Contacts of the helix formed by residues 479 - 487 (chain C) in PDB entry 2VF7
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 479 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452C ASP* 2.6 27.5 + - - -
465C LEU* 3.9 8.7 - - - +
473C LEU* 3.6 16.3 - - - +
476C VAL* 3.5 22.3 + - - +
477C PRO 2.9 2.0 + - - +
478C GLU* 1.3 78.0 - - - +
480C GLN* 1.3 60.1 + - - +
482C GLY* 2.9 20.3 + - - -
483C GLN* 3.2 30.1 + - - +
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Residues in contact with GLN 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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44C VAL* 3.6 21.1 - - + +
452C ASP* 4.5 1.8 + - - -
455C PRO 3.0 24.9 + - - +
456C GLU* 3.8 13.9 - - - +
465C LEU* 5.3 0.4 - - - +
478C GLU 3.6 6.4 + - - +
479C SER* 1.3 71.7 - - - +
481C THR* 1.3 61.4 + - - +
483C GLN* 3.9 19.2 - - - +
484C TYR* 3.4 29.8 + - - -
489C ARG* 4.3 10.2 + - - +
765C HIS* 3.4 12.1 + - + +
767C ALA* 3.4 25.2 - - + +
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Residues in contact with THR 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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42C THR* 4.0 24.7 - - + +
43C GLY* 3.8 5.0 + - - -
441C LEU* 4.9 7.9 - - + -
444C ILE* 4.6 6.5 - - + -
452C ASP* 3.0 24.6 + - - -
473C LEU* 4.2 6.5 - - + -
479C SER* 3.8 3.1 - - - -
480C GLN* 1.3 76.2 - - - +
482C GLY* 1.3 64.5 + - - +
484C TYR* 3.1 14.0 + - - +
485C LEU* 2.9 35.0 + - + +
765C HIS* 2.9 26.7 - - + -
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Residues in contact with GLY 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 LEU* 3.7 24.0 - - - +
476C VAL 5.2 1.8 - - - -
479C SER* 2.9 20.4 + - - -
481C THR* 1.3 75.8 - - - +
483C GLN* 1.3 60.6 + - - +
485C LEU* 4.2 2.7 - - - -
486C PHE* 3.0 36.8 + - - +
487C ALA* 3.5 1.0 + - - +
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Residues in contact with GLN 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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477C PRO* 2.8 27.3 + - + +
478C GLU* 4.1 6.3 + - - +
479C SER 3.2 17.4 + - - +
480C GLN* 3.9 12.0 - - - +
481C THR 3.4 0.2 - - - -
482C GLY* 1.3 74.6 - - - +
484C TYR* 1.3 58.3 + - - +
487C ALA* 3.1 36.0 + - + -
488C ASP 3.2 9.7 + - - -
489C ARG* 2.6 52.8 + - + -
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Residues in contact with TYR 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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441C LEU* 4.1 25.9 - - + +
445C ARG* 5.2 0.7 + - - -
480C GLN 3.4 20.0 + - - +
481C THR* 3.1 11.2 + - - +
483C GLN* 1.3 81.6 - - - +
485C LEU* 1.3 58.9 + - - +
486C PHE 3.5 0.2 - - - -
488C ASP* 4.4 4.3 + - - -
489C ARG* 3.3 66.5 + - + +
491C THR* 5.5 2.3 - - - +
765C HIS* 4.4 1.1 - - - +
766C PRO* 3.5 38.6 + - + -
767C ALA* 3.6 14.8 - - + -
770C GLU* 3.6 24.6 + - - +
794C GLN* 3.7 13.7 + - - -
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Residues in contact with LEU 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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441C LEU* 4.2 23.6 - - + +
444C ILE* 4.4 11.2 - - + -
445C ARG* 3.5 65.2 + - + +
450C LEU* 5.7 0.9 - - + -
470C PRO* 6.0 2.9 - - + +
473C LEU* 4.5 4.7 - - + -
481C THR* 2.9 52.9 + - + +
482C GLY* 4.2 6.1 - - - +
484C TYR* 1.3 77.5 - - - +
486C PHE* 1.3 88.6 + - + +
488C ASP 5.0 0.9 - - - -
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Residues in contact with PHE 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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445C ARG* 6.2 2.9 - - + -
470C PRO* 3.3 29.6 - - + -
471C GLU* 4.0 19.3 - - + -
473C LEU* 4.1 12.6 - - + -
474C LYS* 3.7 45.8 - - + -
482C GLY* 3.0 18.8 + - - +
485C LEU* 1.3 109.4 - - + +
487C ALA* 1.3 59.5 + - + +
488C ASP* 3.4 6.1 + - - +
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Residues in contact with ALA 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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482C GLY 3.5 1.5 + - - +
483C GLN* 3.1 32.0 + - + +
486C PHE* 1.3 76.7 - - + +
488C ASP* 1.3 72.0 + - - +
489C ARG* 3.5 2.0 + - + +
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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