Contacts of the helix formed by residues 476 - 488 (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 SER 476 (chain C).
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Specific contacts
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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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Residues in contact with GLU 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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476C SER* 1.3 71.6 - - - +
478C GLU* 1.3 60.6 + - - +
480C PHE* 3.6 6.2 + - - +
481C ASN* 2.6 46.2 + - - +
502C GLU* 3.4 19.1 - - + +
503C THR* 2.8 47.1 - - - +
506C GLY* 5.3 3.5 - - - -
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Residues in contact with GLU 478 (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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473C TYR* 3.9 26.6 + - + -
476C SER* 3.7 9.0 - - - +
477C GLU* 1.3 78.9 - - - +
479C PHE* 1.3 61.9 + - - +
481C ASN* 3.3 9.1 + - - +
482C LEU* 3.2 33.3 + - + +
502C GLU* 5.6 2.2 - - - -
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Residues in contact with PHE 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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451C ILE* 4.5 2.9 - - + -
473C TYR* 3.1 59.7 - + + +
474C LEU* 2.9 46.4 - - + +
476C SER* 3.3 5.1 + - - +
478C GLU* 1.3 77.2 - - - +
480C PHE* 1.3 69.5 + + - +
481C ASN 3.1 1.1 - - - -
482C LEU* 3.1 25.4 + - + +
483C LEU* 3.3 34.3 + - + +
538C ASP* 4.3 5.4 - - + -
539C ILE* 3.7 33.9 - - + -
542C ALA* 4.2 8.1 - - + -
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Residues in contact with PHE 480 (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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444C ASP* 6.1 0.9 - - - -
447C VAL* 3.5 28.9 - - + -
448C ASN 5.6 0.7 - - - -
451C ILE* 4.4 4.3 - - + -
474C LEU 3.2 26.5 - - - -
475C ILE* 3.3 29.6 - - + -
476C SER 3.3 12.9 + - - +
477C GLU* 3.6 5.8 + - - +
478C GLU 3.4 0.2 - - - -
479C PHE* 1.3 79.1 - + - +
481C ASN* 1.3 56.6 + - - +
483C LEU* 3.5 6.7 + - + +
484C ALA* 3.0 29.8 + - - +
506C GLY* 4.1 17.5 - - - -
509C PHE* 3.8 27.7 - + + -
510C GLU* 3.3 38.8 - - + -
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Residues in contact with ASN 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 GLU* 2.6 26.3 + - - +
478C GLU* 3.5 11.2 - - - +
479C PHE 3.1 0.4 - - - -
480C PHE* 1.3 78.4 - - - +
482C LEU* 1.3 64.5 + - + +
484C ALA* 3.5 4.7 + - - +
485C GLN* 3.2 28.4 + - - +
502C GLU* 3.0 59.2 + - + +
505C ILE* 3.4 26.6 - - - +
506C GLY* 4.5 2.6 - - - +
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Residues in contact with LEU 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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473C TYR* 4.7 12.8 - - - +
478C GLU* 3.2 25.4 + - + +
479C PHE* 3.1 19.4 + - + +
481C ASN* 1.3 79.6 - - + +
483C LEU* 1.3 68.8 + - + +
485C GLN* 3.4 36.7 + - - +
486C LYS* 3.6 9.4 - - - +
538C ASP* 5.4 8.0 - - - +
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Residues in contact with LEU 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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451C ILE* 5.3 2.0 - - + -
479C PHE* 3.3 48.1 + - + +
480C PHE* 3.5 3.3 + - + +
481C ASN 3.4 0.2 - - - -
482C LEU* 1.3 78.6 - - + +
484C ALA* 1.3 66.0 + - - +
485C GLN 3.1 1.8 - - - -
486C LYS* 3.2 22.7 + - + +
487C LEU* 3.6 3.8 + - - +
509C PHE* 3.7 25.8 - - + -
531C PHE* 4.1 11.4 - - + -
535C PHE* 3.4 53.8 - - + -
538C ASP* 4.6 15.0 - - + +
539C ILE* 4.7 1.8 - - + -
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Residues in contact with ALA 484 (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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480C PHE 3.0 19.0 + - - +
481C ASN 4.0 1.8 - - - +
483C LEU* 1.3 73.9 - - - +
485C GLN* 1.3 53.6 - - - +
487C LEU* 3.0 7.2 + - - +
488C GLU 2.8 29.5 + - - -
489C LEU* 3.1 25.2 + - + -
490C HIS* 6.0 0.2 - - - -
505C ILE* 3.8 26.7 - - + -
509C PHE* 3.8 19.4 - - + -
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Residues in contact with GLN 485 (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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481C ASN 3.2 20.2 + - - +
482C LEU* 3.4 31.8 + - - +
484C ALA* 1.3 75.5 - - - +
486C LYS* 1.3 56.2 + - + +
488C GLU* 2.5 31.8 + - - +
490C HIS* 5.2 8.0 + - + -
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Residues in contact with LYS 486 (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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410C LYS* 4.8 10.6 + - - +
482C LEU 3.6 13.7 - - - +
483C LEU* 3.2 17.9 + - + +
485C GLN* 1.3 76.5 - - + +
487C LEU* 1.3 63.0 - - + +
488C GLU* 5.3 0.3 - - - +
534C LEU* 3.0 37.8 + - - +
535C PHE* 3.6 14.6 - - - -
538C ASP* 4.0 26.7 - - - +
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Residues in contact with LEU 487 (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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407C LEU* 4.1 15.1 - - + +
410C LYS* 3.4 30.3 - - + +
411C LEU* 3.8 35.9 - - + -
483C LEU 3.8 2.7 - - - +
484C ALA* 3.0 7.8 + - - +
485C GLN 3.0 0.4 - - - -
486C LYS* 1.3 82.2 - - + +
488C GLU* 1.3 78.5 + - - +
489C LEU* 3.3 7.9 - - + -
492C PHE* 3.6 5.5 - - - -
509C PHE* 5.5 4.3 - - + -
512C LEU* 4.8 7.9 - - + -
513C TRP* 5.1 4.3 - - + +
534C LEU* 4.2 15.5 - - + -
535C PHE* 3.5 37.2 - - + -
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Residues in contact with GLU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLN* 2.6 29.6 - - - +
410C LYS* 2.8 23.2 + - + +
484C ALA 2.8 3.3 + - - -
485C GLN 2.5 22.4 + - - +
486C LYS 3.4 0.8 - - - +
487C LEU* 1.3 79.3 - - - +
489C LEU* 1.3 64.3 + - - +
490C HIS* 3.3 28.4 - - + +
491C LYS* 3.1 31.6 + - - -
492C PHE* 3.1 15.0 - - + -
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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