Contacts of the helix formed by residues 84 - 94 (chain B) in PDB entry 2PO5
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 ASP 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PRO* 3.7 16.8 - - + -
80B GLU* 3.7 10.9 + - - +
81B THR* 2.7 39.0 + - - +
83B GLY* 1.3 77.1 - - - +
85B VAL* 1.3 64.7 + - - +
86B HIS 3.3 2.0 + - - -
87B ASP* 3.5 8.8 + - - +
88B PHE* 3.2 21.5 + - - +
166B VAL* 5.0 5.1 - - + +
167B HIS* 6.0 2.3 - - - -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PRO* 4.0 23.6 - - + -
81B THR 4.1 0.2 - - - +
82B LEU* 3.3 26.8 + - - +
84B ASP* 1.3 77.3 - - - +
86B HIS* 1.3 64.5 + - - +
88B PHE* 3.2 5.6 + - + +
89B LEU* 3.0 31.9 + - + +
116B THR* 3.9 15.0 - - + +
119B ILE* 3.8 29.6 - - + -
120B GLN* 3.7 20.6 - - + -
123B TYR* 4.3 9.2 - - + -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU 4.7 0.4 + - - -
83B GLY 4.3 7.9 + - - +
84B ASP 3.3 1.0 - - - -
85B VAL* 1.3 79.4 - - - +
87B ASP* 1.3 71.1 + - - +
89B LEU* 3.4 3.0 + - - +
90B LEU* 3.0 42.3 + - + +
109B PRO* 4.4 7.1 + - + -
112B ALA* 4.0 4.7 - - + +
113B LYS* 4.1 28.5 + - + +
116B THR* 3.6 31.9 + - + +
120B GLN* 5.5 0.4 - - - +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLY 5.5 3.1 - - - +
84B ASP* 3.5 8.3 + - - +
85B VAL 3.4 0.2 - - - -
86B HIS* 1.3 88.9 + - - +
88B PHE* 1.3 65.6 + - - +
90B LEU* 3.6 14.6 - - + +
91B ARG* 2.9 57.2 + - + +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET* 4.6 7.4 - - + -
77B GLY 3.7 22.9 - - - -
78B GLY* 4.4 0.7 - - - -
79B PRO* 3.8 24.0 - - + -
84B ASP 3.2 15.7 + - - +
85B VAL* 3.3 16.2 - - + +
87B ASP* 1.3 78.4 - - - +
89B LEU* 1.3 74.9 + - + +
91B ARG* 3.4 3.4 + - - +
92B LEU* 3.1 40.9 + - + +
119B ILE* 5.2 3.1 - - + -
123B TYR* 4.3 12.1 - + - -
165B TYR* 3.6 28.7 - + + +
166B VAL* 3.5 24.7 - - + -
501B CHD 4.2 20.6 - - + -
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Residues in contact with LEU 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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85B VAL* 3.0 21.5 + - + +
86B HIS 3.8 3.4 - - - +
88B PHE* 1.3 89.1 - - + +
90B LEU* 1.3 63.0 + - - +
92B LEU* 3.2 6.0 + - + +
93B PHE* 3.0 37.4 + - + -
112B ALA* 3.6 19.7 - - + +
115B LEU* 3.7 12.6 - - + -
116B THR* 3.6 36.6 - - - +
119B ILE* 3.9 15.9 - - + -
501B CHD 4.2 33.2 - - + -
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Residues in contact with LEU 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 HIS* 3.0 27.4 + - + +
87B ASP* 3.6 20.2 - - - +
88B PHE 3.3 0.2 - - - -
89B LEU* 1.3 77.7 - - - +
91B ARG* 1.3 64.6 + - + +
93B PHE* 3.4 1.7 + - - +
94B LEU* 3.2 46.7 + - + +
108B ALA 4.0 2.5 - - - -
109B PRO* 3.5 42.8 - - + -
112B ALA* 3.6 8.7 - - + +
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Residues in contact with ARG 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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84B ASP 5.6 0.2 + - - -
87B ASP* 2.9 49.8 + - + +
88B PHE* 3.9 1.5 - - - +
90B LEU* 1.3 79.2 - - + +
92B LEU* 1.3 62.4 + - - +
94B LEU* 3.4 19.0 + - + +
95B ASP* 3.4 9.9 + - - +
164B ARG 4.6 1.8 - - - +
165B TYR* 3.0 47.4 + - + +
166B VAL* 4.0 6.9 - - - +
167B HIS* 3.3 32.2 + - - +
169B LEU* 3.6 33.4 - - - +
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Residues in contact with LEU 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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76B MET* 4.7 2.0 - - - -
88B PHE* 3.1 29.7 + - + +
89B LEU* 3.5 6.1 - - - +
91B ARG* 1.3 78.2 - - - +
93B PHE* 1.3 75.1 + - + +
94B LEU 3.2 1.0 + - - -
95B ASP* 3.5 9.4 + - - +
98B LEU* 3.6 22.9 - - + +
99B MET* 3.9 7.5 - - + +
165B TYR* 3.5 29.8 - - + -
501B CHD 3.6 69.5 - - + -
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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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89B LEU* 3.0 38.7 + - + +
90B LEU 3.4 1.3 + - - +
92B LEU* 1.3 80.5 - - + +
94B LEU* 1.3 56.3 + - - +
95B ASP 3.4 0.9 - - - -
99B MET* 3.5 27.3 - - + +
101B LEU* 4.2 6.0 - - + +
104B GLN* 2.8 27.9 + - - +
108B ALA* 3.9 25.3 - - + +
111B ILE* 3.8 25.6 - - + -
112B ALA 4.7 3.8 - - - -
115B LEU* 3.6 26.2 - - + -
501B CHD 3.5 28.5 - - + -
502B CHD 3.9 33.7 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.2 41.7 + - + +
91B ARG* 3.7 10.8 - - + +
92B LEU 3.2 0.8 - - - -
93B PHE* 1.3 77.8 - - - +
95B ASP* 1.3 58.0 + - - +
96B ARG* 2.9 23.3 + - - +
104B GLN* 3.6 5.4 - - + +
105B ASN* 3.8 34.1 - - - +
108B ALA* 3.5 21.5 - - + -
109B PRO* 5.0 0.4 - - + -
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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