Contacts of the helix formed by residues 470 - 475 (chain B) in PDB entry 5OQN
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 PHE 470 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 4.1 3.6 - - + -
64A LYS* 3.3 52.0 - - + -
67A PRO* 4.0 13.7 - - + -
467B ASP* 3.1 38.0 + - + +
468B ASP* 3.0 2.5 - - - -
469B SER* 1.3 76.2 - - - +
471B GLU* 1.3 64.0 + - + +
472B ASP 3.1 0.7 - - - -
473B LYS* 2.7 44.2 + - + +
474B VAL* 3.2 25.5 + - + -
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Residues in contact with GLU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 3.4 32.1 + - + +
63A THR* 3.9 24.2 + - + -
121A HIS* 4.2 14.4 - - - -
124A ARG* 4.2 12.0 + - - -
468B ASP* 2.7 29.9 + - + +
470B PHE* 1.3 80.2 - - + +
472B ASP* 1.3 64.8 + - - +
474B VAL* 3.1 22.6 + - - +
475B PHE* 3.6 21.6 + - + -
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Residues in contact with ASP 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 5.4 5.5 + - - -
469B SER* 3.4 11.7 + - - +
470B PHE 3.1 1.0 - - - -
471B GLU* 1.3 81.8 + - - +
473B LYS* 1.3 65.3 + - - +
475B PHE* 3.2 19.5 + - - +
476B ALA* 3.2 14.2 + - - +
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Residues in contact with LYS 473 (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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67A PRO* 5.0 9.6 - - - -
128A SER* 4.7 2.8 + - - -
129A PRO* 5.5 0.9 - - - +
130A ASP* 4.0 29.7 + - - +
133A VAL* 4.7 3.0 - - - +
469B SER 4.0 2.2 + - - +
470B PHE* 2.7 41.2 + - + +
472B ASP* 1.3 73.1 - - - +
474B VAL* 1.3 69.4 + - + +
475B PHE 3.4 0.2 + - - -
476B ALA* 3.6 16.8 + - - +
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 4.4 8.1 - - + -
66A LEU* 4.5 12.6 - - + -
67A PRO* 3.8 15.9 - - + -
128A SER* 3.1 27.6 + - - -
133A VAL* 3.4 29.8 - - + +
470B PHE* 3.7 35.2 - - + +
471B GLU 3.1 11.3 + - - +
473B LYS* 1.3 85.4 - - + +
475B PHE* 1.3 76.1 + - + +
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Residues in contact with PHE 475 (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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63A THR* 4.1 17.7 - - + -
66A LEU* 5.0 7.4 - - + -
121A HIS* 4.0 18.8 - + - -
122A VAL 5.4 0.4 - - - -
124A ARG* 3.0 87.6 - - + +
125A GLY* 3.6 5.4 - - - -
128A SER* 5.1 0.7 - - - -
471B GLU* 3.7 26.9 - - + -
472B ASP* 3.2 14.5 + - - +
474B VAL* 1.3 95.1 - - + +
476B ALA* 1.3 66.8 + - - +
477B SER* 3.6 0.7 + - - -
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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