Contacts of the helix formed by residues 0 - 22 (chain J) in PDB entry 5JHC
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 PRO 0 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1J GLY* 1.3 84.0 - - - +
1J MET* 1.3 58.9 + - - +
2J GLU 3.2 0.2 - - - -
3J GLU* 3.1 12.5 + - + +
4J GLN* 2.9 30.0 + - - +
10O GLN* 5.1 1.7 - - - +
0j PRO* 4.3 22.2 - - + -
2j GLU* 5.5 13.2 - - + +
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Residues in contact with MET 1 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1J GLY 3.0 6.2 - - - +
0J PRO* 1.3 79.6 - - - +
2J GLU* 1.3 68.4 + - - +
4J GLN* 3.4 2.1 + - - +
5J ARG* 2.9 29.7 + - - +
-1j GLY 5.5 0.2 - - - +
0j PRO* 4.3 14.6 - - + +
3j GLU* 4.2 18.4 - - - +
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Residues in contact with GLU 2 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1J GLY* 2.7 45.5 + - - +
0J PRO 3.2 0.2 - - - -
1J MET* 1.3 83.9 - - - +
3J GLU* 1.3 62.8 + - - +
5J ARG* 3.2 12.8 + - - +
6J GLU* 2.9 23.0 + - - +
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Residues in contact with GLU 3 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1J GLY 4.0 1.5 + - - +
0J PRO* 3.1 16.5 + - + +
2J GLU* 1.3 78.7 - - - +
4J GLN* 1.3 57.9 + - - +
6J GLU* 3.0 9.6 + - - +
7J ILE* 2.9 36.3 + - + +
10O GLN* 5.5 1.8 - - - +
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Residues in contact with GLN 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I GLU* 3.3 19.3 - - - +
0J PRO 2.9 15.2 + - - +
1J MET 3.8 3.8 - - - +
3J GLU* 1.3 76.0 - - - +
5J ARG* 1.3 57.5 + - - +
7J ILE* 3.4 9.0 + - - +
8J LEU* 3.0 31.0 + - - +
10O GLN* 3.8 9.3 + - - +
-1j GLY 3.2 30.7 - - - +
0j PRO* 4.6 5.2 - - + -
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Residues in contact with ARG 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J MET 2.9 18.6 + - - +
2J GLU* 3.4 12.1 - - - +
3J GLU 3.1 0.2 - - - -
4J GLN* 1.3 75.8 - - - +
6J GLU* 1.3 68.7 + - - +
8J LEU* 3.1 10.9 + - - +
9J GLU* 2.9 36.6 + - + +
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Residues in contact with GLU 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J GLU 2.9 12.4 + - - +
3J GLU* 3.3 12.3 - - - +
5J ARG* 1.3 81.3 - - - +
7J ILE* 1.3 61.8 + - + +
9J GLU* 3.0 9.3 + - - +
10J GLN* 2.9 35.9 + - + +
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Residues in contact with ILE 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I GLU* 3.4 20.2 - - - +
3J GLU* 2.9 24.2 + - + +
4J GLN* 3.5 6.5 - - - +
6J GLU* 1.3 75.0 - - + +
8J LEU* 1.3 59.5 + - - +
10J GLN* 3.1 16.2 + - - +
11J LEU* 2.9 37.6 + - + +
3O GLU* 5.0 4.9 - - + +
6O GLU* 3.7 32.1 - - + +
7O ILE* 4.0 13.5 - - + -
10O GLN* 3.6 35.9 - - + +
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Residues in contact with LEU 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I LEU* 3.6 21.1 - - + -
21I GLU* 3.6 31.6 - - + +
22I LEU* 3.7 24.9 - - + -
4J GLN 3.0 13.2 + - - +
5J ARG* 3.3 13.2 - - + +
7J ILE* 1.3 79.7 - - - +
9J GLU* 1.3 55.9 + - - +
11J LEU* 3.2 9.3 + - - +
12J LYS* 2.9 26.3 + - - +
1S MET* 4.6 14.4 - - + -
22e LEU* 3.6 31.5 - - + +
-1j GLY 5.1 4.0 - - - +
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Residues in contact with GLU 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J ARG* 2.9 27.4 + - - +
6J GLU* 3.0 11.2 + - - +
8J LEU* 1.3 74.0 - - - +
10J GLN* 1.3 66.1 + - + +
12J LYS* 3.1 33.1 + - - +
13J LYS* 3.0 21.3 + - - +
22e LEU* 5.5 4.9 - - - +
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Residues in contact with GLN 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J GLU* 2.9 30.6 + - - +
7J ILE* 3.2 9.0 - - - +
9J GLU* 1.3 77.4 - - + +
11J LEU* 1.3 56.1 + - - +
13J LYS* 3.0 9.9 + - - +
14J THR* 3.0 29.6 + - - -
2O GLU* 4.5 9.3 + - - +
3O GLU* 3.5 23.8 - - - +
6O GLU* 2.7 42.1 + - - +
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Residues in contact with LEU 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I THR* 3.8 27.8 - - + +
17I MET* 4.0 15.5 - - + -
18I LEU* 4.1 22.0 - - + +
21I GLU* 4.0 22.9 - - + -
7J ILE* 2.9 34.0 + - + +
8J LEU* 3.3 8.7 - - - +
10J GLN* 1.3 77.8 - - - +
12J LYS* 1.3 63.5 + - - +
