Contacts of the helix formed by residues 36 - 50 (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 ASN 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.2 19.5 + - + +
35B ASP* 1.3 83.8 - - + +
37B PHE* 1.3 65.8 + - - +
38B LEU* 3.6 14.5 - - - +
39B GLN* 3.0 39.5 + - + +
40B PHE 3.0 17.7 + - - -
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Residues in contact with PHE 37 (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* 3.4 24.1 + - - +
34B ASN 4.7 1.9 + - - +
35B ASP 4.0 0.8 - - - -
36B ASN* 1.3 74.0 - - - +
38B LEU* 1.3 64.5 + - - +
40B PHE* 3.1 13.9 + + - +
41B ALA* 2.9 26.8 + - + +
65B LEU* 4.2 17.7 - - + -
68B GLU* 3.8 20.0 - - + -
69B LEU* 4.4 7.2 - - + -
80B PHE 5.9 0.2 - - - -
83B ARG* 3.4 65.5 - - + -
84B TRP* 4.4 9.9 - + - -
87B GLN* 4.7 8.3 - - + -
88B VAL* 3.8 27.1 - - + -
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Residues in contact with LEU 38 (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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36B ASN* 3.6 11.9 - - - +
37B PHE* 1.3 84.4 - - - +
39B GLN* 1.3 64.3 + - + +
41B ALA* 3.4 3.5 + - - +
42B GLY* 3.1 16.8 + - - -
87B GLN* 3.9 14.9 - - + +
88B VAL* 3.9 12.1 - - + -
89B SER* 3.6 35.4 - - - +
92B ALA* 3.8 22.1 - - + +
96B ILE* 5.4 0.5 - - - +
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Residues in contact with GLN 39 (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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1B MET* 3.0 38.8 + - - +
32B LEU* 3.3 22.2 - - - +
36B ASN* 3.0 30.4 + - - +
38B LEU* 1.3 80.0 - - + +
40B PHE* 1.3 67.0 + - - +
42B GLY* 3.2 2.2 + - - -
43B LEU* 2.9 48.9 + - + +
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Residues in contact with PHE 40 (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* 3.8 28.8 - + - -
29B LEU* 3.5 34.1 - - + -
32B LEU* 3.9 19.6 - - + +
33B SER* 3.9 22.9 - - - -
36B ASN 3.0 11.9 + - - +
37B PHE* 3.5 15.7 - + - +
39B GLN* 1.3 76.6 - - - +
41B ALA* 1.3 63.5 + - - +
43B LEU* 3.9 3.9 - - - +
44B SER* 2.6 45.2 + - - -
64B THR* 3.4 24.0 - - - -
65B LEU* 4.1 13.5 - - + -
68B GLU* 4.1 19.5 - - + -
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Residues in contact with ALA 41 (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* 2.9 31.6 + - + +
38B LEU 3.6 4.0 - - - +
40B PHE* 1.3 73.9 - - - +
42B GLY* 1.3 63.4 + - - +
44B SER* 3.3 3.0 + - - -
45B SER* 3.0 23.2 + - - -
65B LEU* 3.8 31.2 - - + +
84B TRP* 4.7 2.7 - - + -
88B VAL* 4.7 3.4 - - + -
96B ILE* 3.5 22.7 - - + -
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Residues in contact with GLY 42 (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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38B LEU 3.1 10.6 + - - -
39B GLN* 3.2 3.6 + - - -
41B ALA* 1.3 78.9 - - - +
43B LEU* 1.3 61.3 + - - +
45B SER* 2.8 25.4 + - - -
46B GLN* 3.2 19.2 + - - +
92B ALA* 5.8 4.5 - - - -
96B ILE* 4.1 9.5 - - - +
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Residues in contact with LEU 43 (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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1B MET* 3.7 27.1 - - + +
3B THR* 3.4 30.7 - - - +
6B PHE* 3.9 34.8 - - + -
32B LEU* 4.8 1.1 - - + -
39B GLN* 2.9 55.5 + - + +
40B PHE 4.0 2.7 - - - +
42B GLY* 1.3 69.4 - - - -
44B SER* 1.3 65.3 + - - +
46B GLN* 3.0 10.9 + - - +
47B VAL* 2.9 28.4 + - - +
