Contacts of the helix formed by residues 79 - 92 (chain B) in PDB entry 1O90
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 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B ILE* 1.3 73.4 - - - +
80B TYR* 1.3 57.8 + - - +
81B GLN* 3.2 16.0 + - - +
82B ARG* 2.9 76.5 + - + +
83B VAL* 3.0 14.8 + - - +
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Residues in contact with TYR 80 (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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42B VAL* 3.6 27.6 - - + -
46B HIS* 3.0 8.3 + - - -
68B LEU* 3.7 20.6 - - + -
72B ILE* 3.0 21.8 - - + +
78B ILE* 3.4 23.8 + - + -
79B ASP* 1.3 72.8 + - - +
81B GLN* 1.3 62.8 + - + +
83B VAL* 3.7 6.7 - - + -
84B VAL* 3.0 31.7 + - - +
109B VAL* 4.0 30.5 - - + -
111B LEU* 3.6 16.3 - - + +
113B GLN* 2.6 33.3 + - + -
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Residues in contact with GLN 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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79B ASP* 3.1 12.2 + - - +
80B TYR* 1.3 76.3 - - - +
82B ARG* 1.3 59.0 + - - +
84B VAL* 4.0 0.3 - - - +
85B ARG* 2.8 82.2 + - - +
107B VAL* 3.0 35.6 + - - +
109B VAL* 4.2 9.1 - - + +
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Residues in contact with ARG 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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77B MET 5.4 4.0 + - - -
79B ASP* 2.9 53.9 + - - +
81B GLN* 1.3 79.7 - - - +
83B VAL* 1.3 58.5 + - + +
85B ARG* 4.9 2.7 - - - +
86B ASP* 2.9 55.5 + - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 5.3 0.6 - - - +
41B ALA* 4.2 9.3 - - + +
42B VAL* 3.9 29.2 - - + +
45B ALA* 4.0 18.2 - - + -
78B ILE* 3.8 18.4 - - + -
79B ASP 3.0 13.1 + - - +
80B TYR* 3.3 23.3 - - + +
82B ARG* 1.3 81.0 - - + +
84B VAL* 1.3 59.5 + - + +
86B ASP* 4.3 4.3 - - - +
87B THR* 2.6 32.1 + - - -
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Residues in contact with VAL 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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38B ILE* 3.8 27.3 - - + +
66B VAL* 3.8 26.9 - - + -
68B LEU* 4.0 22.9 - - + -
80B TYR 3.0 20.9 + - - +
81B GLN 4.0 0.2 - - - +
83B VAL* 1.3 79.8 - - + +
85B ARG* 1.3 64.4 + - - +
87B THR* 3.3 4.6 + - - -
88B ILE* 3.1 39.6 + - + +
107B VAL* 3.9 25.4 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLN* 2.8 50.8 + - - +
82B ARG* 4.3 2.7 - - - +
84B VAL* 1.3 71.9 - - - +
86B ASP* 1.3 63.2 + - - +
88B ILE* 3.2 4.0 + - - -
89B LYS* 2.9 25.6 + - - +
102B PHE* 2.8 63.0 + - + +
103B LYS* 4.1 11.6 + - - +
104B THR 4.5 0.2 - - - -
105B CYS* 3.0 32.5 + - - -
106B ASN* 4.8 0.2 - - - +
107B VAL* 3.5 22.4 - - + +
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Residues in contact with ASP 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 ARG* 2.9 43.0 + - - +
83B VAL* 4.3 5.0 - - - +
85B ARG* 1.3 79.1 - - - +
87B THR* 1.3 58.1 + - - +
89B LYS* 3.3 15.6 + - - +
90B HIS* 2.9 28.6 + - - +
102B PHE* 5.5 2.4 - - - -
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Residues in contact with THR 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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37B GLN* 4.1 11.2 - - + -
38B ILE* 3.9 34.5 - - + +
41B ALA* 3.2 15.4 - - - +
83B VAL 2.6 23.6 + - - -
84B VAL 3.3 5.3 + - - -
85B ARG 3.2 0.6 - - - -
86B ASP* 1.3 76.5 - - - +
88B ILE* 1.3 64.0 + - - +
90B HIS* 3.5 6.7 + - - +
91B ILE* 3.1 33.5 + - + +
373B GLN* 3.8 21.3 + - - +
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Residues in contact with ILE 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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34B ILE* 4.9 6.1 - - + -
38B ILE* 4.2 12.8 - - + -
66B VAL* 4.0 13.9 - - + -
84B VAL* 3.1 32.4 + - + +
85B ARG* 3.7 8.3 - - - +
87B THR* 1.3 73.9 - - - +
89B LYS* 1.3 64.6 + - - +
91B ILE* 3.4 10.1 + - + +
92B GLY 3.3 4.5 + - - -
93B TYR* 3.1 51.4 + - + +
100B PHE* 4.0 17.7 - - + -
102B PHE* 3.9 7.4 - - + +
105B CYS* 3.6 27.8 - - - -
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Residues in contact with LYS 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 ARG 2.9 16.7 + - - +
86B ASP* 3.5 15.1 + - - +
88B ILE* 1.3 75.3 - - - +
90B HIS* 1.3 61.8 + - - +
92B GLY* 2.8 21.7 + - - -
93B TYR 4.0 2.4 + - - -
94B ASP* 5.3 5.0 - - + +
102B PHE* 3.7 47.2 - - + +
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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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28B GLU* 4.4 8.0 + - - -
37B GLN* 4.5 12.9 + - - -
86B ASP 2.9 16.7 + - - +
87B THR* 3.6 8.1 - - - +
89B LYS* 1.3 78.1 - - - +
91B ILE* 1.3 57.9 + - + +
92B GLY 3.2 0.7 + - - -
169B ARG* 4.0 0.5 + - - -
170B ARG* 2.6 52.7 + - - -
373B GLN* 4.3 20.4 + - - +
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Residues in contact with ILE 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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28B GLU* 3.2 40.1 - - + +
34B ILE* 3.8 27.6 - - + -
37B GLN* 3.6 26.7 - - - +
87B THR* 3.1 25.0 + - + +
88B ILE* 3.6 10.1 - - - +
89B LYS 3.2 0.2 - - - -
90B HIS* 1.3 77.8 - - + +
92B GLY* 1.3 55.1 + - - +
93B TYR* 3.5 23.3 - - + -
169B ARG* 2.6 27.9 + - - -
170B ARG* 3.9 5.8 - - - +
179B PRO* 3.4 7.0 - - + +
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Residues in contact with GLY 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 ILE 3.3 0.2 + - - -
89B LYS 2.8 13.5 + - - -
90B HIS 3.1 1.3 - - - -
91B ILE* 1.3 80.9 - - - +
93B TYR* 1.3 60.5 + - - +
94B ASP* 3.4 13.7 + - - +
98B LYS* 3.6 24.1 + - - +
169B ARG* 4.2 8.3 - - - -
179B PRO* 3.8 13.7 - - - +
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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