Contacts of the helix formed by residues 10 - 28 (chain A) in PDB entry 2JQK
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 1.3 68.0 + - - +
12A GLN* 3.4 5.7 - - - +
13A LYS* 3.2 28.5 + - - +
14A ALA* 3.2 9.4 + - - +
43A TYR* 3.0 54.1 + - - +
46A HIS* 3.3 38.1 + - - +
47A VAL* 3.5 21.1 - - + +
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Residues in contact with LEU 11 (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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10A ASN* 1.3 79.1 - - - +
12A GLN* 1.3 53.8 + - - +
14A ALA* 2.8 20.7 + - + +
15A ILE* 2.7 34.5 - - + +
44A PHE* 5.8 5.4 - - + -
47A VAL* 4.0 33.9 - - + -
51A GLU* 6.1 5.2 - - + -
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Residues in contact with GLN 12 (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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10A ASN 3.4 2.8 - - - +
11A LEU* 1.3 79.1 - - - +
13A LYS* 1.3 67.1 + - + +
15A ILE* 3.7 6.7 + - - -
16A ASP* 2.5 60.3 + - - +
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Residues in contact with LYS 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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10A ASN* 3.2 28.5 + - - +
11A LEU 3.0 0.6 - - - -
12A GLN* 1.3 89.2 - - + +
14A ALA* 1.3 59.4 + - - +
16A ASP* 4.2 5.6 - - + -
17A LEU* 2.8 49.0 + - + +
43A TYR* 3.6 27.9 + - + +
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Residues in contact with ALA 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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10A ASN 3.2 6.9 + - - +
11A LEU* 2.8 17.9 + - + +
13A LYS* 1.3 76.9 - - - +
15A ILE* 1.3 59.9 + - + +
18A ALA* 2.8 32.2 + - - +
40A ALA* 3.8 6.6 - - - +
43A TYR* 3.7 26.9 - - + +
44A PHE* 4.0 31.1 - - + +
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Residues in contact with ILE 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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11A LEU* 2.7 43.5 - - + +
12A GLN* 4.1 6.3 - - - +
14A ALA* 1.3 76.2 - - + +
16A ASP* 1.3 61.1 - - - +
18A ALA* 4.1 4.7 - - + -
19A SER* 2.6 51.2 + - - +
44A PHE* 4.7 14.6 - - + -
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Residues in contact with ASP 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 GLN* 2.5 51.6 + - - +
13A LYS* 4.0 7.6 - - + +
15A ILE* 1.3 79.9 - - - +
17A LEU* 1.3 62.5 + - + +
19A SER* 4.1 3.7 - - - -
20A LYS* 3.3 24.6 + - - +
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Residues in contact with LEU 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 LYS* 2.8 41.1 + - + +
16A ASP* 1.3 77.9 - - + +
18A ALA* 1.3 64.0 + - - +
20A LYS* 4.1 3.0 - - - +
21A ALA* 3.3 23.4 + - - +
36A LEU* 3.6 28.1 - - + +
39A HIS* 4.3 19.7 - - + +
40A ALA* 3.1 17.8 - - + +
43A TYR* 3.7 31.9 - - + -
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Residues in contact with ALA 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 ALA 2.8 22.3 + - - +
15A ILE* 3.8 4.5 - - - +
17A LEU* 1.3 77.4 - - - +
19A SER* 1.3 63.7 + - - +
21A ALA* 3.8 4.4 - - - +
22A ALA* 3.3 22.7 + - - +
37A TYR* 6.0 0.2 - - - -
40A ALA* 3.0 14.1 - - + +
44A PHE* 4.0 18.6 - - + -
68A TYR* 4.3 25.3 + - + +
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Residues in contact with SER 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 ILE* 2.6 34.1 + - - +
