Contacts of the helix formed by residues 80 - 91 (chain B) in PDB entry 2O38
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 SER 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B GLU* 5.5 2.2 - - - -
36B LYS* 4.3 2.9 - - - +
78B GLY 4.2 1.2 + - - -
79B PHE* 1.3 74.1 - - - +
81B VAL* 1.3 66.1 + - - +
82B GLU* 3.4 19.0 - - - +
83B ARG* 2.9 32.2 + - - +
84B LEU* 2.9 26.0 + - - +
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Residues in contact with VAL 81 (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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81A VAL* 4.7 3.6 - - + -
82A GLU* 3.8 34.8 - - + +
85A MSE 3.9 25.6 - - + -
32B GLU* 4.5 9.5 + - + +
35B THR* 4.2 9.4 - - + -
36B LYS* 3.9 24.1 - - + +
39B LEU* 3.6 22.1 - - + +
79B PHE 4.0 0.4 + - - -
80B SER* 1.3 70.7 - - - +
82B GLU* 1.3 66.1 + - + +
84B LEU* 3.2 8.1 + - - +
85B MSE 3.0 31.8 + - + +
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Residues in contact with GLU 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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32A GLU* 2.7 46.1 - - + +
36A LYS* 4.2 3.2 - - - -
80A SER* 3.4 15.6 - - - -
81A VAL* 2.9 44.3 + - + +
82A GLU 5.6 0.2 - - - +
111A ILE* 5.2 2.2 - - - +
80B SER* 3.4 20.0 - - - +
81B VAL* 1.3 76.2 - - + +
83B ARG* 1.3 54.3 + - - +
85B MSE 3.2 15.4 + - - +
86B THR* 3.0 30.8 + - - -
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Residues in contact with ARG 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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28A PRO* 5.0 4.4 - - - +
61B LEU 4.0 7.1 + - - -
62B GLY 4.4 4.0 + - - -
63B ILE* 3.4 27.3 - - - +
79B PHE* 4.2 13.5 - - + -
80B SER* 2.9 31.3 + - - +
82B GLU* 1.3 69.2 - - - +
84B LEU* 1.3 60.3 + - - +
86B THR* 3.1 35.9 + - - +
87B LEU* 2.9 64.3 + - + +
90B ALA* 6.0 0.8 - - - +
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Residues in contact with LEU 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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36B LYS* 3.7 46.9 - - + +
39B LEU* 4.0 18.6 - - + +
40B ALA* 4.7 10.5 - - + -
43B LEU* 4.3 10.3 - - + +
71B LEU* 3.6 31.0 - - + -
76B LEU* 4.9 3.1 - - + -
79B PHE* 3.9 20.9 - - + -
80B SER 2.9 23.4 + - - +
81B VAL* 3.6 7.2 - - - +
83B ARG* 1.3 71.4 - - - +
85B MSE 1.3 57.4 + - - +
87B LEU* 3.3 5.8 + - + +
88B LEU* 2.9 35.3 + - - +
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Residues in contact with MSE 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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35A THR* 5.0 2.2 - - - -
81A VAL* 4.4 17.0 - - - -
85A MSE 5.0 2.0 - - - -
97A ILE* 3.7 27.1 - - + -
111A ILE* 3.8 24.7 - - + -
39B LEU* 4.2 10.8 - - + -
81B VAL* 3.0 22.5 + - + +
82B GLU* 3.2 10.3 + - - +
84B LEU* 1.3 76.3 - - - +
86B THR* 1.3 60.7 + - - +
88B LEU* 3.3 9.8 + - - +
89B ASN* 3.0 26.0 + - - +
95B VAL* 3.4 32.3 - - + +
97B ILE* 3.7 27.8 - - + -
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Residues in contact with THR 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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28A PRO* 3.6 39.5 + - + +
31A GLU* 5.8 1.9 - - - +
32A GLU* 5.4 3.8 - - - +
111A ILE* 4.6 5.1 - - - +
82B GLU 3.0 17.4 + - - -
83B ARG* 3.1 35.7 + - - +
85B MSE 1.3 75.0 - - - +
87B LEU* 1.3 57.9 + - - +
89B ASN* 3.2 14.6 + - + +
90B ALA* 3.0 25.8 + - + +
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Residues in contact with LEU 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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43B LEU* 3.7 26.0 - - + -
61B LEU* 3.3 34.9 - - + +
63B ILE* 3.9 13.2 - - + -
71B LEU* 4.4 6.3 - - + -
79B PHE* 3.9 30.3 - - + -
83B ARG* 2.9 60.7 + - + +
84B LEU* 3.7 6.7 - - + +
86B THR* 1.3 73.2 - - - +
88B LEU* 1.3 67.1 + - - +
90B ALA* 3.2 3.8 + - + -
91B LEU* 3.1 19.2 + - - +
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Residues in contact with LEU 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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99A ILE* 3.8 45.3 - - + -
39B LEU* 3.9 23.8 - - + +
42B ALA 4.0 4.5 - - - +
43B LEU* 3.7 40.2 - - + +
46B VAL* 4.3 1.1 - - + -
84B LEU 2.9 17.9 + - - +
85B MSE 3.5 9.9 - - - +
86B THR 3.3 0.2 - - - -
87B LEU* 1.3 77.0 - - - +
89B ASN* 1.3 62.2 - - - +
91B LEU* 3.0 9.9 + - - -
92B ASP 3.3 0.3 + - - -
93B GLN* 3.0 37.6 + - + +
95B VAL* 4.1 13.5 - - + -
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Residues in contact with ASN 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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31A GLU* 4.0 13.7 + - - +
109A ALA* 3.6 15.3 + - + +
110A ARG* 3.5 22.7 + - - +
111A ILE* 3.2 35.9 - - - +
85B MSE 3.0 14.7 + - - +
86B THR* 3.2 12.7 + - + +
88B LEU* 1.3 76.3 - - - +
90B ALA* 1.3 56.9 + - - +
92B ASP* 2.9 22.5 + - - +
93B GLN 2.9 25.8 - - - +
95B VAL* 3.8 6.6 - - - +
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Residues in contact with ALA 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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60B ARG* 4.1 17.3 - - - +
61B LEU* 3.9 28.0 - - + +
83B ARG* 6.0 0.4 - - - +
86B THR* 3.0 14.0 + - + +
87B LEU* 3.2 13.0 + - + +
89B ASN* 1.3 75.0 - - - +
91B LEU* 1.3 62.2 + - - +
92B ASP* 3.2 8.8 + - - +
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Residues in contact with LEU 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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43B LEU* 3.6 18.6 - - + +
46B VAL* 3.8 23.2 - - + +
47B ILE* 3.5 33.2 - - + +
52B LEU* 4.5 11.9 - - + -
57B ALA* 5.4 0.7 - - - +
60B ARG* 3.5 30.1 - - + +
61B LEU* 3.4 30.1 - - + -
87B LEU 3.1 5.1 + - - +
88B LEU 3.0 9.2 + - - +
90B ALA* 1.3 75.1 - - - +
92B ASP* 1.3 66.4 + - - +
93B GLN* 2.9 22.9 + - + -
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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