Contacts of the helix formed by residues 36 - 49 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.1 23.7 + - + +
35D ASP* 1.3 83.7 - - + +
37D PHE* 1.3 65.7 + - - +
38D LEU* 3.9 10.6 - - - +
39D GLN* 3.2 40.5 + - - +
40D PHE 3.0 17.0 + - - -
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Residues in contact with PHE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D SER* 3.6 26.0 + - - +
34D ASN 4.7 1.6 + - - +
35D ASP 4.1 0.6 - - - -
36D ASN* 1.3 71.1 - - - +
38D LEU* 1.3 70.5 + - - +
40D PHE* 3.1 14.4 + + - -
41D ALA* 3.0 24.6 + - + +
65D LEU* 4.1 12.1 - - + -
68D GLU* 3.9 26.9 - - + -
69D LEU* 4.0 14.6 - - + -
80D PHE 6.0 0.2 - - - -
83D ARG* 3.7 55.0 - - + -
84D TRP* 4.3 12.8 - + - -
87D GLN* 4.6 9.4 - - + -
88D VAL* 3.9 26.9 - - + -
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Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASN* 3.2 9.1 + - - +
37D PHE* 1.3 81.2 - - - +
39D GLN* 1.3 62.4 + - + +
41D ALA* 3.8 2.8 - - - +
42D GLY* 3.2 17.2 + - - -
87D GLN* 3.9 16.9 - - + +
88D VAL* 3.7 13.5 - - + -
89D SER* 3.4 36.6 - - - +
92D ALA* 3.7 23.7 - - + +
96D ILE* 5.1 1.2 - - - +
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Residues in contact with GLN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.0 42.6 + - - +
32D LEU* 3.3 21.1 - - - +
36D ASN* 3.2 31.9 + - - +
38D LEU* 1.3 80.2 - - + +
40D PHE* 1.3 66.6 + - - +
42D GLY* 3.3 1.9 + - - -
43D LEU* 2.9 41.5 + - + +
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 3.7 31.9 - + - -
10D LEU* 6.1 0.2 - - + -
29D LEU* 3.3 37.0 - - + -
32D LEU* 3.8 17.6 - - + +
33D SER* 3.7 26.9 - - - -
36D ASN 3.0 14.0 + - - +
37D PHE* 3.1 14.3 + + - +
39D GLN* 1.3 76.2 - - - +
41D ALA* 1.3 62.7 + - - +
43D LEU* 3.9 1.3 - - - +
44D SER* 2.9 48.8 + - - -
64D THR* 3.5 24.9 - - - -
65D LEU* 4.2 15.5 - - + -
68D GLU* 4.2 8.1 - - + -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.0 29.4 + - + +
38D LEU 3.8 2.9 - - - +
40D PHE* 1.3 79.7 - - - +
42D GLY* 1.3 63.3 + - - +
44D SER* 3.2 2.6 + - - -
45D SER* 3.0 23.4 + - - -
65D LEU* 3.8 31.0 - - + +
84D TRP* 4.6 3.8 - - + -
88D VAL* 4.7 2.9 - - + -
96D ILE* 3.5 20.9 - - + -
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Residues in contact with GLY 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU 3.2 11.5 + - - -
39D GLN* 3.3 3.6 + - - -
41D ALA* 1.3 78.2 - - - +
43D LEU* 1.3 58.9 + - - +
45D SER* 2.7 20.7 + - - -
46D GLN* 3.2 21.2 + - - +
92D ALA* 5.6 4.0 - - - -
95D GLN* 6.3 1.3 - - - -
96D ILE* 3.7 15.8 - - - +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.9 22.7 - - + +
3D THR* 3.4 35.4 - - - +
6D PHE* 3.8 37.9 - - + -
32D LEU* 4.8 1.8 - - + -
39D GLN* 2.9 51.2 + - + +
40D PHE 4.0 1.8 - - - +
42D GLY* 1.3 68.4 - - - -
44D SER* 1.3 67.1 + - - +
46D GLN* 3.0 20.1 + - - +
47D VAL* 3.0 18.4 + - - +
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Residues in contact with SER 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 3.4 23.4 - - - -
10D LEU* 5.9 0.5 - - - +
40D PHE* 2.9 38.5 + - - -
41D ALA 3.4 4.9 - - - -
43D LEU* 1.3 76.5 - - - +
45D SER* 1.3 62.1 + - - +
48D LEU* 3.2 20.0 + - - +
61D ALA* 3.3 33.5 + - - +
62D ALA* 5.6 0.6 - - - -
64D THR* 4.9 0.5 + - - -
65D LEU* 3.8 15.3 - - - -
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 3.0 11.5 + - - -
42D GLY* 2.7 15.6 + - - -
43D LEU 3.2 0.2 - - - -
44D SER* 1.3 76.8 - - - +
46D GLN* 1.3 58.7 + - - +
48D LEU* 3.6 18.3 - - - +
49D ILE* 3.7 3.1 - - - +
65D LEU* 4.5 4.4 - - - +
95D GLN* 5.4 0.5 - - - +
96D ILE* 3.6 32.1 + - - +
99D ASN* 2.6 48.9 + - - +
100D ALA 5.5 0.4 - - - -
118D LEU* 5.6 2.7 - - - -
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Residues in contact with GLN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 2.8 37.1 + - + +
42D GLY* 3.2 19.8 + - - +
43D LEU* 3.0 12.8 + - - +
45D SER* 1.3 79.3 + - - +
47D VAL* 1.3 65.8 + - - +
48D LEU 3.1 1.6 - - - -
49D ILE* 3.2 13.3 + - + +
50D ASP* 3.1 21.5 + - - +
95D GLN* 5.8 6.0 + - - +
99D ASN* 4.3 8.7 - - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 3.7 18.8 - - + +
6D PHE* 3.8 14.8 - - + -
7D ALA* 3.7 22.9 - - + -
10D LEU* 3.9 15.9 - - + -
43D LEU 3.0 14.1 + - - +
44D SER 4.1 3.6 - - - +
46D GLN* 1.3 75.4 - - - +
48D LEU* 1.3 65.0 + - - +
50D ASP* 3.1 16.8 + - - +
53D THR* 3.7 30.7 - - + +
57D GLY 4.0 8.5 - - - +
58D ARG* 3.2 10.9 - - - +
61D ALA* 4.1 4.9 - - + -
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D SER 3.2 14.7 + - - +
45D SER* 3.6 16.4 - - - +
47D VAL* 1.3 76.2 - - - +
49D ILE* 1.3 58.0 + - + +
58D ARG* 2.8 54.5 + - - +
61D ALA* 4.0 1.9 - - + +
62D ALA* 3.7 25.8 - - + +
99D ASN 4.5 1.6 - - - +
100D ALA* 4.4 13.0 - - - +
103D ALA* 3.6 30.5 - - + -
111D ILE* 4.1 17.8 - - + +
114D ALA* 5.2 0.9 - - + -
115D ALA* 4.6 4.5 - - + -
118D LEU* 4.3 17.0 - - + -
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER 3.7 4.9 - - - +
46D GLN* 3.4 15.0 - - + +
48D LEU* 1.3 77.1 - - + +
50D ASP* 1.3 61.0 + - - +
51D GLU* 3.4 11.6 + - - +
58D ARG* 3.9 10.9 + - - +
99D ASN* 2.9 61.9 - - + +
102D THR* 4.0 22.7 - - + -
103D ALA* 4.1 10.5 - - + +
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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