Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 2BZN
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 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B TYR* 1.3 76.0 - - - +
82B LEU* 1.3 65.0 + - - +
83B VAL* 3.6 8.6 + - - +
84B GLN* 2.9 40.9 + - - +
85B TRP* 3.0 23.5 + - - -
116B ILE* 5.8 0.4 - - - -
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Residues in contact with LEU 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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80B TYR 4.1 0.2 + - - -
81B SER* 1.3 73.4 - - - +
83B VAL* 1.3 59.9 + - + +
85B TRP* 3.1 10.0 + - + +
86B GLN* 2.8 52.6 + - + +
115B GLN* 3.7 51.8 - - + +
116B ILE* 3.9 21.5 - - + +
119B ALA* 3.9 15.5 - - + -
120B ILE* 5.4 0.9 - - + -
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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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81B SER* 3.2 8.2 + - - +
82B LEU* 1.3 79.6 - - + +
84B GLN* 1.3 60.9 + - + +
86B GLN* 3.3 16.9 + - - +
87B GLU* 2.8 35.7 + - + +
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Residues in contact with GLN 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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61B PHE* 3.9 5.9 - - + -
79B HIS 4.5 1.9 - - - +
80B TYR* 3.5 32.3 - - + -
81B SER* 2.9 45.6 + - - +
83B VAL* 1.3 79.5 - - + +
85B TRP* 1.3 61.6 + - - +
87B GLU* 3.3 7.5 + - - +
88B PHE* 3.0 24.3 + - - +
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Residues in contact with TRP 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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61B PHE* 3.8 17.3 - + - -
76B VAL* 3.6 40.8 - - + +
77B HIS 4.8 5.9 + - - -
80B TYR* 3.8 22.5 + - + +
81B SER 3.0 25.6 + - - -
82B LEU* 3.1 11.4 + - + +
84B GLN* 1.3 74.4 - - - +
86B GLN* 1.3 58.5 + - - +
88B PHE* 3.4 5.5 + + - +
89B ALA* 2.9 31.0 + - - +
96B LEU* 5.4 1.8 - - + -
99B LEU* 4.1 16.4 - - + -
100B ALA 4.3 1.3 - - - -
101B ALA* 4.3 26.7 - - + -
102B SER 5.6 0.2 - - - -
116B ILE* 3.4 43.3 - - + +
120B ILE* 3.6 17.0 - - + +
123B VAL* 4.0 22.2 - - + -
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Residues in contact with GLN 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 LEU* 2.8 50.1 + - + +
83B VAL* 3.6 20.7 - - - +
85B TRP* 1.3 73.4 - - - +
87B GLU* 1.3 62.2 + - - +
89B ALA* 4.0 1.1 - - - +
90B GLY* 3.1 19.8 + - - -
119B ALA* 4.1 16.8 - - + +
120B ILE* 3.9 15.3 - - + -
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Residues in contact with GLU 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* 2.8 24.4 + - + +
84B GLN* 3.4 9.2 - - - +
85B TRP 3.1 0.2 - - - -
86B GLN* 1.3 75.3 - - - +
88B PHE* 1.3 65.9 + - - +
90B GLY* 3.4 2.6 + - - -
91B GLN* 3.3 46.6 + - - +
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Residues in contact with PHE 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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61B PHE* 3.5 61.9 - + + -
64B ALA* 4.3 10.1 - - + -
65B LYS* 3.9 11.4 - - + -
84B GLN 3.0 13.3 + - - +
85B TRP* 3.7 6.1 - + - +
87B GLU* 1.3 80.2 + - - +
89B ALA* 1.3 61.6 + - - +
91B GLN* 3.4 0.8 + - - -
92B ASN* 2.8 60.8 + - + +
95B CYS* 3.6 26.0 - - + -
96B LEU* 4.0 11.9 - - + -
99B LEU* 3.6 24.7 - - + -
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Residues in contact with ALA 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 TRP* 2.9 7.6 + - + +
86B GLN* 4.0 3.1 - - - +
88B PHE* 1.3 78.1 - - + +
90B GLY* 1.3 62.6 + - - +
92B ASN 3.6 0.4 - - - -
93B PRO* 3.4 25.8 - - - +
96B LEU* 3.8 34.5 - - + +
120B ILE* 3.4 35.4 - - + -
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Residues in contact with GLY 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 GLN 3.1 17.4 + - - -
87B GLU 3.9 1.8 - - - -
88B PHE 3.3 0.4 - - - -
89B ALA* 1.3 76.9 - - - +
91B GLN* 1.3 61.1 + - - +
93B PRO* 4.0 7.3 - - - +
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Residues in contact with GLN 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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65B LYS* 5.7 5.1 - - - +
87B GLU* 3.3 35.7 + - - +
88B PHE* 5.0 0.4 - - - -
89B ALA 3.3 0.4 - - - -
90B GLY* 1.3 75.9 - - - +
92B ASN* 1.3 75.7 + - - +
93B PRO* 3.3 9.7 - - - +
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Residues in contact with ASN 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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65B LYS* 3.5 34.8 + - - +
69B LYS* 5.8 1.8 - - - +
88B PHE* 2.8 48.2 + - + +
89B ALA 3.4 4.2 + - - -
91B GLN* 1.3 92.8 + - - +
93B PRO* 1.3 65.8 - - - +
94B ASP 3.0 4.5 + - - -
95B CYS* 3.1 28.9 + - - +
96B LEU* 3.7 10.4 - - - +
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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