Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 1JPM
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 GLY 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLY 3.8 5.8 - - - -
125A GLY 4.1 9.9 - - - -
78B SER* 3.1 13.0 + - - +
80B ALA* 1.3 78.5 - - - +
82B TYR* 1.3 62.2 + - - -
83B GLU 3.4 2.5 - - - -
84B ALA* 3.5 10.8 + - - +
85B ILE* 3.3 23.6 + - - +
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Residues in contact with TYR 82 (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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121A GLN 5.4 2.2 - - - +
124A GLY* 3.4 13.0 + - - +
79B LEU* 3.7 43.0 + - + +
80B ALA 3.4 3.0 - - - -
81B GLY* 1.3 72.6 - - - +
83B GLU* 1.3 67.5 + - - +
85B ILE* 3.0 9.4 + - + +
86B LEU* 2.9 56.9 + - + +
107B LEU* 3.1 12.3 + - + +
108B TYR* 3.1 64.8 + + - -
111B TRP* 3.7 42.4 - + + +
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Residues in contact with GLU 83 (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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123A LEU 4.8 0.2 - - - +
124A GLY* 2.9 26.1 + - - +
126A TYR* 3.8 20.9 - - + -
282A ASN* 5.3 0.5 - - - +
286A GLU* 4.6 10.9 - - - +
313A SER 3.6 18.6 - - - +
314A LYS* 3.6 19.9 + - - +
315A ARG* 3.0 29.7 + - + +
316A ASN 4.6 1.2 + - - -
82B TYR* 1.3 75.7 - - - +
84B ALA* 1.3 57.4 + - - +
86B LEU* 3.9 10.8 - - - +
87B HIS* 3.1 28.5 + - - +
280B LYS* 6.0 0.3 + - - -
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Residues in contact with ALA 84 (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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126A TYR* 4.1 27.2 - - + +
81B GLY* 3.5 11.5 + - - +
82B TYR 3.2 0.4 - - - -
83B GLU* 1.3 76.4 - - - +
85B ILE* 1.3 66.6 + - + +
87B HIS* 3.8 5.2 - - - +
88B ASP* 3.1 33.9 + - - +
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Residues in contact with ILE 85 (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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3B ILE* 4.7 4.3 - - + -
74B LEU* 3.5 25.1 - - + -
77B LYS* 4.0 29.2 - - + -
78B SER 3.4 29.8 - - - +
79B LEU* 4.3 17.3 - - + -
81B GLY 3.3 10.7 + - - +
82B TYR* 3.0 13.7 + - + +
84B ALA* 1.3 79.2 - - + +
86B LEU* 1.3 63.5 + - + +
88B ASP* 3.2 8.3 + - - +
89B ILE* 3.0 33.3 + - + +
107B LEU* 3.9 12.1 - - + -
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Residues in contact with LEU 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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82B TYR* 2.9 52.4 + - + +
83B GLU* 3.9 10.3 - - - +
85B ILE* 1.3 77.3 - - + +
87B HIS* 1.3 63.1 + - - +
89B ILE* 3.3 10.0 + - + +
90B GLN* 3.0 30.7 + - + +
104B GLU* 3.5 34.8 - - + +
107B LEU* 5.1 3.6 - - + -
108B TYR* 3.6 10.3 - - + +
276B SER* 3.6 25.4 - - - +
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Residues in contact with HIS 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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126A TYR* 5.9 0.2 - - + -
286A GLU* 5.1 7.0 - - - -
315A ARG* 3.3 58.1 + - - -
83B GLU* 3.1 18.9 + - + +
84B ALA* 3.8 5.8 - - - +
85B ILE 3.3 0.2 - - - -
86B LEU* 1.3 76.2 - - - +
88B ASP* 1.3 65.8 + - - +
90B GLN* 4.8 1.1 - - - -
91B HIS* 2.9 78.8 + + + +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ALA* 5.3 7.9 - - + +
74B LEU* 5.5 3.8 - - + -
77B LYS* 5.4 8.3 - - - -
84B ALA* 3.1 26.1 + - - +
85B ILE* 3.6 7.2 - - - +
87B HIS* 1.3 80.8 + - - +
89B ILE* 1.3 65.5 + - + +
91B HIS* 4.5 0.9 - - - +
92B LEU* 2.9 54.7 + - + +
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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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70B LEU* 3.7 25.4 - - + +
74B LEU* 4.0 16.6 - - + -
85B ILE* 3.0 25.7 + - + +
86B LEU* 3.3 11.4 + - + +
88B ASP* 1.3 77.5 - - - +
90B GLN* 1.3 79.2 + - - +
93B LEU* 3.8 3.3 - - - +
100B LYS* 3.4 40.0 - - + +
103B VAL* 3.8 9.9 - - + -
104B GLU* 4.6 8.7 - - + -
107B LEU* 3.1 36.1 - - + -
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Residues in contact with GLN 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 LEU* 3.0 19.0 + - + +
87B HIS* 4.8 0.4 - - - -
89B ILE* 1.3 93.7 - - - +
91B HIS* 1.3 77.6 + - + +
92B LEU 3.8 0.2 - - - -
93B LEU 3.5 2.6 - - - +
97B MET* 4.2 8.1 - - - +
100B LYS* 3.1 36.0 + - - +
104B GLU* 3.0 18.9 + - - +
272B ALA 4.0 12.7 - - - +
273B GLY 3.0 25.8 + - - +
276B SER* 4.4 6.0 + - - +
277B GLY* 6.1 0.9 - - - -
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Residues in contact with HIS 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 HIS* 2.9 67.7 + + + +
88B ASP* 5.2 0.9 - - - -
90B GLN* 1.3 93.9 + - + +
92B LEU* 1.3 64.7 + - - +
93B LEU* 3.1 6.4 + - - -
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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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69B VAL* 3.6 30.0 - - + +
70B LEU* 4.9 5.2 - - + -
73B ALA* 3.3 35.0 - - + -
88B ASP* 2.9 42.8 + - + +
89B ILE 4.3 0.4 + - - -
90B GLN 3.8 0.6 - - - -
91B HIS* 1.3 78.8 - - - +
93B LEU* 1.3 62.4 + - + +
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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