Contacts of the helix formed by residues 461 - 473 (chain C) in PDB entry 3K0J
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 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C HIS* 3.9 3.2 - - - +
439C GLN* 4.7 1.0 + - + +
459C PHE* 3.2 22.4 - - - +
460C LYS* 1.3 114.1 + - + +
462C VAL* 1.3 65.9 + - - +
463C SER* 3.5 12.7 + - - +
464C SER* 3.2 24.6 + - - +
465C ALA 3.5 0.5 + - - -
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Residues in contact with VAL 462 (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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408C PRO* 4.8 4.9 - - + +
409C ASN* 3.4 30.7 - - - +
410C HIS* 3.4 25.8 - - + +
460C LYS 5.4 0.4 - - - +
461C GLU* 1.3 70.9 - - - +
463C SER* 1.3 68.2 + - - +
464C SER 3.1 1.3 - - - -
465C ALA* 3.0 13.0 + - - +
466C THR* 3.0 16.4 + - - +
486C TYR* 5.6 0.2 - - + -
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Residues in contact with SER 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C GLU* 4.2 11.4 + - - +
462C VAL* 1.3 76.1 - - - +
464C SER* 1.3 79.9 + - - +
466C THR* 2.7 21.6 + - - -
467C ASN* 2.9 22.3 + - - -
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Residues in contact with SER 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C PHE* 3.0 26.4 + - - +
438C GLY* 4.3 6.3 - - - -
439C GLN 4.8 1.9 + - - -
459C PHE* 3.7 15.0 - - - -
461C GLU* 3.2 30.1 + - - +
463C SER* 1.3 84.9 + - - +
465C ALA* 1.3 66.5 + - - +
467C ASN* 2.9 10.0 + - - +
468C ALA* 2.9 23.5 + - - +
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Residues in contact with ALA 465 (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 15.7 - - - +
410C HIS* 3.6 25.8 - - - +
412C ILE* 3.6 19.1 - - + +
459C PHE* 3.6 14.3 - - + -
461C GLU 3.5 1.4 + - - +
462C VAL 3.0 10.4 + - - +
464C SER* 1.3 79.0 - - - +
466C THR* 1.3 62.4 + - - +
468C ALA* 3.3 2.5 + - - +
469C LEU* 3.0 25.1 + - - +
486C TYR* 4.6 3.1 - - + -
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Residues in contact with THR 466 (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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408C PRO* 5.5 2.1 - - - +
462C VAL* 3.0 14.7 + - - +
463C SER* 2.7 23.3 + - - -
465C ALA* 1.3 73.9 - - - +
467C ASN* 1.3 62.6 + - - +
469C LEU* 3.4 2.5 + - - +
470C ARG* 3.1 40.8 + - + +
486C TYR* 2.9 27.6 + - - +
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Residues in contact with ASN 467 (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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437C PHE* 3.9 17.5 + - + +
463C SER* 2.9 32.2 + - - -
464C SER* 2.9 8.3 + - - +
466C THR* 1.3 74.9 - - - +
468C ALA* 1.3 67.6 + - - +
470C ARG* 4.2 24.2 + - - +
471C SER* 2.9 32.4 + - - +
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Residues in contact with ALA 468 (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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412C ILE* 4.4 3.1 - - + -
434C PHE* 4.0 11.4 - - + -
437C PHE* 3.7 20.8 - - + -
459C PHE* 3.6 31.4 - - + -
464C SER 2.9 12.2 + - - +
465C ALA 3.3 9.4 - - - +
467C ASN* 1.3 79.5 - - - +
469C LEU* 1.3 68.1 + - - +
471C SER* 3.9 0.2 - - - -
472C MET* 3.1 23.4 + - - +
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Residues in contact with LEU 469 (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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412C ILE* 4.9 3.7 - - + +
465C ALA 3.0 12.9 + - - +
466C THR* 3.6 5.4 - - - +
468C ALA* 1.3 81.5 - - - +
470C ARG* 1.3 76.0 + - + +
473C GLN* 2.9 49.0 + - + +
484C ILE* 3.4 38.1 - - + +
485C GLN* 3.8 17.9 - - - +
486C TYR* 3.9 30.7 - - + +
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Residues in contact with ARG 470 (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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236A ARG* 3.1 18.8 + - - -
466C THR* 3.1 32.6 + - + +
467C ASN* 3.7 21.8 + - - +
469C LEU* 1.3 90.7 - - + +
471C SER* 1.3 72.3 + - - +
473C GLN* 3.1 10.3 + - - +
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Residues in contact with SER 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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236A ARG* 2.8 26.7 + - - +
437C PHE* 3.5 27.2 - - - -
467C ASN* 2.9 23.1 + - - +
470C ARG* 1.3 79.9 + - - +
472C MET* 1.3 69.2 + - - +
475C PHE* 5.0 2.6 - - - +
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Residues in contact with MET 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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433C ILE* 3.2 29.2 - - + -
434C PHE* 3.4 28.5 - - + -
436C ARG* 3.4 14.8 - - - +
437C PHE* 3.4 29.2 - - + -
468C ALA 3.1 9.0 + - - +
469C LEU 3.8 0.4 - - - -
471C SER* 1.3 84.4 - - - +
473C GLN* 1.3 53.7 + - - +
474C GLY 3.0 1.2 + - - -
475C PHE* 2.7 53.6 + - + +
482C MET* 3.4 23.4 - - + +
484C ILE* 4.0 3.4 - - + -
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Residues in contact with GLN 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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231A HIS* 5.4 4.6 - - - +
232A ALA* 3.1 33.2 - - - +
233A ILE* 4.5 0.7 - - - -
235A SER* 5.4 8.7 + - - -
236A ARG* 2.3 29.3 + - + +
469C LEU* 2.9 25.9 + - + +
470C ARG* 3.1 19.8 + - - +
471C SER 3.2 0.6 - - - -
472C MET* 1.3 74.2 - - - +
474C GLY* 1.3 59.6 + - - +
475C PHE 3.2 0.4 - - - -
483C ARG* 3.5 9.4 - - - -
484C ILE* 2.9 46.3 + - - +
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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
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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