Contacts of the helix formed by residues 74 - 82 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R SER* 1.3 83.0 - - - +
75R LEU* 1.3 60.2 + - - +
76R LYS* 4.0 4.3 + - - +
77R GLU* 2.9 30.3 + - - +
78R PHE* 3.1 36.5 + - - -
25T VAL* 3.8 6.0 - - - +
29T GLN* 4.0 2.0 - - - +
86T GLU* 3.3 29.8 - - + +
87T ALA* 3.6 33.0 - - - +
88T PRO* 3.8 6.2 - - + +
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Residues in contact with LEU 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R THR* 1.3 69.0 - - - +
76R LYS* 1.3 65.5 + - - +
78R PHE* 3.1 7.6 + - + +
79R LEU* 2.8 28.6 + - - +
21T ASN* 3.8 21.1 - - + +
22T VAL* 3.9 14.1 - - + -
25T VAL* 3.9 18.8 - - + -
75T LEU* 3.7 35.3 - - + +
78T PHE* 3.7 34.3 - - + -
79T LEU* 3.6 24.9 - - + -
86T GLU* 2.9 18.1 + - - +
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Residues in contact with LYS 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R THR* 4.3 4.9 - - - +
75R LEU* 1.3 74.5 - - - +
77R GLU* 1.3 65.9 + - + +
79R LEU* 3.3 9.0 + - + +
80R GLU* 3.0 50.2 + - + +
79T LEU* 3.8 20.0 - - + +
86T GLU* 3.2 15.2 + - - +
88T PRO* 6.0 4.7 - - + -
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Residues in contact with GLU 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R ALA* 4.4 0.3 - - - +
71R PRO 5.2 0.3 - - - +
72R PHE* 3.5 38.3 - - + -
73R SER* 3.0 24.9 + - - -
74R THR* 2.9 26.5 + - - +
76R LYS* 1.3 76.0 - - + +
78R PHE* 1.3 67.7 + - - +
80R GLU* 4.3 10.3 - - - +
81R ASN* 3.0 32.6 + - - +
88T PRO* 3.9 28.8 - - + +
89T TYR 5.1 1.0 + - - -
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Residues in contact with PHE 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R VAL* 4.0 10.3 - - + -
18R ALA* 3.6 26.3 - - + +
21R ASN* 3.1 44.4 - - + -
22R VAL* 5.0 0.2 - - - -
72R PHE* 3.5 40.2 - - + -
73R SER* 4.1 3.4 - - - -
74R THR 3.1 28.7 + - - -
75R LEU* 3.1 4.7 + - + +
77R GLU* 1.3 76.3 - - - +
79R LEU* 1.3 61.6 + - - +
82R ALA* 3.1 30.9 + - - +
25T VAL* 3.9 23.1 - - + -
32T TRP* 5.0 5.4 - + - -
75T LEU* 3.6 24.9 - - + -
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Residues in contact with LEU 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R VAL* 5.1 4.7 - - + -
75R LEU 2.8 16.3 + - - +
76R LYS* 3.7 10.8 - - + +
78R PHE* 1.3 75.7 - - - +
80R GLU* 1.3 63.6 + - + +
81R ASN 3.4 0.7 + - - -
82R ALA* 4.1 10.3 + - - +
86R GLU* 3.5 30.1 - - + +
75T LEU* 3.8 16.8 - - + -
76T LYS* 4.0 26.7 - - + +
79T LEU* 4.1 19.5 - - + -
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Residues in contact with GLU 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76R LYS* 3.0 50.1 + - + +
77R GLU* 3.8 10.0 - - - +
79R LEU* 1.3 78.7 - - + +
81R ASN* 1.3 72.8 + - - +
82R ALA 5.2 1.2 - - - +
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Residues in contact with ASN 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R HIS* 2.8 40.4 + - + -
18R ALA* 4.2 5.8 - - + -
72R PHE* 3.2 45.9 - - + -
77R GLU* 3.0 24.3 + - - +
80R GLU* 1.3 89.7 + - - +
82R ALA* 1.3 57.1 + - - +
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Residues in contact with ALA 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R HIS* 4.1 0.4 - - - -
18R ALA* 4.0 12.1 - - - +
19R ASN* 3.5 13.2 - - - +
22R VAL* 3.9 24.5 - - + -
78R PHE 3.1 17.8 + - - +
79R LEU* 4.1 8.2 + - - +
80R GLU 3.8 1.1 - - - +
81R ASN* 1.3 78.0 - - - +
83R SER* 1.3 60.5 + - - +
84R VAL 4.2 8.4 - - - +
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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
------------------------------------------------------------
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