Contacts of the helix formed by residues 74 - 82 (chain S) in PDB entry 2BKC
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 THR 74 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25Q VAL* 3.7 3.6 - - - -
29Q GLN* 3.8 2.9 - - - +
86Q GLU* 3.4 27.1 - - + +
87Q ALA* 3.5 34.3 - - - +
88Q PRO* 3.9 3.4 - - + +
73S SER* 1.3 84.3 - - - +
75S LEU* 1.3 63.0 + - - +
76S LYS* 3.6 3.7 + - - +
77S GLU* 3.0 35.2 + - - +
78S PHE* 3.1 29.6 + - - -
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Residues in contact with LEU 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q ASN* 4.1 9.4 - - + +
22Q VAL* 4.2 17.3 - - + +
25Q VAL* 3.5 34.3 - - + -
75Q LEU* 4.0 24.2 - - + +
78Q PHE* 3.9 38.8 - - + -
79Q LEU* 3.7 17.0 - - + -
86Q GLU* 2.9 19.2 + - - +
74S THR* 1.3 72.2 - - - +
76S LYS* 1.3 57.8 + - - +
78S PHE* 3.3 9.0 + - + +
79S LEU* 3.0 32.2 + - - +
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Residues in contact with LYS 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q LEU* 4.1 30.6 - - + +
86Q GLU* 3.3 13.2 + - - +
74S THR* 3.2 4.4 - - - +
75S LEU* 1.3 73.6 - - - +
77S GLU* 1.3 67.5 + - + +
79S LEU* 3.2 6.9 + - + +
80S GLU* 3.0 45.9 + - + +
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Residues in contact with GLU 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q PRO* 3.7 25.9 - - + +
89Q TYR 4.9 2.1 + - - +
71S PRO 4.9 0.4 - - - +
72S PHE* 3.8 35.2 - - + -
73S SER* 3.0 26.3 + - - -
74S THR* 3.0 27.4 + - - +
76S LYS* 1.3 78.7 - - + +
78S PHE* 1.3 62.9 + - - +
80S GLU* 3.4 12.7 + - - +
81S ASN* 3.1 29.0 + - - +
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Residues in contact with PHE 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q VAL* 3.6 25.6 - - + -
32Q TRP* 4.9 4.7 - + - -
75Q LEU* 3.8 15.7 - - + -
17S VAL* 3.8 10.5 - - + -
18S ALA* 3.6 29.0 - - - +
21S ASN* 3.6 36.3 - - + -
22S VAL* 4.7 0.4 - - + -
72S PHE* 3.4 38.6 - - + -
73S SER* 3.9 3.4 - - - -
74S THR 3.1 28.6 + - - -
75S LEU* 3.7 11.4 - - + +
76S LYS 3.2 0.4 - - - -
77S GLU* 1.3 76.0 - - - +
79S LEU* 1.3 58.4 + - - +
82S ALA* 2.9 36.2 + - - +
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Residues in contact with LEU 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Q LEU* 3.8 22.7 - - + -
76Q LYS* 4.0 34.8 - - + -
79Q LEU* 4.7 7.6 - - + -
22S VAL* 4.6 6.7 - - + -
75S LEU 3.0 17.4 + - - +
76S LYS* 3.2 8.7 + - + +
78S PHE* 1.3 74.1 - - - +
80S GLU* 1.3 64.4 + - + +
81S ASN 3.4 0.3 + - - -
82S ALA* 4.2 9.4 + - + +
86S GLU* 3.5 26.5 - - + +
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Residues in contact with GLU 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S LYS* 3.0 38.1 + - + +
77S GLU* 4.0 13.7 + - - +
79S LEU* 1.3 77.2 - - + +
81S ASN* 1.3 71.5 + - - +
82S ALA 5.1 1.0 - - - +
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Residues in contact with ASN 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S HIS* 3.1 28.7 + - + -
18S ALA* 4.0 8.7 - - + -
72S PHE* 3.1 45.3 - - + -
77S GLU* 3.1 24.3 + - - +
80S GLU* 1.3 90.1 + - - +
82S ALA* 1.3 67.9 + - - +
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Residues in contact with ALA 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S HIS* 4.6 0.4 - - - -
18S ALA* 4.0 10.0 - - - +
19S ASN* 3.4 15.0 - - - +
22S VAL* 3.8 23.8 - - + -
78S PHE 2.9 19.1 + - - +
79S LEU* 4.2 9.8 + - + +
80S GLU 3.9 0.9 - - - +
81S ASN* 1.3 79.6 - - - +
83S SER* 1.3 59.0 + - - +
84S VAL 4.1 10.6 - - - +
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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