Contacts of the helix formed by residues 79 - 96 (chain B) in PDB entry 1O94
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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708A ARG* 2.9 35.6 + - - -
77B ILE 3.5 1.0 - - - -
78B TRP* 1.3 79.7 - - + +
80B GLU* 1.3 65.3 + - - +
81B GLY* 3.0 14.9 + - - -
82B ASP* 3.1 18.7 + - - +
83B VAL* 3.2 13.0 + - - +
157B ARG* 3.8 13.3 - - - +
717B HIS* 3.9 4.4 + - - -
718B MET* 5.3 20.6 - - + +
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Residues in contact with GLU 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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79B ASP* 1.3 73.7 - - - +
81B GLY* 1.3 64.8 + - - +
82B ASP 3.2 0.2 - - - -
83B VAL* 3.5 14.0 - - + +
84B ARG* 3.0 23.4 + - - +
157B ARG* 5.8 3.1 - - + -
718B MET* 5.8 4.1 - - - -
719B PRO* 4.3 20.1 - - + +
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Residues in contact with GLY 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* 3.0 9.0 + - - -
80B GLU* 1.3 79.0 - - - +
82B ASP* 1.3 62.2 + - - +
84B ARG* 3.3 29.2 + - - +
85B ASN* 3.2 21.0 + - - +
717B HIS* 3.6 21.8 - - - -
718B MET* 4.9 0.8 - - - +
719B PRO* 3.9 8.3 - - - +
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Residues in contact with ASP 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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708A ARG* 2.8 44.7 + - - -
35B SER* 3.5 15.3 - - - +
76B ARG 3.2 24.7 - - - +
77B ILE* 3.8 7.4 - - + -
78B TRP* 2.9 21.5 + - - +
79B ASP* 3.1 9.8 + - - +
81B GLY* 1.3 75.2 - - - +
83B VAL* 1.3 65.5 + - - +
85B ASN* 4.0 4.7 - - - +
86B LEU* 2.9 30.8 + - - +
717B HIS* 3.9 5.0 + - - -
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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
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77B ILE* 4.5 5.2 - - + -
79B ASP 3.2 12.4 + - - +
80B GLU* 3.3 17.9 + - + +
82B ASP* 1.3 79.3 - - - +
84B ARG* 1.3 57.3 + - - +
87B LYS* 2.9 34.9 + - + +
157B ARG* 3.7 39.9 - - + +
160B ASP* 3.9 14.8 - - + +
161B ALA* 3.8 30.0 - - - +
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Residues in contact with ARG 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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712A ALA* 3.5 23.5 - - - +
713A TRP* 3.7 33.0 - - + +
80B GLU 3.0 15.5 + - - +
81B GLY* 3.3 14.8 + - - +
83B VAL* 1.3 79.6 - - - +
85B ASN* 1.3 78.7 + - - +
87B LYS* 3.5 6.9 + - - +
88B ALA 3.4 13.9 + - - -
716B PRO 4.4 1.4 + - - -
717B HIS* 2.7 53.1 + - - -
719B PRO* 3.8 23.9 - - + +
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Residues in contact with ASN 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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711A ILE* 2.9 24.8 + - - +
713A TRP* 3.0 20.1 + - - -
35B SER* 2.9 32.2 + - - +
38B PRO* 3.7 26.9 - - + +
41B GLN* 5.8 1.6 - - - +
81B GLY 3.2 13.2 + - - +
82B ASP* 4.0 5.2 - - - +
84B ARG* 1.3 102.0 + - - +
86B LEU* 1.3 62.1 + - - +
88B ALA* 3.3 19.1 + - - +
89B MET* 4.1 1.9 + - - +
717B HIS* 4.1 5.9 + - - -
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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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34B GLY 4.3 14.1 - - - +
35B SER* 3.5 19.3 - - - +
41B GLN* 4.7 9.9 - - + +
58B THR* 4.2 20.2 - - + -
61B CYS* 4.1 16.6 - - - -
75B ALA* 4.8 3.6 - - + -
76B ARG 3.6 21.8 - - - +
77B ILE* 4.1 18.8 - - + -
82B ASP 2.9 17.1 + - - +
83B VAL 4.2 1.3 - - - +
85B ASN* 1.3 72.2 - - - +
87B LYS* 1.3 61.2 + - - +
88B ALA 3.0 2.0 - - - -
89B MET* 2.9 24.1 + - + +
90B THR* 3.2 14.7 + - - +
102B VAL* 5.0 0.2 - - + -
161B ALA* 4.5 2.2 - - + -
163B PHE* 4.0 20.4 - - + -
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Residues in contact with LYS 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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83B VAL* 2.9 22.6 + - + +
84B ARG* 3.8 7.4 - - - +
85B ASN 3.4 0.2 - - - -
86B LEU* 1.3 73.4 - - - +
88B ALA* 1.3 65.4 + - - +
89B MET 3.1 0.2 - - - -
90B THR* 3.6 1.1 - - - +
91B ASP* 2.8 61.5 + - - +
160B ASP 4.0 19.5 - - - +