16A ASP* 4.1 4.7 - - - -
18A ALA* 1.3 72.7 - - - +
20A LYS* 1.3 60.4 + - - +
22A ALA* 3.5 4.2 + - - +
23A GLN* 2.9 29.7 + - - +
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Residues in contact with LYS 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 ASP 3.3 17.7 + - - +
17A LEU 3.8 2.9 + - - +
19A SER* 1.3 78.6 - - - +
21A ALA* 1.3 59.2 + - - +
23A GLN* 4.1 20.2 - - - +
24A GLU* 2.5 64.4 + - - +
36A LEU* 4.2 16.4 - - + -
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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 LEU 3.3 18.1 + - - +
18A ALA* 3.8 5.6 - - - +
19A SER 3.2 0.6 - - - -
20A LYS* 1.3 80.0 - - - +
22A ALA* 1.3 62.3 + - - +
24A GLU 3.2 9.4 + - - -
25A ASP 3.2 8.5 + - - -
33A ALA* 3.5 14.8 - - - +
36A LEU* 3.6 24.6 - - + +
37A TYR* 3.5 34.9 + - + +
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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 ALA 3.3 14.8 + - - +
19A SER* 4.0 3.8 - - - +
21A ALA* 1.3 75.6 - - - +
23A GLN* 1.3 66.3 + - - +
25A ASP* 3.0 13.0 + - - +
26A LYS* 3.3 15.1 + - - +
37A TYR* 3.3 16.3 + - - +
68A TYR* 4.3 17.7 - - + +
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Residues in contact with GLN 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 SER 2.9 19.7 + - - +
20A LYS* 3.5 21.2 - - - +
22A ALA* 1.3 76.8 - - - +
24A GLU* 1.3 77.1 + - - +
26A LYS* 3.8 4.3 + - - +
27A ALA* 3.2 33.5 + - + +
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Residues in contact with GLU 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 LYS* 2.5 49.7 + - - +
21A ALA 3.2 3.0 + - - +
22A ALA 3.1 0.6 - - - -
23A GLN* 1.3 96.1 + - - +
25A ASP* 1.3 60.1 + - - +
26A LYS 3.2 0.7 - - - -
27A ALA* 4.0 5.6 - - + -
28A GLY 2.8 25.8 + - - -
29A ASN* 2.9 43.3 + - + +
32A GLU* 3.7 8.9 - - + +
33A ALA* 3.4 21.5 - - + -
36A LEU* 3.3 12.9 - - - +
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Residues in contact with ASP 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 3.2 3.2 + - - +
22A ALA 3.0 8.4 + - - +
24A GLU* 1.3 80.6 - - - +
26A LYS* 1.3 65.3 + - + +
28A GLY* 3.8 4.9 + - - -
29A ASN 3.9 7.6 + - - -
30A TYR* 4.3 12.0 + - - -
33A ALA* 4.2 1.7 - - - +
37A TYR* 3.1 29.1 + - + +
71A ARG* 3.5 32.0 + - - +
75A LEU* 3.7 27.2 - - - +
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Residues in contact with LYS 26 (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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22A ALA 3.3 10.5 + - - +
23A GLN* 4.3 4.0 - - - +
25A ASP* 1.3 83.9 + - + +
27A ALA* 1.3 66.0 + - - +
28A GLY* 3.3 0.6 - - - -
71A ARG* 5.4 9.0 - - - +
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Residues in contact with ALA 27 (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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23A GLN* 3.2 27.0 + - + +
24A GLU* 3.2 9.6 + - + +
26A LYS* 1.3 80.1 - - - +
28A GLY* 1.3 58.2 + - - +
29A ASN* 3.7 5.4 - - + +
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Residues in contact with GLY 28 (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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24A GLU 2.8 3.0 + - - -
25A ASP 4.3 5.2 - - - -
26A LYS 3.3 3.2 - - - -
27A ALA* 1.3 79.5 - - - +
29A ASN* 1.3 68.1 + - - +
30A TYR* 3.0 33.8 - - - -
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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