Contacts of the helix formed by residues 85 - 94 (chain B) in PDB entry 1P27
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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B GLU 4.0 7.6 - - - +
84B ALA* 1.3 76.2 - - - +
86B GLU* 1.3 64.2 + - - +
87B GLU* 3.2 11.9 + - - +
88B ASP* 2.7 41.1 + - - +
89B ILE* 3.1 20.4 - - - +
104B LEU* 3.0 8.7 - - - -
113B LEU* 5.5 0.2 - - - -
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Residues in contact with GLU 86 (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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85B THR* 1.3 73.5 - - - +
87B GLU* 1.3 64.9 + - + +
88B ASP 3.1 0.3 + - - -
89B ILE* 3.2 4.3 + - - +
90B HIS* 2.9 24.7 + - + +
102B ILE* 2.9 49.9 + - + +
104B LEU* 2.8 22.9 + - + +
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Residues in contact with GLU 87 (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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85B THR* 3.2 10.5 + - - +
86B GLU* 1.3 80.0 - - + +
88B ASP* 1.3 57.9 + - - +
90B HIS* 3.8 7.4 - - - +
91B ASP* 2.9 42.4 + - - +
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Residues in contact with ASP 88 (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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83B GLU 4.3 0.9 - - - +
84B ALA* 3.3 17.2 - - + -
85B THR* 2.7 40.8 + - - +
86B GLU 3.1 0.8 - - - -
87B GLU* 1.3 79.0 - - - +
89B ILE* 1.3 60.3 + - + +
91B ASP* 3.3 9.4 + - - +
92B LYS* 3.1 28.9 + - - +
139B LEU* 4.6 11.9 - - + +
140B MET* 3.8 16.4 - - - +
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Residues in contact with ILE 89 (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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77B VAL* 6.1 0.7 - - + -
80B VAL* 4.1 9.4 - - + -
84B ALA* 4.0 17.9 - - + -
85B THR 3.1 22.2 - - - +
86B GLU 3.2 5.5 + - - +
88B ASP* 1.3 81.3 - - + +
90B HIS* 1.4 57.2 + - - +
92B LYS* 3.3 2.5 + - - -
93B PHE* 2.9 56.2 + - + +
102B ILE* 4.2 11.2 - - + -
104B LEU* 3.7 26.0 - - + -
117B THR* 4.1 17.9 - - + +
119B VAL* 3.8 21.5 - - + -
139B LEU* 4.4 12.8 - - + -
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Residues in contact with HIS 90 (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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86B GLU* 2.9 18.8 + - + +
87B GLU* 3.9 8.7 - - + +
89B ILE* 1.4 77.9 - - - +
91B ASP* 1.3 58.4 + - - +
94B ALA* 3.0 50.8 + - + +
99B ILE* 3.4 40.4 + - + +
102B ILE* 3.8 17.0 - - + +
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Residues in contact with ASP 91 (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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87B GLU* 2.9 31.3 + - - +
88B ASP* 3.6 9.2 - - - +
89B ILE 3.3 0.2 - - - -
90B HIS* 1.3 78.5 + - - +
92B LYS* 1.3 65.2 + - - +
94B ALA* 4.2 5.7 + - - +
95B GLU* 3.3 15.1 + - - +
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Residues in contact with LYS 92 (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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88B ASP 3.1 17.1 + - - +
89B ILE* 3.9 5.2 - - - +
91B ASP* 1.3 82.8 - - - +
93B PHE* 1.3 66.7 + - + +
95B GLU* 3.1 18.0 - - - +
96B TYR* 4.1 2.9 - - - -
134B LEU* 3.3 40.4 - - + +
137B GLN* 6.2 0.2 - - + -
138B ASP 3.9 22.5 + - - +
139B LEU* 4.4 21.0 - - + +
144B ILE* 5.0 6.5 - - + -
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Residues in contact with PHE 93 (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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75B LEU* 4.5 5.2 - - + -
77B VAL* 3.7 37.2 - - + -
89B ILE* 2.9 44.8 + - + +
92B LYS* 1.3 85.5 - - + +
94B ALA* 1.3 60.5 + - - +
95B GLU 3.1 6.9 + - - -
96B TYR* 3.3 8.5 + - - -
99B ILE* 3.8 13.0 - - + -
119B VAL* 4.1 16.6 - - + -
121B TYR* 2.6 42.6 + + - +
130B ALA* 4.4 2.7 - - + -
134B LEU* 3.6 23.6 - - + -
139B LEU* 6.1 1.1 - - + -
144B ILE* 4.1 20.6 - - + -
146B VAL* 4.1 17.9 - - + -
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Residues in contact with ALA 94 (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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90B HIS* 3.0 41.3 + - + +
91B ASP* 4.2 4.4 + - - +
92B LYS 3.7 0.8 - - - -
93B PHE* 1.3 72.5 - - - +
95B GLU* 1.3 64.6 + - - +
96B TYR 3.0 4.5 + - - -
97B GLY 3.4 17.1 + - - +
99B ILE* 3.7 9.6 - - + +
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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