Contacts of the helix formed by residues 76 - 84 (chain A) in PDB entry 2B6V
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 PHE 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TYR* 5.8 0.6 - - - +
33A PHE* 3.5 32.9 - + + +
71A SER 3.4 11.7 - - - +
72A LEU* 3.1 43.3 - - + -
73A THR* 5.6 2.0 - - + -
75A PRO* 1.3 67.7 - - - +
77A LYS* 1.3 78.7 + - + +
78A ILE* 3.2 5.0 - - - +
79A LEU* 3.5 29.2 - - + +
80A GLY* 3.0 21.5 + - - -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A THR* 3.3 27.6 - - - +
74A PHE 3.4 8.1 - - - +
75A PRO 3.0 2.9 + - - +
76A PHE* 1.3 93.5 - - + +
78A ILE* 1.3 57.7 + - - +
80A GLY* 3.5 2.1 + - - -
81A ASP* 3.0 27.4 + - - +
87A TRP* 3.5 6.7 - - - -
93A VAL* 4.0 24.5 - - + +
96A VAL* 3.6 32.2 - - + +
97A SER* 3.9 4.7 - - - +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.2 57.3 - - + +
74A PHE* 3.2 32.2 + - + +
75A PRO* 3.6 13.9 - - + -
76A PHE 3.2 0.4 - - - +
77A LYS* 1.3 79.0 - - - +
79A LEU* 1.4 67.4 + - - +
81A ASP* 4.2 2.7 - - - -
82A SER* 3.1 22.2 + - - -
87A TRP* 4.3 5.8 - - + -
97A SER* 4.2 0.6 + - - +
170A ILE* 2.9 47.1 - - + +
171A LYS* 4.6 5.8 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO* 2.8 46.9 - - + +
29A TYR* 4.5 5.6 - - + -
30A CYS* 4.1 21.1 - - + +
33A PHE* 6.0 6.7 - - + -
76A PHE* 3.5 27.7 + - + +
77A LYS 3.3 0.2 - - - -
78A ILE* 1.4 84.2 - - - +
80A GLY* 1.3 58.0 - - - +
82A SER 3.5 0.2 + - - -
83A GLY* 2.9 26.7 + - - -
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PHE 3.0 17.1 + - - -
77A LYS 3.8 2.5 - - - -
79A LEU* 1.3 78.3 - - - +
81A ASP* 1.3 56.7 + - - +
83A GLY* 3.0 3.1 + - - -
84A LEU* 2.9 30.7 + - - +
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Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS 3.0 8.0 + - - +
78A ILE 3.7 4.3 - - - +
79A LEU 3.3 0.4 - - - -
80A GLY* 1.3 74.5 - - - +
82A SER* 1.3 58.9 + - - +
84A LEU* 3.1 2.3 - - - -
85A GLY* 2.9 43.9 + - - +
86A PRO 2.9 22.6 - - - +
87A TRP* 2.9 49.4 + - + -
88A GLN 4.4 0.2 + - - -
93A VAL* 5.1 0.9 - - - +
169A GLN 2.9 26.2 - - - +
170A ILE* 3.3 11.8 - - - +
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 2.8 32.9 + - - +
25A ILE* 3.2 34.2 - - - +
26A PRO* 3.7 12.8 - - - -
78A ILE 3.1 13.1 + - - -
81A ASP* 1.3 75.1 - - - +
83A GLY* 1.4 65.5 + - - +
84A LEU 3.4 6.2 - - - +
170A ILE* 3.4 33.4 - - - +
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO* 4.1 9.4 - - - +
79A LEU 2.9 15.3 + - - -
80A GLY* 3.0 5.8 + - - -
82A SER* 1.4 79.6 - - - +
84A LEU* 1.4 61.1 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 4.8 7.5 + - - -
22A GLN* 5.1 5.9 + - - +
80A GLY 2.9 14.0 + - - +
81A ASP* 3.1 5.6 - - - +
82A SER* 3.4 6.9 - - - +
83A GLY* 1.4 79.7 - - - +
85A GLY* 1.4 66.2 + - - +
86A PRO* 4.1 27.8 - - + +
88A GLN* 4.5 24.9 - - + +
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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