14J THR* 3.3 6.7 + - - -
15J LEU* 3.0 28.8 + - - +
3O GLU* 3.6 22.2 - - + +
7O ILE* 4.2 9.4 - - + -
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Residues in contact with LYS 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J LEU 2.9 12.8 + - - +
9J GLU* 3.1 33.7 + - - +
11J LEU* 1.3 77.5 - - - +
13J LYS* 1.3 57.6 + - - +
15J LEU* 3.1 10.9 + - - +
16J GLN* 2.9 43.3 + - - +
19e THR* 3.1 28.9 + - + +
20e VAL* 4.5 4.2 + - - +
22e LEU* 2.8 48.2 + - + +
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Residues in contact with LYS 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J GLU 3.0 11.8 + - - +
10J GLN* 3.0 11.2 + - - +
12J LYS* 1.3 76.1 - - - +
14J THR* 1.3 64.5 + - - +
16J GLN* 2.9 25.7 + - - +
17J MET* 3.0 13.5 + - - +
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Residues in contact with THR 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I THR* 3.8 26.0 - - + +
17I MET* 6.1 0.2 - - + -
10J GLN 3.0 12.3 + - - -
11J LEU 3.5 7.9 - - - -
13J LYS* 1.3 75.8 - - - +
15J LEU* 1.3 58.2 + - - +
17J MET* 3.4 6.0 + - - +
18J LEU* 3.0 35.4 + - + +
-1O GLY 5.8 0.3 - - - -
0O PRO* 4.8 19.2 - - + +
3O GLU* 3.0 29.7 + - - +
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Residues in contact with LEU 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I LEU* 5.9 0.4 - - + -
14I THR* 3.5 23.8 - - + -
15I LEU* 3.6 21.8 - - + -
18I LEU* 3.4 32.8 - - + -
11J LEU 3.0 16.5 + - - +
12J LYS* 3.1 9.6 + - + +
14J THR* 1.3 74.9 - - - +
16J GLN* 1.3 60.5 + - - +
18J LEU* 3.8 8.1 - - + +
19J THR* 2.7 36.4 + - - +
15e LEU* 5.6 7.0 - - + -
18e LEU* 4.5 15.9 - - + -
19e THR* 4.6 14.4 - - + +
22e LEU* 4.4 10.8 - - + -
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Residues in contact with GLN 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J LYS* 2.9 34.3 + - - +
13J LYS* 2.9 16.4 + - - +
15J LEU* 1.3 78.7 - - - +
17J MET* 1.3 63.2 + - - +
19J THR* 3.2 4.5 + - - -
20J VAL* 3.0 29.9 + - + +
19e THR* 3.3 27.6 - - + +
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Residues in contact with MET 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LYS 3.0 11.0 + - - +
14J THR* 3.8 8.5 - - - +
16J GLN* 1.3 75.5 - - - +
18J LEU* 1.3 66.5 + - + +
20J VAL* 2.9 20.4 + - - +
21J GLU* 3.0 23.5 + - - +
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Residues in contact with LEU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE* 4.0 21.1 - - + +
10I GLN* 4.2 14.6 - - + +
11I LEU* 3.4 29.4 - - + +
14I THR* 3.1 31.0 - - + +
14J THR* 3.0 27.1 + - + +
15J LEU* 3.8 8.3 - - + +
17J MET* 1.3 76.2 - - + +
19J THR* 1.3 62.0 + - - +
21J GLU* 3.3 31.7 + - - +
22J LEU* 3.4 23.2 + - + +
15e LEU* 6.0 0.9 - - + -
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Residues in contact with THR 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 2.7 26.8 + - - +
16J GLN* 3.7 5.2 - - - -
18J LEU* 1.3 75.2 - - - +
20J VAL* 1.3 65.9 + - + +
21J GLU 3.5 0.3 + - - -
22J LEU* 3.5 19.6 + - + +
12e LYS* 3.8 21.5 - - + +
15e LEU* 3.6 42.8 - - + +
16e GLN* 3.8 17.7 - - + +
19e THR* 4.2 6.6 + - - -
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Residues in contact with VAL 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J GLN* 3.0 22.9 + - + +
17J MET* 2.9 11.9 + - - +
19J THR* 1.3 79.5 - - - +
21J GLU* 1.3 65.8 + - + +
22J LEU 3.1 9.4 - - - +
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Residues in contact with GLU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE* 3.1 40.4 - - + +
17J MET* 3.0 23.8 + - - +
18J LEU* 3.7 16.7 - - - +
19J THR 3.3 0.4 - - - -
20J VAL* 1.3 79.7 - - + +
22J LEU* 1.3 67.7 + - + +
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Residues in contact with LEU 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I GLN 5.9 0.7 - - - +
7I ILE* 3.6 28.7 - - + -
8I LEU* 5.5 1.6 - - + +
11I LEU* 3.7 28.0 - - + -
18J LEU* 3.4 16.2 + - + +
19J THR* 3.8 14.4 - - + +
20J VAL 3.1 10.3 - - - +
21J GLU* 1.3 86.1 - - + +
8e LEU* 5.4 4.3 - - - +
11e LEU* 3.9 22.2 - - + -
12e LYS* 4.3 20.7 - - + +
15e LEU* 5.0 6.1 - - + -
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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