Contacts of the helix formed by residues 52 - 60 (chain B) in PDB entry 2OFK
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 LYS 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B THR* 3.3 23.5 + - - +
49B VAL* 2.9 10.3 + - - +
51B LYS* 1.3 79.8 - - + +
53B ARG* 1.3 65.4 + - - +
54B GLU 3.4 2.5 - - - -
55B ASN* 3.0 14.9 + - - +
56B TYR* 2.9 30.9 + - + -
83B THR 3.1 27.5 + - - -
84B GLY* 3.2 17.9 + - - +
85B ILE* 3.3 18.7 + - - -
86B ILE* 3.7 28.5 - - + -
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Residues in contact with ARG 53 (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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16B TYR* 4.7 3.6 - - - +
20B GLU* 2.8 42.4 + - - -
33B GLU* 3.6 2.9 + - - +
34B MET* 4.6 13.9 - - - -
37B LEU* 3.6 28.7 - - + -
46B TRP* 5.4 2.3 - - - -
49B VAL 3.1 7.6 + - - +
50B LEU* 3.1 40.6 + - - +
51B LYS 3.4 0.8 - - - -
52B LYS* 1.3 76.7 - - - +
54B GLU* 1.3 60.3 + - + +
56B TYR* 3.2 10.0 + - + +
57B ARG* 2.9 69.3 + - - +
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Residues in contact with GLU 54 (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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51B LYS 5.0 1.7 + - - +
52B LYS 3.4 0.6 - - - -
53B ARG* 1.3 79.2 + - + +
55B ASN* 1.3 62.2 + - - +
57B ARG* 2.7 42.4 + - - +
58B ALA* 3.0 28.4 + - - +
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Residues in contact with ASN 55 (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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51B LYS 4.6 3.8 + - - -
52B LYS* 3.0 16.8 + - - +
54B GLU* 1.3 79.4 - - - +
56B TYR* 1.3 60.4 + - - +
58B ALA* 3.2 6.2 + - - +
59B CYS* 2.9 35.3 + - - +
82B ASN* 5.3 0.4 - - - +
84B GLY* 3.0 45.5 + - - +
85B ILE* 4.1 4.0 - - + -
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Residues in contact with TYR 56 (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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37B LEU* 3.8 28.5 - - + -
40B GLN* 3.0 41.6 + - + +
49B VAL* 4.6 9.4 - - + -
52B LYS* 2.9 44.9 + - + -
53B ARG* 3.5 7.2 - - - +
55B ASN* 1.3 76.4 - - - +
57B ARG* 1.3 63.7 + - - +
60B PHE* 2.9 57.1 + + - +
63B PHE* 3.9 8.7 - + + -
85B ILE* 3.8 22.2 - - + +
86B ILE* 3.1 28.5 + - + +
95B ILE* 4.0 6.3 - - + -
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Residues in contact with ARG 57 (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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20B GLU* 5.5 0.4 + - - -
33B GLU* 2.8 41.4 + - - +
53B ARG* 2.9 48.9 + - - +
54B GLU* 2.7 46.6 + - - +
56B TYR* 1.3 76.6 - - - +
58B ALA* 1.3 59.4 + - - +
61B HIS 3.5 0.3 + - - -
62B GLN* 2.8 45.8 + - + +
63B PHE* 4.1 10.8 - - + -
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Residues in contact with ALA 58 (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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54B GLU 3.0 16.9 + - - +
55B ASN* 3.7 6.7 - - - +
57B ARG* 1.3 79.5 - - - +
59B CYS* 1.3 60.6 + - - +
60B PHE 3.7 0.2 + - - -
61B HIS* 4.0 6.9 + - - -
62B GLN* 4.1 10.3 + - - +
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Residues in contact with CYS 59 (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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55B ASN* 2.9 20.7 + - - +
58B ALA* 1.3 77.2 - - - +
60B PHE* 1.3 74.7 + - + +
61B HIS* 3.5 5.4 + - - -
71B MET* 3.4 19.8 - - - +
79B LEU* 3.6 25.1 - - + +
82B ASN* 3.0 38.6 - - - -
85B ILE* 3.9 11.4 - - + -
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Residues in contact with PHE 60 (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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56B TYR* 2.9 49.8 + + + +
57B ARG 4.0 0.7 - - - -
59B CYS* 1.3 89.0 - - + +
61B HIS* 1.3 76.5 + - - +
62B GLN 3.2 2.7 - - - -
63B PHE* 2.9 20.8 + + + -
68B ILE* 3.4 19.7 - - + +
71B MET* 4.1 18.8 - - + -
79B LEU* 3.9 27.8 - - + -
85B ILE* 4.2 9.6 - - + -
92B ILE* 4.2 18.6 - - + -
95B ILE* 3.6 39.9 - - + -
96B ILE* 4.8 1.6 - - + -
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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