Contacts of the helix formed by residues 74 - 82 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73J SER* 1.3 84.7 - - - +
75J LEU* 1.3 62.7 - - - +
76J LYS* 3.9 5.5 - - + +
77J GLU* 2.8 40.7 + - - +
78J PHE* 3.0 33.5 + - - -
25L VAL* 3.9 2.5 - - - -
29L GLN* 4.1 0.2 - - - +
86L GLU* 3.4 29.4 - - + +
87L ALA 3.6 10.1 - - - +
88L PRO* 3.6 27.1 - - + -
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Residues in contact with LEU 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74J THR* 1.3 71.6 - - - +
76J LYS* 1.3 62.6 + - - +
78J PHE* 3.2 9.0 + - + +
79J LEU* 2.9 27.9 + - - +
21L ASN* 3.8 9.9 - - + +
22L VAL* 3.9 17.5 - - + -
25L VAL* 3.7 32.5 - - + -
75L LEU* 3.9 25.0 - - + +
78L PHE* 3.8 38.8 - - + -
79L LEU* 3.9 16.2 - - + -
86L GLU* 3.1 20.5 + - - +
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Residues in contact with LYS 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74J THR* 3.2 8.7 - - - +
75J LEU* 1.3 77.4 - - - +
77J GLU* 1.3 73.0 + - + +
79J LEU* 3.3 4.5 + - - +
80J GLU* 3.0 64.2 + - - +
79L LEU* 3.7 18.2 - - + +
86L GLU* 3.2 15.3 + - - +
88L PRO* 3.7 28.6 - - + +
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Residues in contact with GLU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ALA* 4.4 0.7 - - - +
71J PRO 5.3 0.2 - - - +
72J PHE* 3.7 33.7 - - + -
73J SER* 3.1 22.1 + - - -
74J THR* 2.8 37.6 + - - +
76J LYS* 1.3 91.7 - - + +
78J PHE* 1.3 65.0 + - - +
80J GLU* 4.2 8.7 - - - +
81J ASN* 2.7 30.6 + - - +
88L PRO* 3.6 21.5 - - - +
89L TYR 4.9 2.1 + - - +
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Residues in contact with PHE 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 3.8 5.2 - - + -
18J ALA* 3.5 28.6 - - - +
21J ASN* 3.4 42.8 - - + -
22J VAL* 4.7 0.4 - - + -
72J PHE* 3.3 39.7 - - + -
73J SER* 4.0 1.3 - - - -
74J THR 3.0 26.8 + - - -
75J LEU* 3.2 7.2 + - + +
77J GLU* 1.3 75.5 - - - +
79J LEU* 1.3 58.1 + - - +
81J ASN 3.3 0.2 + - - -
82J ALA* 3.0 35.9 + - - +
25L VAL* 3.5 33.7 - - + -
32L TRP* 5.1 4.7 - + - -
75L LEU* 3.6 19.7 - - + -
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Residues in contact with LEU 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J VAL* 4.9 5.2 - - + -
75J LEU 2.9 13.9 + - - +
76J LYS* 3.3 4.7 + - - +
78J PHE* 1.3 79.1 - - - +
80J GLU* 1.3 61.8 + - + +
81J ASN 3.3 0.7 + - - -
82J ALA* 3.9 11.8 + - + +
86J GLU* 3.3 30.7 - - + +
75L LEU* 3.9 15.3 - - + -
76L LYS* 3.8 37.7 - - + +
79L LEU* 4.2 16.4 - - + -
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Residues in contact with GLU 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J LYS* 3.0 53.3 + - + +
77J GLU* 3.8 4.3 - - - +
78J PHE 3.3 0.2 - - - -
79J LEU* 1.3 77.5 - - - +
81J ASN* 1.3 69.9 + - - +
82J ALA 3.8 1.0 - - - +
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Residues in contact with ASN 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J HIS* 2.9 37.4 + - + -
18J ALA* 4.0 7.6 - - + -
72J PHE* 3.1 46.5 - - + -
77J GLU* 2.7 25.0 + - - +
78J PHE 3.3 1.8 + - - -
79J LEU 3.2 0.2 - - - -
80J GLU* 1.3 88.9 + - - +
82J ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ALA* 3.9 9.6 - - - +
19J ASN* 3.2 14.1 - - - +
22J VAL* 3.7 26.0 - - + -
78J PHE 3.0 17.1 + - - +
79J LEU* 3.9 9.2 + - + +
80J GLU 3.8 0.5 - - - +
81J ASN* 1.3 79.5 - - - +
83J SER* 1.3 59.5 + - - +
84J VAL 4.0 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