Contacts of the helix formed by residues 471 - 477 (chain B) in PDB entry 1O95
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 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B PRO* 4.6 4.7 - - + +
470B MET* 1.3 77.7 - - - +
472B ALA* 1.3 63.1 + - - +
473B ASP* 3.6 7.8 + - - +
474B ASP* 2.7 47.3 + - - +
475B VAL* 3.0 15.9 + - - +
650B LEU* 4.2 4.0 - - - -
653B GLU* 5.3 3.4 - - - -
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Residues in contact with ALA 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B THR* 1.3 76.3 - - - +
473B ASP* 1.3 60.7 + - - +
475B VAL* 3.5 2.0 - - - +
476B LEU* 3.0 33.9 + - + +
650B LEU* 3.6 19.7 - - + +
653B GLU* 3.7 27.3 + - + +
654B LEU* 3.3 24.8 - - + +
657B ARG* 5.1 10.1 - - - +
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Residues in contact with ASP 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B THR* 3.0 7.8 + - - +
472B ALA* 1.3 76.6 - - - +
474B ASP* 1.3 65.4 + - - +
475B VAL 2.9 3.2 + - - -
476B LEU* 4.1 2.8 - - - +
477B GLN* 2.9 31.1 + - + +
657B ARG* 2.4 48.2 + - - -
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Residues in contact with ASP 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PRO 4.0 4.2 - - - +
470B MET* 3.5 26.4 - - + +
471B THR* 2.7 41.6 + - - +
473B ASP* 1.3 74.2 - - - +
475B VAL* 1.3 56.0 + - - +
477B GLN* 3.4 4.2 - - - -
478B TYR* 3.1 31.2 + - + +
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 4.0 11.8 - - + +
395B VAL* 4.5 7.0 - - + -
470B MET* 3.6 26.9 - - + -
471B THR 3.0 18.9 + - - +
472B ALA* 3.5 6.3 - - - +
473B ASP 2.9 0.2 - - - -
474B ASP* 1.3 76.7 - - - +
476B LEU* 1.3 64.5 + - - +
478B TYR* 3.0 25.5 + - - +
479B GLY 4.4 1.4 + - - -
480B ALA* 6.0 0.2 - - - +
483B VAL* 4.5 21.1 - - + +
485B ILE* 5.2 0.2 - - + -
650B LEU* 4.5 7.9 - - + -
654B LEU* 3.6 32.1 - - + -
666B ILE* 4.2 5.1 - - + +
669B ILE* 4.7 4.3 - - + -
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Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B ALA 3.0 15.7 + - - +
473B ASP* 4.1 3.4 - - - +
475B VAL* 1.3 81.2 - - + +
477B GLN* 1.3 60.0 + - + +
478B TYR 3.3 2.6 + - - -
479B GLY 4.8 0.9 + - - -
654B LEU* 4.5 13.0 - - + -
657B ARG* 3.3 46.4 - - + +
660B GLU* 3.4 17.0 - - - +
661B TRP* 3.6 18.2 - - + -
664B ASN* 3.2 56.3 - - - +
666B ILE* 3.3 24.0 - - + +
669B ILE* 5.6 0.2 - - + -
195C ARG* 4.2 1.4 + - - -
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Residues in contact with GLN 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B ASP* 2.9 21.6 + - + +
474B ASP* 3.4 6.7 - - - +
476B LEU* 1.3 78.2 - - + +
478B TYR* 1.3 60.6 + - - +
479B GLY 3.6 1.1 - - - -
664B ASN* 4.9 4.3 - - - +
193C SER* 5.1 2.4 - - - -
195C ARG* 3.4 45.4 - - - +
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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