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Residues in contact with SER 44 (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* 3.5 22.6 - - - -
40B PHE* 2.6 37.8 + - - -
41B ALA 3.3 5.8 - - - -
43B LEU* 1.3 77.5 - - - +
45B SER* 1.3 62.6 + - - +
47B VAL 3.4 0.5 + - - -
48B LEU* 3.2 20.5 + - - +
61B ALA* 3.4 31.8 + - - +
62B ALA* 6.1 0.2 - - - -
64B THR* 4.9 0.5 + - - -
65B LEU* 3.9 14.3 - - - +
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Residues in contact with SER 45 (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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41B ALA 3.0 12.7 + - - -
42B GLY* 2.8 16.0 + - - -
44B SER* 1.3 75.6 - - - +
46B GLN* 1.3 59.8 + - - +
48B LEU* 3.5 20.9 - - - +
49B ILE* 3.7 4.9 - - - +
65B LEU* 4.6 4.4 - - - +
95B GLN* 4.6 0.5 - - - +
96B ILE* 3.8 32.6 + - - +
99B ASN* 2.7 44.7 + - - +
118B LEU* 5.6 2.2 - - - -
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Residues in contact with GLN 46 (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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3B THR* 2.5 38.5 + - + +
42B GLY* 3.2 20.2 + - - +
43B LEU* 3.0 12.8 + - - +
45B SER* 1.3 81.7 + - - +
47B VAL* 1.3 65.7 + - - +
48B LEU 3.1 1.3 - - - -
49B ILE* 3.2 13.0 + - + +
50B ASP* 3.0 22.3 + - - +
99B ASN* 4.2 8.2 - - - +
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Residues in contact with VAL 47 (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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3B THR* 3.7 24.0 - - + +
6B PHE* 3.6 22.7 - - + -
7B ALA* 3.8 9.9 - - + -
10B LEU* 4.0 4.7 - - + -
43B LEU 2.9 20.0 + - - +
44B SER 4.0 3.1 - - - +
46B GLN* 1.3 75.3 - - - +
48B LEU* 1.3 63.4 + - - +
50B ASP* 3.1 17.3 + - - +
53B THR* 3.7 30.5 - - + +
57B GLY 3.9 16.8 - - - +
58B ARG* 3.2 12.5 - - - +
61B ALA* 4.1 5.2 - - + -
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Residues in contact with LEU 48 (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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44B SER 3.2 13.0 + - - +
45B SER* 3.5 16.4 - - - +
46B GLN 3.1 0.4 - - - -
47B VAL* 1.3 77.1 - - - +
49B ILE* 1.3 53.7 + - - +
58B ARG* 2.7 56.0 + - - +
61B ALA* 4.0 2.2 - - + +
62B ALA* 3.8 23.3 - - + +
99B ASN 4.4 2.0 - - - +
100B ALA* 4.3 15.7 - - - +
103B ALA* 3.5 30.5 - - + -
111B ILE* 4.1 19.3 - - + +
114B ALA* 5.2 1.1 - - + -
115B ALA* 4.5 4.7 - - + -
118B LEU* 4.3 13.2 - - + -
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Residues in contact with ILE 49 (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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45B SER 3.7 6.5 - - - +
46B GLN* 3.5 14.8 - - + +
48B LEU* 1.3 77.9 - - + +
50B ASP* 1.3 60.8 + - - +
51B GLU* 3.4 12.3 + - - +
58B ARG* 3.7 11.5 + - - +
99B ASN* 3.1 58.3 - - + +
102B THR* 4.2 15.0 - - + +
103B ALA* 4.0 17.9 - - + +
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Residues in contact with ASP 50 (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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3B THR* 4.8 13.3 - - + +
7B ALA* 5.3 0.7 - - - +
46B GLN 3.0 15.6 + - - +
47B VAL* 3.1 14.3 + - - +
48B LEU 3.4 0.2 - - - -
49B ILE* 1.3 75.2 - - - +
51B GLU* 1.3 63.8 + - - +
52B ASN* 3.3 20.5 + - - +
53B THR* 2.7 36.5 + - - +
58B ARG* 3.1 23.2 + - - -
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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