161B ALA* 3.4 24.6 + - - +
162B GLY* 5.2 4.5 - - - +
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Residues in contact with ALA 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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713A TRP* 3.3 50.2 - - + +
38B PRO 4.6 2.2 - - - +
42B SER* 3.6 11.6 - - - -
84B ARG 3.4 4.2 + - - -
85B ASN 3.3 14.4 + - - +
86B LEU 3.0 1.0 - - - -
87B LYS* 1.3 78.2 - - - +
89B MET* 1.3 63.6 + - - +
91B ASP* 4.0 5.1 - - - +
92B GLU* 3.2 24.4 + - - +
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Residues in contact with MET 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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38B PRO 5.3 0.4 + - - +
41B GLN* 3.7 40.6 - - + +
42B SER* 3.6 16.9 - - - +
45B ARG* 3.8 17.0 - - + -
56B LEU 5.0 2.2 - - - +
57B ASN 4.9 0.9 - - - -
58B THR* 3.5 37.9 - - + +
85B ASN 4.1 1.0 + - - +
86B LEU* 2.9 11.3 + - + +
88B ALA* 1.3 79.3 - - - +
90B THR* 1.3 68.2 + - - +
92B GLU* 3.3 1.2 + - - +
93B VAL* 2.9 38.0 + - - +
100B ALA* 4.3 7.0 - - + -
101B GLY 4.5 0.9 - - - +
163B PHE* 3.6 18.8 - - + -
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Residues in contact with THR 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 3.2 5.0 + - - +
87B LYS* 3.4 8.7 + - - +
89B MET* 1.3 76.2 - - - +
91B ASP* 1.3 67.1 + - - +
93B VAL* 3.4 0.3 + - - +
94B HIS* 2.9 34.0 + - - -
100B ALA* 3.9 16.6 - - + -
161B ALA 2.5 29.3 + - - +
162B GLY* 3.6 19.5 - - - -
163B PHE* 3.5 44.0 - - + -
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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 LYS* 2.8 58.7 + - - +
88B ALA* 4.0 5.4 - - - +
90B THR* 1.3 82.7 + - - +
92B GLU* 1.3 65.8 + - - +
94B HIS* 3.4 10.9 + - - +
95B LYS* 3.2 20.8 + - - +
162B GLY* 5.9 0.5 - - - -
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Residues in contact with GLU 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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725A ILE* 3.9 24.8 - - + +
42B SER* 4.3 8.1 - - - +
46B SER* 3.4 28.0 - - - +
88B ALA 3.2 17.4 + - - +
89B MET 3.9 2.5 - - - +
90B THR 3.2 0.2 - - - -
91B ASP* 1.3 84.2 - - - +
93B VAL* 1.3 61.7 + - - +
95B LYS* 3.3 23.5 + - - +
96B TYR* 3.4 27.0 + - + -
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Residues in contact with VAL 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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45B ARG* 3.8 31.4 - - + +
46B SER* 4.1 2.7 - - - +
49B ALA* 3.8 9.2 - - + +
56B LEU* 4.0 8.5 - - + -
89B MET* 2.9 37.3 + - + +
90B THR* 3.8 5.4 - - - +
92B GLU* 1.3 76.0 - - - +
94B HIS* 1.3 56.3 + - + +
96B TYR* 3.0 18.7 + - - -
97B GLY 3.6 0.2 + - - -
98B ALA* 3.5 29.7 + - + +
99B LEU 3.5 29.4 - - - +
100B ALA* 4.2 4.0 - - + -
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Residues in contact with HIS 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 THR* 2.9 27.4 + - - +
91B ASP* 3.7 11.6 + - - +
92B GLU 3.3 0.2 - - - -
93B VAL* 1.3 74.0 - - + +
95B LYS* 1.3 65.1 + - - +
97B GLY* 3.0 14.1 + - - -
98B ALA 3.4 21.5 - - - -
99B LEU* 5.8 0.4 - - + -
100B ALA* 4.3 6.5 + - + +
162B GLY* 3.1 27.0 + - - -
164B ASP* 2.6 30.1 + - - -
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Residues in contact with LYS 95 (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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91B ASP 3.2 12.4 + - - +
92B GLU* 3.4 17.3 - - - +
93B VAL 3.2 0.4 - - - -
94B HIS* 1.3 77.2 - - - +
96B TYR* 1.4 83.9 + - + +
97B GLY 3.3 1.0 + - - -
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Residues in contact with TYR 96 (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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727A TYR* 5.8 3.6 - - - -
21B ARG* 2.7 29.8 + - - -
46B SER* 3.8 27.6 - - - -
49B ALA* 3.6 20.3 - - + +
50B GLU* 3.6 45.2 + - + +
92B GLU* 3.4 29.4 + - + -
93B VAL 3.0 3.8 + - - -
95B LYS* 1.4 91.9 - - + +
97B GLY* 1.3 51.0 + - - +
98B ALA 3.4 1.7 + - - -
382B LYS* 5.7 1.0 + - - -
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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