Contacts of the helix formed by residues 466 - 474 (chain C) in PDB entry 5Q14
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 THR 466 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292C THR* 4.9 9.6 - - - +
293C GLU* 6.1 0.7 - - - -
296C THR* 3.1 37.1 + - + +
465C PHE* 1.3 74.0 - - - +
467C PRO* 1.4 74.0 - - - +
468C LEU* 3.8 3.6 + - - -
469C LEU* 3.0 30.2 + - + +
470C CYS* 3.0 10.5 + - - -
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Residues in contact with PRO 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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465C PHE 4.5 1.6 - - - +
466C THR* 1.4 84.0 - - - +
468C LEU* 1.4 61.3 + - - +
470C CYS* 3.3 11.9 + - + +
471C GLU* 3.2 24.6 + - - +
748D LEU* 3.8 17.0 - - + -
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Residues in contact with LEU 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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296C THR* 4.1 13.5 - - + +
299C VAL* 4.0 20.0 - - + -
300C GLN* 3.7 38.4 - - + +
466C THR* 3.2 6.5 + - - +
467C PRO* 1.4 77.4 - - - +
469C LEU* 1.3 63.0 + - - +
471C GLU* 3.2 13.1 + - - +
472C ILE* 3.2 36.2 + - + +
748D LEU* 3.5 30.5 - - + +
749D LEU* 4.5 4.5 - - + +
752D LEU* 3.9 23.6 - - + -
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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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292C THR* 3.4 40.6 - - + +
295C ALA* 3.8 29.8 - - + +
296C THR* 3.3 15.7 - - - +
299C VAL* 4.1 11.9 - - + -
465C PHE* 4.2 8.3 - - + -
466C THR* 3.0 20.3 + - - +
468C LEU* 1.3 75.8 - - + +
470C CYS* 1.4 54.0 + - - +
472C ILE* 3.2 2.3 + - + +
473C TRP* 2.8 77.5 + - + +
475C VAL* 4.7 1.3 - - - -
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Residues in contact with CYS 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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465C PHE* 3.8 24.7 - - - -
466C THR 3.0 16.6 + - - -
467C PRO* 3.5 13.0 - - + +
468C LEU 3.2 0.2 - - - -
469C LEU* 1.4 75.4 - - - +
471C GLU* 1.3 60.7 + - - +
474C ASP* 3.3 22.2 + - - +
475C VAL* 3.6 27.1 + - - +
476C GLN* 3.8 15.9 - - - -
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Residues in contact with GLU 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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325C LYS* 2.8 19.2 + - - +
467C PRO 3.2 8.8 + - - +
468C LEU* 3.2 11.7 + - - +
470C CYS* 1.3 79.0 - - + +
472C ILE* 1.3 61.6 + - + +
474C ASP* 4.4 1.7 - - - +
746D HIS* 3.4 46.5 + - + +
747D GLN* 3.2 8.5 + - - +
748D LEU* 2.9 38.2 + - - +
749D LEU* 3.0 29.9 + - + +
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Residues in contact with ILE 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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299C VAL* 3.6 39.3 - - + -
324C LEU 5.5 0.7 - - - +
325C LYS* 2.8 36.1 + - + +
328C ALA* 3.5 29.6 - - + -
329C VAL* 5.1 3.3 - - + +
468C LEU* 3.2 28.4 + - + +
469C LEU* 3.2 4.1 + - + +
471C GLU* 1.3 77.3 - - + +
473C TRP* 1.3 78.9 + - + +
474C ASP* 4.3 0.5 - - - +
749D LEU* 3.6 37.0 - - + -
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Residues in contact with TRP 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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291C LEU* 4.8 9.2 - - + -
292C THR* 4.9 3.1 - - + -
295C ALA* 3.3 35.9 - - + -
299C VAL* 5.4 2.2 - - + +
328C ALA 5.5 1.0 - - - -
329C VAL* 3.4 23.4 - - + +
332C MET* 4.2 15.4 - - + +
451C HIS* 3.2 38.6 + + + -
452C ALA* 4.9 6.6 + - - +
455C LEU* 3.5 35.4 - - + -
465C PHE* 3.9 20.9 - + - -
469C LEU* 2.8 43.4 + - + +
472C ILE* 1.3 88.0 - - + +
474C ASP* 1.4 69.8 + - - +
475C VAL* 3.5 15.2 + - + +
501C 9MM 5.7 0.2 - - + -
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Residues in contact with ASP 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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325C LYS* 3.0 33.2 + - - -
452C ALA* 5.3 4.2 - - - +
470C CYS 3.3 13.3 + - - +
471C GLU 4.4 2.3 - - - +
472C ILE 3.5 0.7 - - - +
473C TRP* 1.4 78.8 - - - +
475C VAL* 1.3 61.4 + - - +
746D HIS* 4.7 4.9 + - - -
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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