Contacts of the helix formed by residues 73 - 88 (chain B) in PDB entry 2BKU
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 ASP 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLU* 4.1 16.9 - - + +
71B SER* 3.2 11.9 + - - +
72B LYS* 1.3 77.5 - - - +
74B SER* 1.3 58.4 + - - +
75B VAL* 3.0 33.3 + - - +
76B LYS* 3.3 21.6 + - + +
77B THR* 3.0 30.1 + - - -
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS 3.7 3.1 + - - -
73B ASP* 1.3 72.0 + - - +
75B VAL* 1.3 70.3 + - - +
77B THR* 3.8 9.1 - - - +
78B GLN* 3.6 26.7 + - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASP* 3.0 10.4 + - - +
74B SER* 1.3 80.3 - - - +
76B LYS* 1.3 62.4 + - + +
77B THR 3.1 1.1 - - - -
78B GLN* 3.0 17.2 + - + +
79B GLN* 2.9 47.1 + - + +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 2.5 37.6 + - - -
71A LYS* 4.5 9.7 + - - +
76A ARG* 4.4 7.3 - - - +
71B SER* 3.3 21.1 - - - +
73B ASP* 3.3 19.4 + - + +
75B VAL* 1.3 78.5 - - + +
77B THR* 1.3 52.1 + - - +
79B GLN* 3.5 19.9 - - - +
80B PHE* 2.8 66.5 + - + -
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU 4.6 3.1 - - - +
70B VAL* 5.0 10.9 - - + +
71B SER* 2.8 37.7 + - - +
73B ASP 3.0 11.9 + - - -
74B SER* 3.8 10.4 - - - +
75B VAL 3.1 0.2 - - - -
76B LYS* 1.3 77.0 - - - +
78B GLN* 1.3 59.1 + - + +
80B PHE* 3.6 5.0 + - - +
81B ALA* 2.9 29.8 + - + +
125B ILE* 5.7 0.6 - - + +
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B SER 3.6 16.8 + - - +
75B VAL* 3.0 16.3 + - + +
77B THR* 1.3 77.6 - - + +
79B GLN* 1.3 65.8 + - + +
81B ALA* 3.3 7.2 + - - +
82B GLN* 3.0 26.0 + - - +
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 2.9 30.5 + - + +
76B LYS* 3.5 37.7 - - - +
78B GLN* 1.3 76.0 - - + +
80B PHE* 1.3 64.2 + - + +
82B GLN* 3.4 5.5 + - - +
83B ARG* 2.9 29.6 + - - +
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 5.9 0.9 - - - -
76A ARG* 6.2 1.3 - - - -
30B LYS* 5.9 2.0 - - - -
37B PHE* 5.9 0.2 - - - -
67B ASN 3.2 24.2 - - - -
68B GLU* 3.4 30.9 - - - +
69B LEU* 3.3 24.4 - - - +
70B VAL 3.8 6.7 - - - -
71B SER* 4.0 15.3 - - - -
76B LYS* 2.8 50.0 + - + +
77B THR 3.8 2.7 - - - +
79B GLN* 1.3 76.8 - - + +
81B ALA* 1.3 66.0 + - - +
83B ARG* 3.7 30.3 + - - +
84B TRP* 3.1 23.6 + - - +
125B ILE* 4.2 1.7 - - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU 4.4 0.6 + - - -
77B THR* 2.9 21.0 + - + +
78B GLN* 3.5 9.4 - - - +
80B PHE* 1.3 77.8 - - - +
82B GLN* 1.3 62.6 + - - +
84B TRP* 3.3 3.1 + - - +
85B ILE* 3.1 32.8 + - + +
125B ILE* 3.8 30.3 - - + +
129B HIS* 6.1 2.7 - - + -
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLN 3.0 17.1 + - - +
79B GLN* 3.8 5.1 + - - +
81B ALA* 1.3 73.2 - - - +
83B ARG* 1.3 65.6 + - - +
85B ILE* 3.2 10.5 + - + +
86B THR* 2.8 61.7 + - + +
87B GLN* 4.3 3.6 - - - +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 3.9 11.9 + - - -
34B ASN* 5.1 7.1 + - - +
37B PHE* 3.4 42.7 - - + -
68B GLU* 2.8 59.8 + - - +
79B GLN 2.9 19.3 + - - +
80B PHE* 3.7 21.6 + - - +
82B GLN* 1.3 83.9 - - - +
84B TRP* 1.3 56.3 + - - +
86B THR* 3.9 1.6 - - - -
87B GLN* 2.7 53.2 + - + +
88B VAL 3.8 0.3 + - - -
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Residues in contact with TRP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 4.4 6.3 - + + -
41B ALA* 4.7 4.7 - - + -
65B LEU* 5.2 1.3 - - + -
69B LEU* 3.4 36.3 - - + -
80B PHE 3.1 10.6 + - - +
81B ALA 3.6 7.0 - - - +
83B ARG* 1.3 80.6 - - - +
85B ILE* 1.3 61.6 + - + +
88B VAL* 3.4 33.2 + - + +
93B LYS* 2.8 52.7 + - + +
96B ILE* 3.6 48.2 - - + -
97B LYS* 4.6 3.1 - - - -
122B ILE* 3.7 25.7 - - + +
125B ILE* 3.6 26.2 - - + -
126B GLU* 2.8 27.7 + - + +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA* 3.1 26.8 + - + +
82B GLN* 3.6 10.1 - - + +
84B TRP* 1.3 80.1 - - + +
86B THR* 1.3 69.0 + - + +
88B VAL 4.2 1.2 - - - +
93B LYS* 2.9 22.9 + - - +
125B ILE* 4.1 18.6 - - + +
126B GLU* 5.6 3.1 - - + -
129B HIS* 4.4 28.9 - - + +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B GLN* 2.8 46.9 + - + +
83B ARG 3.7 0.5 + - - -
85B ILE* 1.3 86.7 - - + +
87B GLN* 1.3 90.5 + - - +
88B VAL 4.5 2.1 - - - +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 4.7 13.0 - - + -
38B LEU* 3.9 18.8 - - + +
82B GLN* 4.3 5.1 - - - +
83B ARG* 2.7 44.6 + - + +
86B THR* 1.3 102.4 + - - +
88B VAL* 1.3 60.7 + - - +
89B SER* 3.4 3.3 + - - -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.8 24.9 - - + -
38B LEU* 3.9 9.2 - - + -
41B ALA* 4.7 6.3 - - + -
84B TRP* 3.4 39.4 + - + +
85B ILE 4.2 2.6 - - - +
86B THR 4.5 2.2 - - - +
87B GLN* 1.3 75.2 - - - +
89B SER* 1.3 68.1 + - - +
90B PRO* 3.7 2.6 - - - +
92B ALA* 3.7 12.1 - - + -
93B LYS* 3.0 54.1 + - + +
96B ILE* 4.3 9.2 - - + -
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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