Contacts of the helix formed by residues 54 - 67 (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 LYS 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLU* 3.0 35.5 + - + +
15D LEU* 3.7 23.6 - - + +
52D ASN 4.0 1.3 + - - +
53D THR* 1.3 77.1 - - - +
55D LEU* 1.3 65.7 + - - +
56D GLU* 3.3 15.3 + - - +
57D GLY 3.3 2.3 + - - +
58D ARG* 3.2 18.4 + - - +
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Residues in contact with LEU 55 (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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82C GLN* 5.1 2.9 - - - +
53D THR 3.7 0.6 + - - -
54D LYS* 1.3 72.3 - - - +
56D GLU* 1.3 63.0 + - - +
58D ARG* 3.0 9.7 + - - +
59D ILE* 2.8 49.9 + - + +
108D GLU* 3.8 30.1 - - + +
110D ARG* 4.1 23.3 - - + +
111D ILE* 3.5 39.3 - - + +
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Residues in contact with GLU 56 (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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81C ILE* 3.4 24.9 - - + +
82C GLN* 3.1 45.5 + - + +
14D ILE* 3.6 13.5 - - + +
15D LEU* 3.8 32.9 - - + +
54D LYS* 3.9 12.4 + - - +
55D LEU* 1.3 86.9 + - + +
57D GLY* 1.3 58.2 + - - +
59D ILE* 4.5 1.1 - - - -
60D LEU* 2.9 29.6 + - - +
110D ARG* 5.3 0.2 - - - +
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Residues in contact with GLY 57 (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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10D LEU* 3.8 18.0 - - - +
11D GLU* 4.1 19.6 - - - +
15D LEU* 4.9 0.4 - - - +
47D VAL* 4.3 1.6 - - - -
53D THR* 4.1 15.3 - - - -
54D LYS* 3.3 6.6 + - - +
55D LEU 3.3 0.4 - - - -
56D GLU* 1.3 76.0 - - - +
58D ARG* 1.3 60.2 + - - +
60D LEU* 3.4 3.9 + - - +
61D ALA* 3.0 28.4 + - - +
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Residues in contact with ARG 58 (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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47D VAL* 3.2 21.5 - - - +
48D LEU* 2.8 41.2 + - - +
49D ILE* 3.9 13.5 + - - +
50D ASP 3.2 23.0 + - - -
51D GLU* 4.3 24.8 + - - +
53D THR* 3.3 23.2 + - - -
54D LYS 3.2 10.9 + - - +
55D LEU* 3.0 9.4 + - - +
57D GLY* 1.3 74.5 - - - +
59D ILE* 1.3 64.8 + - - +
61D ALA* 3.3 10.4 + - - +
62D ALA 3.4 9.0 + - - -
103D ALA* 6.1 0.4 - - - +
106D SER* 4.7 5.9 + - - -
108D GLU* 5.7 0.8 - - - +
111D ILE* 3.3 41.0 - - + +
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Residues in contact with ILE 59 (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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81C ILE* 3.5 30.3 - - + -
111C VAL* 5.0 5.4 - - + -
48D LEU* 5.3 0.4 - - - -
55D LEU* 2.8 36.0 + - + +
56D GLU 3.9 0.4 - - - +
58D ARG* 1.3 77.5 - - - +
60D LEU* 1.3 60.8 + - - +
62D ALA* 3.5 3.8 + - - +
63D LEU* 3.1 33.2 + - + +
110D ARG* 3.3 64.4 - - + +
111D ILE* 4.6 2.7 - - + -
114D ALA* 4.1 13.0 - - + +
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Residues in contact with LEU 60 (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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75C LEU* 4.0 13.2 - - + -
78C GLY* 3.4 34.1 - - - +
81C ILE* 3.3 9.3 - - + +
10D LEU* 3.4 38.6 - - + +
13D SER* 4.0 15.3 - - - -
14D ILE* 4.0 10.1 - - + -
29D LEU* 5.1 0.2 - - + -
56D GLU 2.9 20.0 + - - +
57D GLY* 3.8 4.9 - - - +
59D ILE* 1.3 73.7 - - - +
61D ALA* 1.3 66.2 + - - +
63D LEU* 4.4 1.8 - - + -
64D THR* 2.8 53.9 + - + +
