Contacts of the helix formed by residues 80 - 87 (chain A) in PDB entry 1BKL
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 LEU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TRP* 3.8 21.5 - - + -
6A TYR* 4.8 4.5 - - + -
31A VAL* 4.5 12.3 - - + -
41A TYR* 4.0 35.4 - - + -
61A ILE* 4.0 37.7 - - + -
69A PHE* 3.9 26.0 - - + -
79A SER* 1.3 71.2 - - - +
81A GLN* 1.3 67.3 + - - +
83A LEU* 3.5 7.5 - - + +
84A VAL* 3.0 29.4 + - + +
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Residues in contact with GLN 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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3A GLU* 4.9 5.4 + - - -
5A TRP* 3.2 37.5 + - + +
79A SER* 3.4 7.4 + - - +
80A LEU* 1.3 80.3 - - - +
82A GLN* 1.3 66.2 + - - +
84A VAL* 4.7 3.4 - - - +
85A ALA* 2.9 44.6 + - - +
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Residues in contact with GLN 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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77A PHE* 4.0 18.6 - - + -
78A SER* 4.6 10.1 - - - +
79A SER* 2.8 38.6 + - - +
81A GLN* 1.3 87.0 + - - +
83A LEU* 1.3 68.0 + - - +
85A ALA* 3.8 8.5 - - - +
86A TYR* 2.9 26.5 + - - +
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Residues in contact with LEU 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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43A LEU* 4.5 13.9 - - + -
61A ILE* 3.7 47.3 - - + -
69A PHE* 4.7 6.1 - - + -
71A ILE* 4.2 17.9 - - + +
77A PHE* 3.5 38.3 - - + -
79A SER 3.1 11.5 + - - +
80A LEU* 3.5 12.6 - - + +
82A GLN* 1.3 77.2 - - - +
84A VAL* 1.4 78.9 + - + +
86A TYR* 3.1 2.9 + - - +
87A TYR* 3.0 33.8 + - + -
98A LEU* 5.5 0.9 - - + -
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Residues in contact with VAL 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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5A TRP* 3.7 29.2 - - + +
29A PHE* 3.5 33.9 - - + -
31A VAL* 4.1 22.7 - - + -
43A LEU* 5.4 0.4 - - + -
80A LEU* 3.0 19.0 + - + +
81A GLN* 4.2 6.5 - - - +
83A LEU* 1.4 85.1 - - + +
85A ALA* 1.3 63.7 + - - +
88A SER* 2.8 34.1 + - - +
98A LEU* 4.0 10.0 - - + +
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Residues in contact with ALA 85 (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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81A GLN* 2.9 35.7 + - - +
82A GLN* 4.0 10.8 - - - +
84A VAL* 1.3 74.5 - - - +
86A TYR* 1.3 64.1 + - - +
88A SER* 3.8 8.0 - - - -
89A LYS* 3.7 21.0 + - - +
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Residues in contact with TYR 86 (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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75A THR* 3.6 13.0 - - + +
77A PHE* 3.5 25.1 - + + -
82A GLN 2.9 17.6 + - - +
83A LEU 3.5 3.1 - - - +
85A ALA* 1.3 78.1 - - - +
87A TYR* 1.3 99.0 + + - +
88A SER 3.2 0.4 - - - -
89A LYS* 2.8 21.0 + - - +
90A HIS* 2.9 47.1 + + + +
92A ASP* 3.4 27.4 + - + +
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Residues in contact with TYR 87 (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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43A LEU* 5.4 0.9 - - + -
71A ILE* 4.1 22.9 + - + +
72A THR* 3.8 19.4 + - - -
75A THR* 3.8 10.4 + - - +
77A PHE* 3.8 18.4 - + - -
83A LEU* 3.0 30.1 + - + +
86A TYR* 1.3 101.2 - + - +
88A SER* 1.4 61.1 + - - +
89A LYS 3.2 0.6 + - - -
90A HIS 3.2 22.7 - - - +
91A ALA* 3.7 11.8 - - - -
92A ASP* 3.5 25.9 + - + -
94A LEU* 4.0 24.9 - - + +
96A HIS 4.8 0.2 - - - +
97A ARG* 3.4 6.9 - - - +
98A LEU* 2.8 39.9 + - + -
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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