Contacts of the helix formed by residues 54 - 67 (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 LYS 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLU* 2.8 38.7 + - + +
15B LEU* 3.8 19.5 - - + +
52B ASN 4.1 0.8 + - - +
53B THR* 1.3 77.1 - - - +
55B LEU* 1.3 69.3 + - - +
56B GLU* 3.2 11.6 + - - +
57B GLY* 3.1 10.3 + - - +
58B ARG* 3.2 8.8 + - - +
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Residues in contact with LEU 55 (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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82A GLN* 5.0 2.0 - - - +
53B THR 3.7 1.2 + - - -
54B LYS* 1.3 71.8 - - - +
56B GLU* 1.3 67.8 + - - +
58B ARG* 3.0 9.3 + - - +
59B ILE* 2.9 44.9 + - + +
108B GLU* 3.6 30.7 - - + +
110B ARG* 3.8 27.4 - - + +
111B ILE* 3.6 35.9 - - + +
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Residues in contact with GLU 56 (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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81A ILE* 3.4 24.4 - - + +
82A GLN* 3.3 47.0 + - + +
14B ILE* 3.7 12.7 - - + +
15B LEU* 3.9 33.4 - - + +
54B LYS* 3.2 8.6 + - - +
55B LEU* 1.3 88.3 + - + +
57B GLY* 1.3 56.9 + - - +
59B ILE* 4.5 2.0 - - - -
60B LEU* 2.9 30.3 + - - +
110B ARG* 5.4 0.7 - - - +
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Residues in contact with GLY 57 (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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10B LEU* 3.7 18.7 - - - +
11B GLU* 4.3 18.3 - - - +
15B LEU* 4.9 0.4 - - - +
47B VAL* 3.9 1.2 - - - +
53B THR* 4.2 14.1 - - - -
54B LYS* 3.1 8.3 + - - +
56B GLU* 1.3 76.2 - - - +
58B ARG* 1.3 61.1 + - - +
60B LEU* 3.8 4.8 - - - -
61B ALA* 3.0 26.3 + - - +
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Residues in contact with ARG 58 (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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47B VAL 3.2 18.6 - - - +
48B LEU* 2.7 43.2 + - - +
49B ILE* 3.7 16.4 + - - +
50B ASP 3.1 23.4 + - - -
51B GLU* 4.3 24.6 + - - +
53B THR* 3.3 23.9 + - - -
54B LYS 3.4 10.5 - - - +
55B LEU* 3.0 7.0 + - - +
57B GLY* 1.3 75.4 - - - +
59B ILE* 1.3 65.8 + - - +
61B ALA* 3.2 12.6 + - - +
62B ALA 3.4 8.3 + - - -
103B ALA* 6.0 0.4 - - - +
106B SER* 5.1 4.6 + - - -
108B GLU* 5.6 0.4 - - - +
111B ILE* 3.1 41.8 - - + +
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Residues in contact with ILE 59 (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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81A ILE* 3.6 24.2 - - + -
111A VAL* 5.2 4.7 - - + -
48B LEU* 5.3 0.9 - - - -
55B LEU* 2.9 32.2 + - + +
56B GLU* 3.8 6.5 - - - +
58B ARG* 1.3 76.5 - - - +
60B LEU* 1.3 63.0 + - - +
62B ALA* 3.3 5.2 + - - +
63B LEU* 3.2 31.9 + - + +
110B ARG* 3.5 64.2 - - + +
111B ILE* 4.5 3.8 - - + +
114B ALA* 4.1 15.9 - - + -
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Residues in contact with LEU 60 (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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75A LEU* 4.3 12.1 - - + -
78A GLY* 3.5 33.2 - - - +
81A ILE* 3.6 9.4 - - + +
10B LEU* 3.2 39.3 - - + +
13B SER* 3.9 15.5 - - - -
14B ILE* 3.9 11.0 - - + -
56B GLU 2.9 20.1 + - - +
57B GLY 3.9 4.7 - - - +
58B ARG 3.2 0.2 - - - -
59B ILE* 1.3 73.6 - - - +
61B ALA* 1.3 63.3 + - - +
63B LEU* 4.5 2.2 - - + +
64B THR* 2.7 57.1 + - + +
