Contacts of the helix formed by residues 74 - 82 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73V SER* 1.3 83.9 - - - +
75V LEU* 1.3 64.6 + - - +
76V LYS* 4.1 3.4 - - - +
77V GLU* 2.4 41.2 + - - +
78V PHE* 3.1 29.8 + - - -
25Y VAL* 3.8 2.0 - - - -
29Y GLN* 4.0 2.7 - - - +
86Y GLU* 3.3 28.3 - - + -
87Y ALA* 3.6 37.7 - - - +
88Y PRO* 3.9 3.2 - - + +
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Residues in contact with LEU 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74V THR* 1.3 69.5 - - - +
76V LYS* 1.3 55.7 + - - +
78V PHE* 3.0 10.9 + - + +
79V LEU* 2.8 35.6 + - - +
21Y ASN* 3.8 2.7 - - + +
22Y VAL* 3.7 28.7 - - + +
25Y VAL* 3.6 28.3 - - + -
75Y LEU* 3.8 32.4 - - + +
78Y PHE* 3.6 35.9 - - + -
79Y LEU* 3.9 15.3 - - + -
86Y GLU* 3.0 21.6 + - - +
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Residues in contact with LYS 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74V THR* 4.4 3.1 - - - +
75V LEU* 1.3 76.0 - - - +
77V GLU* 1.3 58.7 + - + +
79V LEU* 3.6 4.3 + - - +
80V GLU* 3.0 52.9 + - - +
79Y LEU* 3.6 18.5 - - + +
86Y GLU* 3.0 17.1 + - - +
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Residues in contact with GLU 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72V PHE* 3.7 37.7 - - + -
73V SER* 3.3 10.3 + - - -
74V THR* 2.4 45.7 + - - +
75V LEU 3.2 0.6 - - - -
76V LYS* 1.3 79.4 - - + +
78V PHE* 1.3 64.2 + - - +
80V GLU* 4.0 15.5 - - - +
81V ASN* 2.8 32.3 + - - +
88Y PRO* 3.8 26.9 - - + +
89Y TYR 5.1 1.0 + - - -
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Residues in contact with PHE 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V VAL* 4.1 4.7 - - + -
18V ALA* 3.9 29.4 - - - +
21V ASN* 3.5 44.0 - - + -
22V VAL* 4.6 0.9 - - + -
72V PHE* 3.3 42.2 - - + -
73V SER* 3.9 3.8 - - - -
74V THR 3.1 24.6 + - - -
75V LEU* 3.0 9.9 + - + +
77V GLU* 1.3 74.6 - - - +
79V LEU* 1.3 65.0 + - - +
80V GLU 3.1 0.3 + - - -
81V ASN 3.2 0.5 + - - -
82V ALA* 3.0 31.6 + - - +
25Y VAL* 3.7 24.0 - - + -
32Y TRP* 5.0 4.7 - + - -
75Y LEU* 3.8 14.8 - - + -
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Residues in contact with LEU 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V VAL* 5.2 5.8 - - + -
75V LEU 2.8 19.7 + - - +
76V LYS* 3.7 6.5 - - - +
78V PHE* 1.3 73.3 - - - +
80V GLU* 1.3 57.9 + - + +
81V ASN 3.8 0.2 + - - -
82V ALA* 4.5 5.6 + - - +
86V GLU* 3.4 28.0 - - + +
75Y LEU* 3.7 21.0 - - + +
76Y LYS* 3.9 44.9 - - + +
79Y LEU* 4.3 13.7 - - + -
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Residues in contact with GLU 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76V LYS* 3.0 45.9 + - - +
77V GLU* 3.9 15.6 - - - +
78V PHE 3.2 0.4 - - - -
79V LEU* 1.3 76.4 - - + +
81V ASN* 1.3 74.0 + - - +
82V ALA 3.8 0.7 - - - -
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Residues in contact with ASN 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V HIS* 3.0 30.5 + - + -
18V ALA* 4.2 6.7 - - + -
72V PHE* 3.4 43.4 - - + -
77V GLU* 2.8 22.9 + - - +
78V PHE 3.2 1.6 + - - -
80V GLU* 1.3 93.7 + - - +
82V ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V HIS* 4.3 0.9 - - - -
18V ALA* 3.8 13.2 - - - +
19V ASN* 3.6 13.9 - - - +
22V VAL* 3.8 23.6 - - + -
78V PHE 3.0 17.4 + - - +
79V LEU* 4.5 5.1 + - - +
80V GLU 3.8 1.1 - - - -
81V ASN* 1.3 79.6 - - - +
83V SER* 1.3 60.0 + - - +
84V VAL 3.5 9.7 - - - +
85V GLU* 5.1 4.0 - - - +
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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