Contacts of the helix formed by residues 470 - 482 (chain C) in PDB entry 5C51
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 LYS 470 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466C MET* 3.9 25.9 - - - +
467C HIS* 3.4 17.5 + - + +
468C ILE 3.3 0.2 - - - -
469C SER* 1.3 81.7 + - - +
471C LEU* 1.3 62.0 + - - +
472C LYS 3.6 0.4 - - - -
473C ASP* 4.3 19.5 - - + +
474C PHE* 3.3 22.5 + - + +
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Residues in contact with LEU 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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402C LEU* 3.7 39.0 - - + -
406C LEU* 4.5 7.6 - - + -
441C VAL* 4.2 20.2 - - + -
453C ILE* 5.0 6.7 - - + -
455C LEU* 4.0 34.8 - - + -
466C MET* 4.4 9.0 - - + -
467C HIS 3.8 4.5 + - - +
468C ILE* 3.6 16.4 - - - +
469C SER 3.2 1.6 - - - -
470C LYS* 1.3 76.0 - - - +
472C LYS* 1.3 67.4 + - - +
474C PHE* 3.2 5.1 + - + +
475C LEU* 2.9 47.4 + - + +
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Residues in contact with LYS 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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402C LEU* 5.8 1.1 - - + +
405C GLU* 4.6 15.3 - - + +
406C LEU* 4.1 21.0 - - + +
409C ASN* 3.3 36.2 + - + +
411C ILE* 5.2 0.2 - - + -
468C ILE 4.8 0.6 + - - -
469C SER 4.4 8.0 + - - +
471C LEU* 1.3 80.1 - - - +
473C ASP* 1.3 77.1 + - - +
475C LEU* 3.3 1.4 + - - +
476C ILE* 2.9 49.3 + - + +
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Residues in contact with ASP 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 SER 4.3 11.3 - - - +
470C LYS* 4.1 17.9 + - + +
471C LEU 3.3 0.6 - - - -
472C LYS* 1.3 98.4 + - - +
474C PHE* 1.3 56.1 + - - +
476C ILE* 4.0 6.6 - - - +
477C LYS* 2.9 33.2 + - - +
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Residues in contact with PHE 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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439C PHE* 4.0 34.5 - + - -
455C LEU* 3.9 27.6 - - + -
464C GLU* 5.2 6.5 - - - -
466C MET* 4.2 20.2 - - + -
470C LYS* 3.3 21.0 + - + +
471C LEU* 3.2 5.7 + - + +
473C ASP* 1.3 80.0 - - - +
475C LEU* 1.3 70.2 + - + +
477C LYS* 3.4 7.6 + - + +
478C TYR* 2.9 39.6 + + + +
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Residues in contact with LEU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C LYS 5.3 1.3 - - - +
383C VAL* 4.2 23.1 - - + -
406C LEU* 3.8 29.4 - - + -
411C ILE* 3.8 23.6 - - + -
439C PHE* 3.8 36.8 - - + -
471C LEU* 2.9 30.0 + - + +
472C LYS 3.8 3.1 - - - +
474C PHE* 1.3 87.0 - - + +
476C ILE* 1.3 58.7 + - - +
478C TYR* 3.2 3.2 + - - +
479C ILE* 2.9 41.0 + - + +
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Residues in contact with ILE 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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409C ASN* 3.7 37.9 - - + +
411C ILE* 3.9 17.0 - - + -
472C LYS* 2.9 32.0 + - + +
473C ASP* 4.0 7.2 - - - +
475C LEU* 1.3 74.6 - - - +
477C LYS* 1.3 59.5 + - - +
479C ILE* 3.3 8.9 + - + +
480C SER* 2.9 31.6 + - - -
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Residues in contact with LYS 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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473C ASP 2.9 19.7 + - - +
474C PHE* 3.8 7.0 - - + +
476C ILE* 1.3 78.6 - - - +
478C TYR* 1.3 54.8 + - - +
480C SER* 3.3 6.3 + - - -
481C SER* 2.6 46.6 + - - +
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Residues in contact with TYR 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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376C PRO* 4.1 27.1 - - + +
438C LEU* 4.2 9.1 - - + +
439C PHE* 3.5 41.3 - + + -
459C ASP* 4.4 17.3 + - - +
474C PHE* 2.9 30.6 + + + +
475C LEU* 3.6 6.1 - - - +
477C LYS* 1.3 78.5 - - - +
479C ILE* 1.3 73.1 + - + +
481C SER* 3.4 15.1 + - - -
482C ALA* 3.5 12.0 + - + +
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Residues in contact with ILE 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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376C PRO* 4.8 11.4 - - + +
377C CYS* 4.0 6.3 - - - +
382C LYS* 4.4 30.3 - - + +
411C ILE* 6.2 2.7 - - + -
438C LEU* 4.0 25.4 - - + -
439C PHE* 5.8 0.2 - - + -
475C LEU* 2.9 29.3 + - + +
476C ILE* 3.7 7.9 - - + +
478C TYR* 1.3 85.0 - - + +
480C SER* 1.3 65.2 + - - +
482C ALA* 3.2 20.0 + - - +
483C LYS* 3.6 18.8 - - - +
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Residues in contact with SER 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C ILE* 2.9 21.3 + - - -
477C LYS* 3.8 7.2 - - - -
479C ILE* 1.3 79.8 - - - +
481C SER* 1.3 61.0 + - - +
483C LYS* 3.4 25.3 + - - +
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Residues in contact with SER 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 LYS* 2.6 32.5 + - - +
478C TYR* 3.7 10.9 - - - -
479C ILE 3.2 0.4 - - - -
480C SER* 1.3 73.9 - - - +
482C ALA* 1.3 58.3 + - - +
483C LYS 3.1 8.8 + - - +
484C ASN* 4.0 11.1 + - - +
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Residues in contact with ALA 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C HIS* 3.8 26.1 + - + +
376C PRO* 4.3 15.5 - - + -
377C CYS* 3.8 16.5 - - - -
478C TYR* 3.5 8.8 + - + +
479C ILE 3.2 11.6 + - - +
480C SER 3.2 0.8 - - - -
481C SER* 1.3 76.0 - - - +
483C LYS* 1.3 61.1 + - - +
484C ASN* 2.9 18.5 + - - +
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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