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Residues in contact with ALA 61 (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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6B PHE* 5.7 0.2 - - - -
10B LEU* 3.6 23.3 - - + +
44B SER* 3.4 33.6 - - - +
47B VAL* 4.1 2.0 - - + -
48B LEU* 4.0 10.1 - - - +
57B GLY 3.0 16.2 + - - +
58B ARG 3.2 9.8 + - - +
60B LEU* 1.3 77.5 - - - +
62B ALA* 1.3 62.4 + - - +
64B THR* 3.9 2.3 + - - -
65B LEU* 3.3 23.2 + - - +
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Residues in contact with ALA 62 (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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48B LEU* 3.8 26.8 - - + +
58B ARG 3.4 1.4 + - - -
59B ILE 3.3 2.6 + - - +
60B LEU 3.3 0.4 - - - -
61B ALA* 1.3 80.5 - - - +
63B LEU* 1.3 62.1 + - - +
65B LEU* 3.9 1.7 - - - +
66B LYS* 3.1 24.3 + - - +
114B ALA* 3.7 38.1 - - + +
118B LEU* 4.0 19.3 - - + +
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Residues in contact with LEU 63 (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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77A ASP* 3.8 41.1 - - - +
78A GLY* 4.2 8.7 - - - +
81A ILE* 4.2 7.0 - - + -
111A VAL* 4.3 9.9 - - + -
59B ILE* 3.2 33.9 + - + +
60B LEU* 3.4 4.2 + - - +
62B ALA* 1.3 77.6 - - - +
64B THR* 1.3 59.8 + - + +
66B LYS* 3.3 10.4 - - - +
67B ASN* 2.8 34.5 + - - +
114B ALA* 4.3 9.6 - - + -
117B GLN* 3.3 40.2 - - + +
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Residues in contact with THR 64 (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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75A LEU* 4.3 20.6 - - + +
6B PHE* 5.9 0.2 - - - -
10B LEU* 4.4 10.7 - - + +
29B LEU* 5.8 1.5 - - + +
40B PHE* 3.4 20.7 - - - -
44B SER* 4.9 0.3 + - - -
60B LEU* 2.7 52.1 + - + +
61B ALA 3.9 3.8 + - - -
63B LEU* 1.3 74.4 - - + +
65B LEU* 1.3 67.3 + - - +
67B ASN* 3.3 11.2 + - - +
68B GLU* 3.2 27.0 + - - +
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Residues in contact with LEU 65 (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* 4.2 15.9 - - + -
40B PHE* 4.1 11.2 - - + -
41B ALA* 3.8 45.3 - - + +
44B SER* 3.9 11.9 - - - -
45B SER 4.6 2.9 - - - +
61B ALA 3.3 15.4 + - - +
62B ALA 3.9 2.9 - - - +
64B THR* 1.3 78.3 + - - +
66B LYS* 1.3 66.0 + - - +
68B GLU* 3.0 11.0 + - - +
69B LEU* 3.1 20.7 + - + +
84B TRP* 5.2 1.6 - - + -
96B ILE* 4.4 14.4 - - + -
118B LEU* 3.8 31.4 - - + -
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Residues in contact with LYS 66 (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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77A ASP* 2.6 31.7 + - - -
62B ALA 3.1 16.1 + - - +
63B LEU* 3.3 14.3 - - - +
65B LEU* 1.3 79.3 - - - +
67B ASN* 1.3 82.5 + - - +
69B LEU* 2.9 21.8 + - - +
70B VAL* 3.0 25.9 + - + +
117B GLN* 3.8 34.4 + - + +
118B LEU* 4.2 15.4 - - - +
121B ALA* 3.6 20.4 - - + -
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Residues in contact with ASN 67 (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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75A LEU* 3.4 18.8 + - - +
76A ARG* 3.8 31.1 + - - +
77A ASP* 3.0 22.4 + - - +
63B LEU* 2.8 23.8 + - - +
64B THR* 3.7 10.4 - - - +
65B LEU 3.2 0.4 - - - -
66B LYS* 1.3 97.9 + - - +
68B GLU* 1.3 63.2 + - + +
69B LEU 3.4 0.2 - - - -
70B VAL* 3.6 10.4 - - - +
80B PHE* 3.2 18.7 - - - -
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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