Contacts of the helix formed by residues 12 - 25 (chain A) in PDB entry 2BKG
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 SER 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASP* 1.3 65.6 + - - +
14A LEU* 4.6 1.7 + - - +
15A GLY* 3.8 21.4 + - - -
16A LYS* 3.5 17.8 + - - +
38A ALA* 6.1 0.2 - - - -
39A ASP* 4.7 12.3 + - - +
42A ALA* 5.5 2.9 - - - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 1.3 74.7 + - - +
14A LEU* 1.3 66.5 + - + +
16A LYS* 3.6 4.8 + - - +
17A LYS* 3.1 48.6 + - - +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 4.4 1.9 + - - +
13A ASP* 1.3 83.7 - - + +
15A GLY* 1.3 64.0 + - - +
16A LYS 3.2 1.1 - - - -
17A LYS* 3.7 24.8 - - + +
18A LEU* 3.1 25.1 + - - +
33A LEU* 3.9 21.0 - - + +
36A ASN* 3.9 33.9 - - + +
37A GLY 4.9 1.1 - - - -
38A ALA* 3.4 30.2 - - + +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 3.8 19.5 + - - -
13A ASP 3.4 0.6 - - - -
14A LEU* 1.3 76.8 - - - +
16A LYS* 1.3 62.5 + - - +
18A LEU* 3.4 5.1 + - - +
19A LEU* 3.1 30.3 + - - +
38A ALA* 4.3 3.1 - - - +
39A ASP 4.7 5.4 - - - +
42A ALA* 3.5 26.4 - - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 3.5 17.2 + - - +
13A ASP* 3.6 5.4 + - - +
14A LEU 3.2 0.2 - - - -
15A GLY* 1.3 77.3 - - - +
17A LYS* 1.3 62.4 + - + +
19A LEU* 3.5 28.5 + - + +
20A GLU* 3.2 39.9 + - + +
43A GLU 4.3 3.0 + - - -
44A ASP* 3.8 22.6 - - - +
45A THR* 4.8 8.3 - - - +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASP* 3.1 46.7 + - - +
14A LEU* 3.4 22.3 + - + +
15A GLY 3.3 0.4 - - - -
16A LYS* 1.3 78.9 - - + +
18A LEU* 1.3 58.3 + - - +
20A GLU* 3.3 10.1 + - - +
21A ALA* 2.9 30.1 + - - +
29A GLU* 5.4 1.3 - - + +
33A LEU* 3.7 22.5 - - + +
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 3.1 17.7 + - - +
15A GLY 3.6 4.7 - - - +
17A LYS* 1.3 75.2 - - - +
19A LEU* 1.3 59.3 + - - +
21A ALA* 4.4 0.2 - - - -
22A ALA* 2.8 33.8 + - - +
30A VAL* 4.0 42.0 - - + +
33A LEU* 3.6 11.8 - - + +
34A MET* 3.5 25.8 - - - -
38A ALA* 4.3 7.0 - - + -
39A ASP 3.4 25.8 - - - +
40A VAL* 4.0 2.9 - - - -
50A PRO* 3.9 19.5 - - + -
66A LEU* 4.6 6.3 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY 3.1 24.1 + - - +
16A LYS* 3.7 28.9 - - + +
17A LYS 3.3 0.2 - - - -
18A LEU* 1.3 75.4 - - - +
20A GLU* 1.3 60.6 + - + +
22A ALA* 3.9 1.4 - - - +
23A ARG* 3.2 17.7 + - - +
42A ALA* 3.4 16.4 - - + +
43A GLU 3.7 8.1 - - - +
44A ASP* 3.6 23.3 - - + +
48A ASP 3.3 25.1 - - - +
49A THR 3.6 1.8 - - - -
50A PRO* 3.5 22.2 - - + -
53A LEU* 3.2 29.3 - - + +
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 3.2 38.0 + - + +
17A LYS* 3.3 9.6 + - - +
19A LEU* 1.3 78.5 - - + +
21A ALA* 1.3 58.7 + - - +
23A ARG* 3.4 12.0 + - - +
24A ALA* 3.0 29.7 + - - +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS 2.9 16.9 + - - +
18A LEU 3.8 3.6 - - - +
20A GLU* 1.3 74.9 - - - +
22A ALA* 1.3 59.4 + - - +
24A ALA* 3.3 3.1 + - - +
25A GLY 2.9 24.6 + - - -
26A GLN* 3.0 19.0 + - + -
29A GLU* 4.0 28.5 - - + -
30A VAL* 3.8 16.6 - - + +
33A LEU* 4.3 4.5 - - + -
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 2.8 22.8 + - + +
19A LEU 3.9 3.4 - - - +
21A ALA* 1.3 72.9 - - - +
23A ARG* 1.3 61.4 + - - +
25A GLY* 3.3 9.4 + - - -
30A VAL* 3.7 6.1 - - + +
50A PRO* 3.7 33.7 - - + +
53A LEU* 5.1 0.7 - - + -
54A ALA* 4.1 7.0 - - - +
59A HIS* 3.4 10.6 + - - -
62A ILE* 3.8 31.4 - - + +
66A LEU* 4.7 0.2 - - + -
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU 3.2 17.3 + - - +
20A GLU* 3.8 11.4 - - - +
21A ALA 3.3 0.2 - - - -
22A ALA* 1.3 75.9 - - - +
24A ALA* 1.3 56.8 + - - +
44A ASP* 4.4 8.3 + - - +
53A LEU* 3.9 36.0 - - + +
56A ARG* 3.9 22.0 - - - +
57A VAL* 3.7 21.0 - - + +
59A HIS* 2.9 20.8 - - - -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU 3.0 18.8 + - - +
21A ALA* 3.3 3.6 + - - +
23A ARG* 1.3 76.1 - - - +
25A GLY* 1.3 61.3 + - - +
26A GLN* 3.4 26.7 + - + +
59A HIS* 3.5 8.7 + - - -
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 2.9 5.7 + - - -
22A ALA 3.3 3.5 + - - -
23A ARG 3.3 4.2 - - - -
24A ALA* 1.3 78.9 - - - +
26A GLN* 1.3 64.8 + - - +
27A ASP* 3.2 10.1 + - - +
59A HIS* 3.4 26.5 - - - -
61A GLU* 4.3 7.9 - - - +
62A ILE* 3.9 11.4 - - - -
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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