Contacts of the helix formed by residues 79 - 93 (chain B) in PDB entry 2ODE
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR* 3.8 39.5 + - - -
183A GLY* 4.0 1.1 - - - -
210A LYS* 3.8 0.7 - - - +
74B LEU* 3.1 31.8 + - - +
77B GLU* 4.1 8.2 - - - +
78B PHE* 1.3 79.6 - - - +
80B GLU* 1.3 64.6 + - - +
81B GLU* 3.1 13.2 + - - -
82B ASN* 3.2 19.4 + - - +
158B SER* 4.0 6.2 + - - -
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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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71B ARG* 4.5 4.0 - - + +
74B LEU* 3.8 25.2 + - + +
75B LYS* 3.8 33.9 - - + +
78B PHE* 3.7 12.4 - - - -
79B SER* 1.3 81.8 + - - +
81B GLU* 1.3 68.4 + - - +
82B ASN 3.1 0.4 - - - -
83B LEU* 3.1 6.4 + - + +
84B GLU* 3.0 38.3 + - + +
119B ARG* 6.5 1.3 - - - -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 4.0 8.1 + - - -
207A GLU* 4.5 2.1 - - - +
210A LYS* 2.7 35.1 + - - -
78B PHE 3.8 1.2 - - - +
79B SER* 3.3 15.9 - - - -
80B GLU* 1.3 84.0 + - - +
82B ASN* 1.3 65.2 + - - +
84B GLU* 4.5 5.4 - - - +
85B PHE* 2.8 33.4 + - - +
112B PHE* 4.0 4.2 - - + -
119B ARG* 3.5 45.8 - - + +
120B GLU 3.9 14.3 - - - +
121B VAL* 3.9 9.9 - - + +
122B ASN 5.2 1.0 + - - -
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Residues in contact with ASN 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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182A THR* 3.2 41.4 + - - +
74B LEU* 5.7 0.2 - - - +
79B SER* 3.5 14.7 + - - +
80B GLU 3.1 0.6 - - - -
81B GLU* 1.3 84.5 + - - +
83B LEU* 1.3 57.8 + - - +
85B PHE* 3.8 0.5 - - - +
86B TRP* 3.0 24.3 + - - +
121B VAL* 3.9 17.2 - - - +
122B ASN 4.4 1.9 + - - -
150B VAL* 3.3 33.3 - - + +
153B LEU* 3.9 15.5 - - - +
154B MET* 3.6 19.5 - - + +
158B SER* 5.3 0.2 + - - -
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Residues in contact with LEU 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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61B LEU* 4.0 27.1 - - + -
67B VAL* 3.9 19.7 - - + +
70B PHE* 4.4 13.2 - - + -
71B ARG* 3.6 40.2 - - + +
74B LEU* 3.7 18.1 - - + +
80B GLU* 3.1 7.1 + - - +
82B ASN* 1.3 77.7 - - - +
84B GLU* 1.3 66.7 + - - +
86B TRP* 3.3 4.9 + - + -
87B LEU* 2.9 47.0 + - + +
154B MET* 3.5 9.1 - - + -
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Residues in contact with GLU 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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71B ARG* 2.7 53.8 + - - +
75B LYS* 5.8 0.5 - - - -
80B GLU* 3.0 26.7 + - + +
81B GLU* 4.2 2.9 - - - +
83B LEU* 1.3 81.5 - - - +
85B PHE* 1.3 57.2 + - - +
87B LEU* 3.4 10.1 - - - +
88B ALA* 3.0 29.3 + - - +
112B PHE* 3.9 8.4 - - + -
119B ARG* 3.8 26.9 - - - +
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Residues in contact with PHE 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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81B GLU 2.8 18.7 + - - +
82B ASN 3.8 1.8 - - - +
84B GLU* 1.3 73.7 - - - +
86B TRP* 1.3 67.6 + - - +
88B ALA* 3.2 2.9 + - - +
89B CYS* 2.9 44.7 + - - -
108B ILE* 3.6 16.4 - - + -
112B PHE* 3.5 34.2 - + + -
113B VAL* 3.8 17.3 - - + -
121B VAL* 3.6 17.9 - - + -
143B PHE* 4.2 4.3 - + - -
146B ALA* 3.7 46.0 - - + -
147B GLN* 3.8 7.0 - - - -
150B VAL* 3.8 23.6 - - + -
