
536C LYS* 1.3 68.5 + - - +
537C GLU 3.1 3.4 - - - -
538C ASP* 3.1 6.9 + - - +
539C ILE* 3.0 32.4 + - + +
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Residues in contact with LYS 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LEU* 3.7 28.0 - - + -
458C TYR* 2.6 48.8 + - - -
532C TYR* 2.7 43.6 + - + +
535C PHE* 1.3 72.4 - - - +
537C GLU* 1.3 53.1 + - - +
539C ILE* 3.4 1.1 + - - +
540C LEU* 2.7 55.3 + - + +
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Residues in contact with GLU 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C LEU 6.1 0.7 - - - +
535C PHE 3.1 0.8 - - - -
536C LYS* 1.3 81.3 - - - +
538C ASP* 1.3 70.4 + - - +
540C LEU* 3.8 6.5 - - + +
541C SER* 3.0 30.9 + - - -
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Residues in contact with ASP 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C PHE* 4.3 6.2 - - + -
482C LEU* 5.4 8.1 - - - +
483C LEU* 4.6 18.0 - - + +
486C LYS* 4.0 26.9 - - - +
534C LEU 5.5 0.7 + - - +
535C PHE* 3.1 10.4 + - - +
537C GLU* 1.3 91.6 - - - +
539C ILE* 1.3 59.7 + - - +
541C SER* 3.0 22.7 + - - -
542C ALA* 3.2 9.7 + - - +
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Residues in contact with ILE 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C PHE 6.0 0.2 - - - +
451C ILE* 4.2 18.2 - - + +
454C LEU* 4.0 25.8 - - + -
455C LEU 6.0 0.2 - - - +
474C LEU* 3.7 31.9 - - + -
479C PHE* 3.7 21.8 - - + -
483C LEU* 4.7 2.0 - - + -
531C PHE* 4.1 26.7 - - + -
532C TYR* 5.7 0.7 - - + -
535C PHE* 3.0 25.2 + - + +
536C LYS 3.9 2.2 - - - +
538C ASP* 1.3 75.9 - - - +
540C LEU* 1.3 66.5 + - - +
542C ALA* 3.2 2.8 + - - +
543C ILE* 3.1 33.6 + - + +
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LEU* 4.0 15.7 - - + -
458C TYR* 3.6 53.6 - - + -
536C LYS* 2.7 46.1 + - + +
537C GLU* 3.8 6.7 - - - +
539C ILE* 1.3 72.0 - - - +
541C SER* 1.3 60.5 + - - +
543C ILE* 3.2 16.5 + - + +
544C LYS* 2.9 44.3 + - - +
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Residues in contact with SER 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C GLU* 3.0 18.7 + - - -
538C ASP* 3.0 12.3 + - - -
540C LEU* 1.3 76.9 - - - +
542C ALA* 1.3 69.1 + - - +
544C LYS* 2.9 26.8 + - - +
545C GLU* 3.2 29.2 + - - +
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Residues in contact with ALA 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LEU* 4.2 3.3 - - - +
473C TYR* 4.2 11.2 - - + +
474C LEU* 4.0 22.4 - - + -
479C PHE* 4.2 9.2 - - + -
538C ASP 3.2 14.2 + - - +
539C ILE 3.6 5.6 - - - +
541C SER* 1.3 82.4 + - - +
543C ILE* 1.3 56.0 + - - +
545C GLU* 4.6 4.0 - - - +
546C GLY* 2.7 36.1 + - - +
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Residues in contact with ILE 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LEU 5.2 1.8 - - - +
455C LEU* 3.7 23.3 - - + +
458C TYR* 4.6 6.1 - - + +
459C SER* 4.4 5.6 - - - -
460C PRO* 3.6 25.8 - - + +
470C LEU* 3.3 37.5 - - + -
474C LEU* 4.1 4.3 - - + -
539C ILE* 3.1 37.9 + - + +
540C LEU* 3.5 20.9 - - + +
541C SER 3.1 0.4 - - - -
542C ALA* 1.3 76.0 - - - +
544C LYS* 1.3 63.6 - - + +
547C ARG* 3.1 26.0 - - - +
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Residues in contact with LYS 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C TYR* 5.1 13.9 - - - -
540C LEU* 2.9 43.7 - - - +
541C SER* 2.9 8.9 + - - +
543C ILE* 1.3 80.5 - - + +
545C GLU* 1.3 67.2 + - - +
547C ARG* 3.5 19.9 + - - +
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Residues in contact with GLU 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C SER* 3.2 34.0 + - - +
542C ALA* 4.3 3.0 - - - +
544C LYS* 1.3 86.9 - - - +
546C GLY* 1.3 58.0 + - - +
547C ARG* 3.2 12.9 + - - +
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Residues in contact with GLY 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C PHE* 5.0 0.2 - - - -
469C PRO* 5.8 2.1 - - - +
470C LEU* 3.9 18.1 + - - +
473C TYR* 6.2 3.8 - - - -
542C ALA* 2.7 22.6 + - - +
545C GLU* 1.3 72.4 - - - +
547C ARG* 1.3 58.4 + - - +
548C HIS 4.3 0.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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