Contacts of the helix formed by residues 461 - 472 (chain C) in PDB entry 3MY0
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 LEU 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296C PRO* 5.7 7.0 - - + -
412C THR* 5.6 8.1 - - + -
414C VAL* 5.2 12.1 - - + -
455C LEU* 5.3 3.0 - - - +
458C ASP* 4.3 12.8 - - + +
459C PRO* 5.3 0.2 - - - +
460C VAL* 1.3 75.4 - - + +
462C SER* 1.3 63.8 + - - +
463C GLY 3.2 3.8 + - - -
464C LEU* 3.4 32.4 + - + +
465C ALA* 3.8 4.3 + - - +
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Residues in contact with SER 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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455C LEU* 3.5 30.0 - - - +
456C ALA* 4.8 6.5 - - - -
458C ASP* 3.1 23.2 + - - +
459C PRO 4.7 4.9 + - - -
460C VAL 3.5 0.7 - - - -
461C LEU* 1.3 75.6 - - - +
463C GLY* 1.3 59.9 + - - +
465C ALA* 3.4 18.7 - - - +
466C GLN* 3.9 4.3 + - - +
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Residues in contact with GLY 463 (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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460C VAL 4.0 6.2 + - - -
461C LEU 3.2 1.2 - - - -
462C SER* 1.3 76.3 + - - +
464C LEU* 1.3 66.8 + - - +
465C ALA 3.2 1.6 - - - -
466C GLN* 3.3 10.1 + - - +
467C MET* 3.2 24.6 + - - +
488C THR* 5.7 3.1 - - - +
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Residues in contact with LEU 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ALA* 5.6 8.7 - - + +
300C LEU* 4.3 18.2 - - + +
303C ALA* 5.4 8.7 - - + -
405C LEU* 4.6 10.7 - - + +
408C ILE* 6.3 2.2 - - + -
409C ALA* 5.7 6.7 - - + -
460C VAL 4.7 4.3 - - - +
461C LEU* 3.5 28.3 - - + +
463C GLY* 1.3 76.0 - - - +
465C ALA* 1.3 59.5 + - - +
467C MET* 3.3 18.6 + - + +
468C MET* 2.8 48.8 + - + +
489C LEU* 4.1 25.4 - - + -
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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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451C ILE* 3.8 27.7 - - + +
455C LEU* 4.4 17.0 - - + -
461C LEU 3.8 2.7 + - - +
462C SER 3.4 15.1 + - - +
463C GLY 3.2 0.4 - - - -
464C LEU* 1.3 79.8 - - - +
466C GLN* 1.3 60.6 + - - +
468C MET* 3.4 9.3 + - - +
469C ARG* 3.1 29.4 + - - +
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Residues in contact with GLN 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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462C SER 3.9 2.2 + - - +
463C GLY* 3.3 15.0 + - - +
464C LEU 3.3 0.2 - - - -
465C ALA* 1.3 78.8 - - - +
467C MET* 1.3 57.4 + - - +
469C ARG* 3.3 22.8 + - - +
470C GLU* 3.1 67.8 + - - +
473C TYR* 4.0 6.9 + - - -
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Residues in contact with MET 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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405C LEU* 3.6 23.6 - - + -
463C GLY 3.2 13.9 + - - +
464C LEU* 3.3 22.2 + - + +
466C GLN* 1.3 75.3 - - - +
468C MET* 1.3 64.4 + - - +
470C GLU* 3.1 10.4 + - - +
471C CYS* 3.0 30.0 + - - -
480C LEU* 3.7 21.6 - - + +
485C ILE* 3.6 33.4 - - + +
488C THR* 3.9 34.5 - - + -
489C LEU* 4.5 13.2 - - + -
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Residues in contact with MET 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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402C GLY* 3.8 14.1 - - - +
405C LEU* 4.0 15.4 - - + +
406C TRP* 4.0 23.8 - - - +
409C ALA* 3.6 29.2 - - + -
451C ILE* 4.0 32.1 - - + -
452C PRO* 5.1 1.3 - - + -
464C LEU* 2.8 36.6 + - + +
465C ALA* 3.4 10.8 - - - +
466C GLN 3.3 0.2 - - - -
467C MET* 1.3 76.8 - - - +
469C ARG* 1.3 63.4 + - - +
471C CYS* 3.1 17.4 + - - +
472C TRP* 3.3 35.9 + - + -
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Residues in contact with ARG 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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451C ILE* 3.3 35.2 + - + +
465C ALA* 3.1 9.9 + - - +
466C GLN* 3.5 25.9 + - - +
468C MET* 1.3 77.9 - - - +
470C GLU* 1.3 59.4 + - + +
472C TRP* 3.0 22.9 + - - +
473C TYR* 3.4 24.6 + - + -
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Residues in contact with GLU 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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466C GLN* 3.1 43.2 + - - +
467C MET* 3.1 8.9 + - - +
469C ARG* 1.3 75.6 - - - +
471C CYS* 1.3 58.2 + - - +
472C TRP 3.4 0.4 - - - -
473C TYR* 3.2 35.8 + - + +
479C ARG* 3.2 11.3 - - - +
480C LEU* 3.2 57.1 + - + +
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Residues in contact with CYS 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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398C ILE* 3.7 29.4 - - - +
399C TRP* 3.5 14.7 - - - -
401C PHE* 4.6 3.1 - - - -
402C GLY* 3.7 30.1 - - - -
405C LEU* 5.1 3.1 - - - -
467C MET* 3.0 23.8 + - - -
468C MET* 3.1 8.5 + - - +
470C GLU* 1.3 79.3 - - - +
472C TRP* 1.3 58.9 + - + +
473C TYR 3.6 1.6 - - - -
479C ARG* 3.2 22.0 + - - -
480C LEU* 5.4 1.1 - - - -
485C ILE* 4.0 19.7 - - - -
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Residues in contact with TRP 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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399C TRP* 3.5 40.8 + + + -
402C GLY* 3.3 37.4 - - - -
403C LEU* 3.5 15.7 - - + +
406C TRP* 4.1 9.9 - + + -
448C THR* 3.9 28.5 - - + +
449C PRO* 3.5 49.4 - - + -
451C ILE* 3.5 25.8 - - + -
468C MET* 3.3 28.9 - - + +
469C ARG* 3.0 10.9 + - - +
471C CYS* 1.3 88.1 - - + +
473C TYR* 1.3 66.7 + - - +
474C PRO* 3.3 7.4 - - - +
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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