Contacts of the helix formed by residues 12 - 25 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ASP* 1.3 70.6 + - - +
14B LEU* 3.3 12.4 + - - +
15B GLY* 3.5 27.4 - - - -
16B LYS* 3.0 27.4 + - - +
19B LEU* 6.1 0.4 - - - +
39B ASP* 6.3 2.9 - - - -
42B ALA* 4.8 6.1 - - - +
43B GLU 5.4 4.9 + - - +
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Residues in contact with ASP 13 (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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12B SER* 1.3 77.6 + - - +
14B LEU* 1.3 66.4 + - + +
16B LYS* 3.6 23.1 + - - +
17B LYS* 3.3 40.6 + - - +
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Residues in contact with LEU 14 (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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12B SER* 3.3 8.7 + - - +
13B ASP* 1.3 80.7 - - + +
15B GLY* 1.3 57.2 + - - +
17B LYS* 3.0 24.7 + - - +
18B LEU* 2.8 34.5 + - - +
33B LEU* 4.2 16.8 - - + +
36B ASN* 3.3 33.7 - - + +
37B GLY 4.1 2.2 - - - -
38B ALA* 3.8 28.4 - - + +
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Residues in contact with GLY 15 (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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12B SER* 3.5 18.6 - - - -
13B ASP 3.4 0.6 - - - -
14B LEU* 1.3 78.9 - - - +
16B LYS* 1.3 55.3 + - - +
18B LEU* 3.2 5.7 + - - +
19B LEU* 2.9 38.2 + - - +
38B ALA* 4.4 5.1 - - - +
39B ASP* 5.2 2.4 - - - +
42B ALA* 3.6 23.6 - - - +
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Residues in contact with LYS 16 (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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12B SER 3.0 22.2 + - - +
13B ASP* 3.7 23.3 + - - +
15B GLY* 1.3 73.4 - - - +
17B LYS* 1.3 59.1 + - + +
19B LEU* 3.5 12.1 + - - +
20B GLU* 3.0 50.5 + - + +
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Residues in contact with LYS 17 (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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13B ASP* 3.3 29.9 + - - +
14B LEU* 3.0 25.6 + - - +
16B LYS* 1.3 76.7 - - + +
18B LEU* 1.3 57.3 + - - +
20B GLU* 3.4 12.9 + - - +
21B ALA* 2.8 28.8 + - - +
29B GLU* 5.3 3.8 - - - +
33B LEU* 3.3 33.7 - - + +
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Residues in contact with LEU 18 (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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14B LEU 2.8 15.1 + - - +
15B GLY 3.5 7.6 - - - +
17B LYS* 1.3 70.6 - - - +
19B LEU* 1.3 60.1 + - - +
21B ALA* 3.8 0.4 - - - +
22B ALA* 3.0 29.8 + - - +
30B VAL* 3.9 44.9 - - + +
33B LEU* 3.5 11.2 - - + +
34B MET* 4.0 11.0 - - + -
38B ALA* 4.0 18.4 - - + -
39B ASP 3.4 25.8 - - - +
40B VAL* 3.9 10.8 - - - -
42B ALA* 5.2 0.4 - - + -
50B PRO* 3.9 19.3 - - + -
66B LEU* 4.7 4.9 - - + -
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Residues in contact with LEU 19 (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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12B SER 6.1 0.2 - - - +
15B GLY 2.9 24.9 + - - +
16B LYS* 3.5 12.1 - - - +
17B LYS 3.3 0.2 - - - -
18B LEU* 1.3 76.4 - - - +
20B GLU* 1.3 57.5 + - + +
22B ALA* 3.4 1.3 + - - +
23B ARG* 3.0 24.8 + - - +
42B ALA* 4.0 6.5 - - + +
43B GLU 3.6 28.9 - - - +
44B ASP* 3.6 11.9 - - + +
48B ASP 3.4 18.2 - - - +
49B THR 3.5 2.5 - - - -
50B PRO* 3.4 36.6 - - + -
53B LEU* 3.4 30.0 - - + +
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Residues in contact with GLU 20 (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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16B LYS* 3.0 39.9 + - + +
17B LYS* 3.9 11.7 - - - +
19B LEU* 1.3 75.8 - - + +
21B ALA* 1.3 57.6 + - - +
23B ARG* 3.3 22.2 + - - +
24B ALA* 2.9 30.8 + - - +
26B GLN* 5.0 0.9 - - - -
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Residues in contact with ALA 21 (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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17B LYS 2.8 21.8 + - - +
18B LEU 3.8 2.0 - - - +
20B GLU* 1.3 69.7 - - - +
22B ALA* 1.3 63.5 + - - +
24B ALA 3.3 0.7 + - - -
25B GLY 3.0 4.2 + - - -
26B GLN* 3.0 42.4 + - - +
29B GLU* 3.9 27.6 - - + -
30B VAL* 3.7 18.7 - - + +
33B LEU* 4.1 4.5 - - + -
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Residues in contact with ALA 22 (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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18B LEU* 3.0 19.4 + - + +
19B LEU 3.8 3.8 - - - +
21B ALA* 1.3 71.7 - - - +
23B ARG* 1.3 66.5 + - - +
25B GLY* 3.2 10.6 + - - -
30B VAL* 3.7 5.4 - - + +
50B PRO* 3.8 31.4 - - + +
53B LEU* 5.0 0.2 - - + -
54B ALA* 4.2 6.6 - - - +
59B HIS* 3.4 10.4 + - - -
62B ILE* 3.7 32.1 - - + +
66B LEU* 4.6 0.7 - - + -
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Residues in contact with ARG 23 (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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19B LEU* 3.0 17.4 + - - +
20B GLU* 3.6 21.4 - - - +
22B ALA* 1.3 78.5 - - - +
24B ALA* 1.3 56.9 + - - +
44B ASP* 5.6 3.0 + - - +
53B LEU* 4.2 34.8 - - + +
56B ARG* 5.8 2.3 - - - +
57B VAL* 3.6 20.4 - - + +
59B HIS* 2.9 21.7 + - - -
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Residues in contact with ALA 24 (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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20B GLU 2.9 17.7 + - - +
21B ALA 3.3 0.4 + - - +
23B ARG* 1.3 77.3 - - - +
25B GLY* 1.3 62.0 + - - +
26B GLN* 3.3 30.6 + - + +
59B HIS* 3.6 7.7 + - - -
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Residues in contact with GLY 25 (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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21B ALA 3.0 4.5 + - - -
22B ALA 3.2 7.4 + - - -
23B ARG 3.3 1.0 - - - -
24B ALA* 1.3 78.8 - - - +
26B GLN* 1.3 59.5 + - - +
27B ASP* 3.2 10.7 + - - +
59B HIS* 3.4 28.5 - - - -
61B GLU* 4.2 7.1 - - - +
62B ILE* 3.9 11.2 - - - +
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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