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Residues in contact with ALA 61 (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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10D LEU* 3.6 29.6 - - + +
44D SER* 3.3 32.8 + - - +
47D VAL* 4.1 1.8 - - + -
48D LEU* 4.0 9.9 - - - +
57D GLY 3.0 10.5 + - - +
58D ARG 3.3 10.9 + - - +
60D LEU* 1.3 78.9 - - - +
62D ALA* 1.3 62.0 + - - +
64D THR* 4.2 1.1 + - - -
65D LEU* 3.2 23.6 + - - +
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Residues in contact with ALA 62 (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 4.9 0.6 + - - -
48D LEU* 3.7 28.2 - - + +
58D ARG 3.4 3.0 + - - -
59D ILE 3.9 1.3 - - - +
60D LEU 3.3 0.2 - - - -
61D ALA* 1.3 79.5 - - - +
63D LEU* 1.3 63.8 + - - +
65D LEU* 3.9 1.6 - - - +
66D LYS* 3.0 23.3 + - - +
114D ALA* 3.7 38.1 - - + +
118D LEU* 4.2 18.6 - - + +
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Residues in contact with LEU 63 (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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77C ASP* 3.7 38.1 - - - +
78C GLY* 4.1 8.7 - - - +
81C ILE* 4.1 6.1 - - + -
111C VAL* 4.2 11.4 - - + -
59D ILE* 3.1 40.3 + - + +
60D LEU* 3.3 4.5 + - - +
62D ALA* 1.3 78.1 - - - +
64D THR* 1.3 59.9 + - + +
66D LYS* 3.1 10.8 + - - +
67D ASN* 2.9 37.0 + - - +
114D ALA* 4.1 13.0 - - + +
117D GLN* 3.3 35.9 - - + +
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Residues in contact with THR 64 (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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75C LEU* 4.1 21.1 - - + +
10D LEU* 4.6 9.2 - - + +
29D LEU* 5.7 2.0 - - + +
40D PHE* 3.5 19.7 - - - -
44D SER* 4.9 0.7 + - - -
60D LEU* 2.8 53.2 + - + +
61D ALA 4.2 2.3 + - - -
63D LEU* 1.3 74.8 - - + +
65D LEU* 1.3 65.7 + - - +
67D ASN* 3.4 14.6 + - - +
68D GLU* 3.1 29.1 + - - +
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Residues in contact with LEU 65 (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* 4.1 16.8 - - + -
40D PHE* 4.2 8.5 - - + -
41D ALA* 3.8 45.3 - - + +
44D SER* 3.8 12.6 - - - -
45D SER 4.5 3.1 - - - +
61D ALA 3.2 16.2 + - - +
62D ALA 3.9 3.1 - - - +
64D THR* 1.3 80.9 + - - +
66D LYS* 1.3 62.5 - - - +
68D GLU* 3.2 10.2 + - - -
69D LEU* 3.2 20.3 + - + +
84D TRP* 5.2 1.1 - - + -
96D ILE* 4.2 14.4 - - + -
118D LEU* 3.7 32.3 - - + -
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Residues in contact with LYS 66 (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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77C ASP* 2.6 30.4 + - - -
107C ASP* 6.4 0.2 - - - -
62D ALA 3.0 15.0 + - - +
63D LEU* 3.1 15.5 - - - +
65D LEU* 1.3 77.4 - - - +
67D ASN* 1.3 83.2 + - - +
68D GLU 3.1 0.4 - - - -
69D LEU* 3.0 11.9 + - - +
70D VAL* 3.0 39.8 + - + +
117D GLN* 3.9 32.9 + - + +
118D LEU* 4.3 9.6 - - - +
121D ALA* 3.9 18.8 - - + -
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Residues in contact with ASN 67 (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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74C GLY 5.8 1.3 - - - +
75C LEU 3.5 16.8 + - - -
76C ARG* 3.8 31.7 + - - +
77C ASP* 3.1 20.8 + - - +
30D LYS* 5.6 0.3 + - - -
63D LEU* 2.9 28.0 + - - +
64D THR* 3.4 11.5 + - - +
65D LEU 3.3 0.4 - - - -
66D LYS* 1.3 100.0 + - - +
68D GLU* 1.3 63.1 + - + +
69D LEU 3.4 1.3 - - - -
70D VAL 3.6 10.0 - - - +
71D SER* 5.4 0.3 - - - -
80D PHE* 3.2 17.7 - - - -
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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