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Residues in contact with TRP 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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58B ASP* 5.4 0.9 - - - -
61B LEU* 3.9 50.5 - - + -
82B ASN 3.0 19.0 + - - +
83B LEU* 3.3 4.7 + - + +
85B PHE* 1.3 80.9 - - - +
87B LEU* 1.3 86.5 + - + +
89B CYS* 3.3 3.5 + - - -
90B GLU* 3.0 48.3 + - + +
147B GLN* 3.3 44.0 + - + +
150B VAL* 4.9 2.5 - - + -
151B HIS* 3.8 32.7 - + + +
154B MET* 3.7 16.4 - - + -
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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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61B LEU 6.0 0.2 - - - +
67B VAL* 4.0 19.5 - - + -
71B ARG* 3.2 31.4 - - - +
83B LEU* 2.9 35.1 + - + +
84B GLU* 3.4 15.7 - - - +
86B TRP* 1.3 93.0 - - + +
88B ALA* 1.3 57.3 + - - +
90B GLU* 3.2 6.7 + - + +
91B GLU* 3.0 37.7 + - + +
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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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84B GLU 3.0 19.4 + - - +
85B PHE* 3.2 5.6 + - - +
87B LEU* 1.3 75.0 - - - +
89B CYS* 1.3 57.3 + - - +
91B GLU* 3.3 8.2 + - - +
92B PHE* 2.8 29.1 + - - +
104B LYS* 5.3 0.9 - - - +
108B ILE* 3.6 21.5 - - + +
112B PHE* 4.1 20.4 - - + -
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Residues in contact with CYS 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 PHE* 2.9 54.4 + - - -
86B TRP 3.6 3.8 - - - +
88B ALA* 1.3 74.0 - - - +
90B GLU* 1.3 64.7 + - - +
92B PHE* 3.3 10.6 + - + +
93B LYS* 3.1 30.1 + - - +
108B ILE* 4.6 2.7 - - - -
143B PHE* 3.6 24.7 - - + -
147B GLN* 3.5 27.4 - - + +
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Residues in contact with GLU 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 TRP* 3.0 52.1 + - + +
87B LEU* 3.2 11.4 + - + +
89B CYS* 1.3 76.5 - - - +
91B GLU* 1.3 64.4 + - + +
93B LYS* 2.6 45.6 + - - +
94B LYS* 3.5 23.9 - - - +
147B GLN* 2.7 13.4 + - - +
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Residues in contact with GLU 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 LEU* 3.0 21.7 + - + +
88B ALA* 3.5 10.1 - - - +
90B GLU* 1.3 74.3 - - + +
92B PHE* 1.3 66.5 + - - +
94B LYS* 3.0 32.5 + - - +
95B THR* 3.7 5.4 + - - -
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Residues in contact with PHE 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 ALA 2.8 20.7 + - - +
89B CYS* 3.3 8.5 + - + +
91B GLU* 1.3 73.2 - - - +
93B LYS* 1.3 59.0 + - + +
94B LYS 3.1 0.2 - - - -
95B THR* 2.8 32.7 + - - -
101B LEU* 3.4 44.0 - - + -
104B LYS* 3.9 23.9 - - + +
105B ALA* 3.7 17.0 - - + -
108B ILE* 3.7 14.8 - - + -
139B SER 3.3 27.8 - - - -
140B LEU* 3.6 25.3 - - - +
142B CYS* 4.1 3.4 - - + -
143B PHE* 3.8 24.0 - + + -
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Residues in contact with LYS 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 CYS* 3.1 17.7 + - - +
90B GLU* 2.6 41.1 + - - +
91B GLU 3.2 0.8 - - - -
92B PHE* 1.3 77.4 - - + +
94B LYS* 1.3 59.0 + - + +
95B THR 3.3 0.9 + - - +
140B LEU* 3.6 44.6 - - + +
144B ASP* 4.1 15.4 + - - +
147B GLN* 3.1 22.3 + - - -
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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