Contacts of the helix formed by residues 465 - 471 (chain C) in PDB entry 6PUO
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 VAL 465 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463C ASN 3.6 1.0 + - - +
464C ARG* 1.3 73.9 - - - +
466C ASP* 1.3 69.6 + - + +
467C ILE 3.2 2.2 - - - -
468C ALA* 3.3 3.7 + - - +
469C ARG* 3.3 35.5 + - - +
498C GLU* 4.3 29.4 - - + +
499C PHE* 3.6 40.6 - - + -
502C LEU* 4.0 17.7 - - + -
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Residues in contact with ASP 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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431C VAL* 4.9 5.4 - - - +
464C ARG* 2.9 44.6 + - - +
465C VAL* 1.3 76.8 - - + +
467C ILE* 1.3 62.4 + - - +
469C ARG* 3.6 13.1 - - - +
470C SER* 2.7 39.4 + - - -
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Residues in contact with ILE 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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431C VAL* 4.6 23.1 - - + +
434C LEU* 4.7 17.5 - - + -
435C GLN* 5.4 10.8 - - + +
438C LEU* 3.7 18.6 - - + -
459C ALA* 5.3 7.4 - - + -
462C TRP* 6.0 4.5 - - + -
464C ARG* 3.8 25.6 - - + +
465C VAL 3.2 0.8 - - - -
466C ASP* 1.3 95.1 - - - +
468C ALA* 1.3 57.7 + - - +
470C SER* 2.9 22.0 + - - +
471C GLU* 2.9 38.2 + - + +
472C ILE* 5.3 0.9 - - + -
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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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456C LEU* 4.6 9.2 - - + -
459C ALA* 4.3 18.5 - - + +
464C ARG 5.1 0.4 + - - +
465C VAL* 3.3 9.6 + - - +
467C ILE* 1.3 80.4 - - - +
469C ARG* 1.3 59.0 + - - +
472C ILE* 3.2 20.8 + - + +
473C PHE* 2.9 34.1 + - + +
499C PHE* 4.6 12.6 - - + -
502C LEU* 4.2 14.1 - - + -
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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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465C VAL* 3.3 24.6 + - - +
466C ASP* 3.6 15.3 - - - +
468C ALA* 1.3 77.9 - - - +
470C SER* 1.3 66.6 + - - +
473C PHE* 4.6 15.5 - - - +
474C MET* 5.4 0.7 - - - -
498C GLU* 4.9 6.7 + - - +
501C LYS* 5.6 2.0 - - - +
502C LEU* 3.5 44.4 - - + +
505C GLU* 3.9 17.2 + - - -
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Residues in contact with SER 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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435C GLN* 4.9 5.7 + - - -
466C ASP* 2.7 20.6 + - - -
467C ILE* 2.9 17.7 + - - +
469C ARG* 1.3 82.4 - - - +
471C GLU* 1.3 72.6 + - - +
474C MET* 4.1 11.2 - - - +
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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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435C GLN* 5.0 17.3 - - + +
438C LEU* 3.3 32.5 - - - +
442C ARG* 3.7 26.0 + - - -
452C TRP* 5.0 4.7 - - - -
467C ILE* 2.9 12.7 + - + +
470C SER* 1.3 96.2 + - - +
472C ILE* 1.3 82.3 + - - +
473C PHE 3.4 0.9 - - - -
474C MET* 3.6 16.8 + - + +
475C ASP 5.1 0.9 + - - +
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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