Contacts of the helix formed by residues 79 - 93 (chain B) in PDB entry 2WOE
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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71B SER* 4.7 0.9 + - - +
75B LYS* 3.9 33.5 + - + +
77B THR* 3.5 5.5 + - + -
78B LEU* 1.3 76.3 - - - +
80B VAL* 1.3 64.4 + - - +
81B ALA* 3.6 9.4 + - - +
82B ASP* 3.1 28.8 + - + +
83B ILE* 3.0 26.6 + - - +
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Residues in contact with VAL 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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78B LEU* 3.9 19.0 - - + -
79B ASP* 1.3 71.2 + - - +
81B ALA* 1.3 56.6 + - - +
83B ILE* 3.3 7.9 + - + +
84B CYS* 2.9 27.4 + - - -
115B THR* 3.7 37.2 - - - +
152B ALA* 3.8 31.4 - - + +
156B ILE* 3.8 16.6 - - + -
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Residues in contact with ALA 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* 3.3 7.7 + - - +
80B VAL* 1.3 78.3 - - - +
82B ASP* 1.3 57.4 + - - +
84B CYS* 3.4 5.0 + - - +
85B GLU* 3.0 31.8 + - + +
109B TYR* 3.9 6.2 + - + +
115B THR* 4.1 20.0 - - + +
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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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71B SER* 2.6 33.2 + - - +
74B ALA* 5.2 2.4 - - - +
75B LYS* 3.4 28.0 + - - +
79B ASP* 3.1 27.0 + - + +
81B ALA* 1.3 74.9 - - - +
83B ILE* 1.3 61.5 + - - +
85B GLU* 3.2 12.9 + - - +
86B GLU* 2.9 38.4 + - - +
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Residues in contact with ILE 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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67B ALA 5.5 0.2 - - - +
68B LEU* 3.5 30.1 - - + -
71B SER* 3.4 25.4 - - - +
72B LEU* 4.7 5.2 - - + -
78B LEU* 3.6 28.7 - - + -
79B ASP 3.0 21.6 + - - +
80B VAL* 3.6 9.6 - - + +
82B ASP* 1.3 75.8 - - - +
84B CYS* 1.3 56.9 - - - +
86B GLU* 3.2 3.6 + - - +
87B PHE* 2.9 52.5 + - + -
153B GLN* 4.8 5.2 - - + -
156B ILE* 3.4 20.6 - - + -
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Residues in contact with CYS 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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80B VAL 2.9 21.4 + - - +
81B ALA 3.4 9.0 - - - +
83B ILE* 1.3 76.1 - - - +
85B GLU* 1.3 57.3 + - - +
87B PHE* 3.3 8.1 + - - +
88B ALA* 2.9 29.8 + - - +
106B ILE* 5.2 0.3 - - - +
109B TYR* 3.5 42.1 - - + -
115B THR* 3.9 17.7 - - - -
156B ILE* 3.8 34.3 - - - -
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Residues in contact with GLU 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 ALA* 3.0 15.5 + - + +
82B ASP* 3.2 16.8 + - - +
84B CYS* 1.3 75.0 - - - +
86B GLU* 1.3 58.2 + - + +
88B ALA* 3.3 8.3 + - - +
89B LEU* 2.9 43.9 + - + +
92B LYS* 5.5 3.8 + - - -
109B TYR* 2.4 31.2 + - - +
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Residues in contact with GLU 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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67B ALA* 3.7 30.9 - - + +
70B ARG* 3.5 35.3 + - - +
71B SER* 4.1 12.4 + - - +
82B ASP* 2.9 27.3 + - - +
83B ILE* 3.2 8.0 + - - +
85B GLU* 1.3 78.5 - - - +
87B PHE* 1.3 57.6 + - - +
89B LEU* 3.4 22.4 + - - +
90B TRP* 2.9 29.2 + - - +
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Residues in contact with PHE 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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64B MET* 3.7 39.9 - - + -
67B ALA* 3.9 14.4 - - + -
68B LEU* 4.0 8.1 - - + -
83B ILE* 2.9 38.3 + - + +
84B CYS* 3.6 8.3 - - - +
86B GLU* 1.3 73.3 - - + +
88B ALA* 1.3 60.1 + - - +
90B TRP* 3.4 10.7 + + - +
91B LEU* 2.9 29.5 + - - +
106B ILE* 3.8 21.0 - - + +
131B ARG* 3.6 44.2 - - - -
153B GLN* 4.4 4.5 - - - -
156B ILE* 3.9 26.2 - - + -
157B THR* 4.7 0.7 - - + -
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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 CYS 2.9 18.1 + - - +
85B GLU* 3.5 12.3 - - - +
87B PHE* 1.3 72.6 - - - +
89B LEU* 1.3 60.3 + - - +
91B LEU* 3.3 2.8 + - - +
92B LYS* 2.9 45.7 + - - +
106B ILE* 3.7 13.8 - - + +
109B TYR* 4.4 6.5 - - + -
110B MET* 4.0 25.9 - - + +
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Residues in contact with LEU 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 GLU* 2.9 30.6 + - + +
86B GLU* 3.7 26.0 - - - +
88B ALA* 1.3 75.4 - - + +
90B TRP* 1.3 64.7 + - - +
92B LYS* 3.3 17.0 + - + +
93B SER* 3.0 22.0 + - - -
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Residues in contact with TRP 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 ASP* 3.7 23.8 - - + -
63B GLU* 3.0 41.6 + - + +
64B MET* 3.6 45.1 - - + -
67B ALA* 4.8 8.1 - - + -
70B ARG* 5.7 3.6 - - - +
86B GLU 2.9 18.1 + - - +
87B PHE* 3.5 12.8 - + - +
88B ALA 3.3 0.2 - - - -
89B LEU* 1.3 76.8 - - - +
91B LEU* 1.3 74.2 + - + +
93B SER* 2.5 32.0 + - - -
95B PRO* 3.5 27.8 - - + +
97B ASN 3.8 0.2 - - - -
98B VAL* 3.8 29.8 - - + -
106B ILE* 3.9 14.1 - - + -
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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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87B PHE 2.9 19.5 + - - +
88B ALA 3.6 4.5 - - - +
90B TRP* 1.3 80.2 - - + +
92B LYS* 1.3 58.4 + - + +
94B ARG* 3.1 19.9 + - - +
95B PRO* 3.4 9.4 - - + +
98B VAL* 4.0 37.5 - - + -
103B ARG* 4.2 19.5 - - + +
106B ILE* 3.6 30.5 - - + -
107B ARG* 3.9 25.1 - - + -
110B MET* 4.5 7.9 - - - -
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Residues in contact with LYS 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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85B GLU* 5.5 3.8 + - - -
88B ALA* 2.9 36.8 + - - +
89B LEU* 3.6 20.1 - - + +
90B TRP 3.3 0.4 - - - -
91B LEU* 1.3 71.6 - - + +
93B SER* 1.3 56.7 + - - +
94B ARG* 3.1 26.6 + - - +
110B MET* 3.7 34.3 - - + +
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Residues in contact with SER 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 LEU 3.0 12.6 + - - -
90B TRP* 2.5 30.0 + - - -
92B LYS* 1.3 74.1 - - - +
94B ARG* 1.3 69.1 + - - +
95B PRO* 4.1 6.4 - - - +
104C ARG* 4.9 25.9 + - - +
107C ARG* 4.6 1.9 + - - -
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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