Contacts of the helix formed by residues 81 - 92 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80H TYR* 1.3 74.2 - - - +
82H LEU* 1.3 65.9 + - - +
83H VAL* 3.4 11.6 + - - +
84H GLN* 2.8 42.1 + - - +
85H TRP* 2.9 25.3 + - - -
116H ILE* 5.8 0.2 - - - -
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Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H TYR 4.2 0.4 + - - -
81H SER* 1.3 72.5 - - - +
83H VAL* 1.3 58.7 + - + +
85H TRP* 3.0 10.7 + - + +
86H GLN* 2.8 57.2 + - + +
115H GLN* 3.9 20.4 - - + +
116H ILE* 3.8 31.7 - - + +
119H ALA* 3.6 29.6 - - + -
120H ILE* 4.9 1.1 - - + -
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Residues in contact with VAL 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H SER* 3.2 9.9 + - - +
82H LEU* 1.3 78.1 - - + +
84H GLN* 1.3 61.0 + - + +
86H GLN* 3.2 16.5 + - + +
87H GLU* 2.8 34.9 + - + +
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Residues in contact with GLN 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H PHE* 3.7 8.2 - - + -
79H HIS 4.4 2.1 - - - +
80H TYR* 3.5 33.2 - - + -
81H SER* 2.8 46.0 + - - +
83H VAL* 1.3 79.3 - - + +
85H TRP* 1.3 55.9 + - - +
87H GLU* 3.6 6.3 + - - +
88H PHE* 3.0 28.8 + - - +
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Residues in contact with TRP 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H PHE* 3.8 19.1 - + - -
76H VAL* 3.4 39.2 - - + +
77H HIS 4.8 4.8 + - - -
80H TYR* 3.8 23.4 + - + +
81H SER 2.9 25.2 + - - -
82H LEU* 3.4 12.1 - - + +
84H GLN* 1.3 74.1 - - - +
86H GLN* 1.3 54.9 + - - +
88H PHE* 3.1 7.0 + + - +
89H ALA* 2.8 35.3 + - - +
96H LEU* 5.8 1.1 - - + -
99H LEU* 3.9 23.3 - - + -
100H ALA 4.3 2.0 - - - -
101H ALA* 4.0 28.7 - - + -
102H SER 5.6 0.4 - - - -
116H ILE* 3.6 39.1 - - + +
120H ILE* 3.8 21.0 - - + +
123H VAL* 4.0 15.9 - - + -
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Residues in contact with GLN 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H LEU* 2.8 49.5 + - + +
83H VAL* 3.7 17.3 - - - +
85H TRP* 1.3 68.0 - - - +
87H GLU* 1.3 56.3 + - - +
89H ALA* 3.2 1.1 + - - +
90H GLY* 2.7 35.2 + - - -
119H ALA* 4.6 10.4 - - + +
120H ILE* 3.8 19.7 - - + -
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Residues in contact with GLU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H VAL* 2.8 23.3 + - + +
84H GLN* 3.6 8.3 - - - +
86H GLN* 1.3 78.0 - - - +
88H PHE* 1.3 65.0 + - - +
90H GLY* 3.4 1.5 + - - +
91H GLN* 2.6 59.4 + - - +
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Residues in contact with PHE 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H PHE* 3.4 57.9 - + + -
64H ALA* 4.1 15.3 - - + -
65H LYS* 3.7 15.7 - - + -
84H GLN 3.0 18.6 + - - +
85H TRP* 3.1 6.5 + + - +
87H GLU* 1.3 80.0 + - - +
89H ALA* 1.3 59.2 + - - +
91H GLN 3.2 0.7 + - - -
92H ASN* 2.8 57.7 + - + +
95H CYS* 3.8 23.6 - - + -
96H LEU* 3.8 15.7 - - + -
99H LEU* 3.8 25.1 - - + -
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Residues in contact with ALA 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H TRP* 2.8 20.6 + - + +
86H GLN 3.8 1.6 - - - +
88H PHE* 1.3 73.4 - - - +
90H GLY* 1.3 63.8 + - - +
92H ASN 3.7 0.4 - - - +
93H PRO* 3.4 24.8 - - - +
96H LEU* 3.8 34.2 - - + +
120H ILE* 3.7 24.5 - - + -
122H GLN* 5.5 0.2 - - - +
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Residues in contact with GLY 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H GLN 2.7 21.2 + - - -
87H GLU* 3.7 2.0 - - - -
89H ALA* 1.3 75.2 - - - +
91H GLN* 1.3 62.2 + - - +
93H PRO* 3.9 7.8 - - - +
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Residues in contact with GLN 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H LYS* 6.2 0.4 - - - +
87H GLU* 2.6 46.5 + - - +
90H GLY* 1.3 79.0 - - - +
92H ASN* 1.3 77.7 + - - +
93H PRO* 3.4 7.9 - - - +
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Residues in contact with ASN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H LYS* 3.8 29.0 + - - +
88H PHE* 2.8 48.5 + - + +
89H ALA 3.7 4.0 - - - -
90H GLY 3.4 0.2 - - - -
91H GLN* 1.3 92.2 + - - +
93H PRO* 1.3 66.5 - - - +
94H ASP 3.1 2.9 - - - -
95H CYS* 3.1 31.2 + - - +
96H LEU* 3.9 8.8 - - - +
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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