Contacts of the helix formed by residues 74 - 82 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Q SER* 1.3 83.2 - - - +
75Q LEU* 1.3 63.7 + - - +
76Q LYS* 3.8 4.0 + - - +
77Q GLU* 2.4 39.6 + - - +
78Q PHE* 3.1 30.1 + - - -
25S VAL* 3.9 4.8 - - - +
29S GLN* 3.7 2.0 - - - +
86S GLU* 3.4 21.8 - - + +
87S ALA* 3.6 38.4 - - - +
88S PRO* 3.6 5.8 - - + +
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Residues in contact with LEU 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Q THR* 1.3 69.4 - - - +
76Q LYS* 1.3 67.2 + - - +
78Q PHE* 3.3 9.5 + - + +
79Q LEU* 3.1 28.6 + - - +
21S ASN* 4.0 9.0 - - + +
22S VAL* 3.9 19.7 - - + +
25S VAL* 3.6 33.0 - - + -
75S LEU* 4.0 29.1 - - + +
78S PHE* 3.8 32.5 - - + -
79S LEU* 3.8 17.5 - - + -
86S GLU* 2.8 19.4 + - - +
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Residues in contact with LYS 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q THR* 4.0 5.2 - - - +
75Q LEU* 1.3 80.7 - - - +
77Q GLU* 1.3 64.4 + - + +
79Q LEU* 3.2 5.5 + - - +
80Q GLU* 3.1 59.8 + - + +
79S LEU* 4.0 21.4 - - + +
86S GLU* 3.3 14.1 + - - +
88S PRO* 6.1 7.2 - - + -
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Residues in contact with GLU 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Q PRO 5.2 0.2 - - - +
72Q PHE* 3.5 38.6 - - + -
73Q SER* 3.3 9.3 + - - -
74Q THR* 2.4 45.0 + - - +
76Q LYS* 1.3 79.2 - - + +
78Q PHE* 1.3 67.4 - - - +
80Q GLU* 3.4 18.1 + - - +
81Q ASN* 2.8 31.0 + - - +
88S PRO* 3.8 24.5 - - + +
89S TYR 5.2 1.4 + - - +
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Residues in contact with PHE 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q VAL* 3.9 9.0 - - + -
18Q ALA* 3.7 28.3 - - - +
21Q ASN* 3.3 45.8 - - + -
22Q VAL* 4.7 1.1 - - + -
72Q PHE* 3.7 32.8 - - + -
73Q SER* 4.2 1.1 - - - -
74Q THR 3.1 26.4 + - - -
75Q LEU* 3.3 13.7 + - + +
77Q GLU* 1.3 77.2 - - - +
79Q LEU* 1.3 57.2 + - - +
82Q ALA* 3.0 36.4 + - - +
25S VAL* 3.7 24.2 - - + -
32S TRP* 5.0 4.9 - + - -
75S LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q VAL* 5.2 4.5 - - + -
75Q LEU 3.1 20.8 + - - +
76Q LYS* 3.2 6.7 + - - +
78Q PHE* 1.3 77.9 - - - +
80Q GLU* 1.3 62.7 + - + +
81Q ASN 3.2 0.9 + - - -
82Q ALA* 3.9 11.6 + - + +
86Q GLU* 3.4 29.6 - - + +
75S LEU* 3.7 35.4 - - + +
76S LYS* 4.1 32.5 - - + +
79S LEU* 4.7 11.7 - - + -
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Residues in contact with GLU 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q LYS* 3.1 44.9 + - + +
77Q GLU* 3.4 22.6 + - - +
79Q LEU* 1.3 76.0 - - + +
81Q ASN* 1.3 69.7 + - - +
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Residues in contact with ASN 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q HIS* 2.7 40.5 + - + -
18Q ALA* 4.1 7.2 - - + -
72Q PHE* 3.2 44.3 - - + -
77Q GLU* 2.8 25.6 + - - +
78Q PHE 3.8 0.2 - - - -
79Q LEU 3.1 0.2 - - - -
80Q GLU* 1.3 92.7 + - - +
82Q ALA* 1.3 55.9 + - - +
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Residues in contact with ALA 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q HIS* 4.2 0.2 - - - -
18Q ALA* 4.0 11.7 - - - +
19Q ASN* 3.6 11.9 - - - +
22Q VAL* 3.7 25.6 - - + -
78Q PHE 3.0 18.0 + - - +
79Q LEU* 3.9 8.3 + - + +
80Q GLU 5.5 0.2 - - - -
81Q ASN* 1.3 77.6 - - - +
83Q SER* 1.3 61.0 + - - +
84Q VAL 4.2 9.4 - - - +
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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