Contacts of the helix formed by residues 11 - 29 (chain A) in PDB entry 1JQI
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLU 3.8 5.4 - - - +
10A LEU* 1.3 98.7 - - + +
12A GLU* 1.3 66.0 + - - +
13A THR* 4.2 6.5 - - - +
14A HIS* 2.9 40.3 + - + +
15A GLN* 3.0 9.7 + - - +
72A LEU* 5.0 5.8 - - + -
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Residues in contact with GLU 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 LEU 3.5 2.7 + - - -
11A PRO* 1.3 72.9 - - - +
13A THR* 1.3 57.1 + - - +
15A GLN* 3.8 15.2 - - + +
16A MET* 3.0 70.2 + - + +
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Residues in contact with THR 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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11A PRO* 3.0 3.7 - - - +
12A GLU* 1.3 80.0 - - - +
14A HIS* 1.3 70.3 + - + +
16A MET* 3.9 15.2 - - + +
17A LEU* 3.2 25.9 + - + +
69A LEU* 5.6 12.8 - - + -
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Residues in contact with HIS 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 LEU* 4.0 17.4 - - + +
11A PRO* 2.9 39.0 + - + +
13A THR* 1.3 86.2 - - + +
15A GLN* 1.3 61.4 + - - +
16A MET 3.3 0.2 - - - -
17A LEU* 3.4 7.1 + - - +
18A ARG* 3.0 28.8 + - - +
69A LEU* 6.0 0.7 - - + -
70A ASP* 3.2 37.4 + - - -
72A LEU* 4.2 16.9 + - + +
73A ALA* 3.5 29.3 + - + +
76A ILE* 4.1 12.2 - - + +
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Residues in contact with GLN 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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9A GLU* 5.9 0.8 + - - -
10A LEU* 2.6 41.6 + - + +
11A PRO 3.0 13.8 + - - +
12A GLU* 3.8 17.8 - - + +
14A HIS* 1.3 72.5 - - - +
16A MET* 1.3 66.5 + - + +
18A ARG* 3.4 29.6 + - - +
19A GLN* 3.2 22.5 + - - +
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Residues in contact with MET 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 GLU* 3.0 62.3 + - + +
13A THR* 3.9 15.5 - - + +
15A GLN* 1.3 74.8 - - + +
17A LEU* 1.3 64.7 + - - +
19A GLN* 3.2 18.8 + - - +
20A THR* 3.0 29.5 + - - +
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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 THR 3.2 16.6 + - - +
14A HIS* 3.5 7.2 - - - +
15A GLN 3.3 0.2 - - - -
16A MET* 1.3 80.3 - - - +
18A ARG* 1.3 62.5 + - - +
20A THR* 3.4 7.8 + - + -
21A CYS* 3.1 41.3 + - - -
55A LEU* 4.7 5.4 - - + -
58A MET* 4.4 15.7 - - + -
69A LEU* 4.5 14.4 - - + -
73A ALA* 3.6 20.9 - - + +
76A ILE* 4.3 6.7 - - + -
77A ALA* 3.6 31.0 - - + +
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Residues in contact with ARG 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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5A TYR* 2.9 44.4 + - - -
7A SER* 4.6 5.7 + - - -
10A LEU* 3.7 22.3 - - - +
14A HIS 3.0 16.1 + - - +
15A GLN* 3.5 31.1 + - - +
16A MET 3.2 0.2 - - - -
17A LEU* 1.3 78.0 - - - +
19A GLN* 1.3 63.1 + - - +
21A CYS* 3.3 3.2 + - - +
22A ARG* 2.9 43.1 + - - +
76A ILE* 3.6 22.4 - - + -
80A GLU* 3.5 26.1 - - - +
305A TRP* 4.9 0.2 - - - -
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Residues in contact with GLN 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 GLN 3.2 10.2 + - - +
16A MET* 3.5 19.0 + - - +
18A ARG* 1.3 79.3 - - - +
20A THR* 1.3 75.2 + - - +
22A ARG* 3.3 11.8 + - - +
23A ASP* 3.0 48.7 + - - +
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Residues in contact with THR 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 MET* 3.0 18.6 + - - +
17A LEU* 3.7 10.2 - - + -
18A ARG 3.3 0.2 - - - -
19A GLN* 1.3 89.0 + - - +
21A CYS* 1.3 60.8 + - - +
23A ASP* 3.5 6.2 + - - +
24A PHE* 3.1 26.0 + - + +
53A LEU* 4.8 24.7 - - + -
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Residues in contact with CYS 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* 3.1 27.6 + - - +
18A ARG 3.9 1.1 - - - +
20A THR* 1.3 78.3 - - - +
22A ARG* 1.3 61.2 + - - +
24A PHE* 3.3 6.9 + - - +
25A ALA* 2.9 31.0 + - - +
53A LEU* 6.1 1.3 - - - -
55A LEU* 3.8 25.4 - - - -
77A ALA* 3.6 33.4 - - - +
80A GLU* 3.8 19.7 - - + -
81A ILE* 4.3 8.0 - - + +
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Residues in contact with ARG 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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4A VAL 5.4 7.2 - - - +
5A TYR* 5.1 8.1 - - - -
18A ARG* 2.9 39.5 + - - +
19A GLN* 3.7 11.4 - - - +
20A THR 3.3 0.2 - - - -
21A CYS* 1.3 76.8 - - - +
23A ASP* 1.3 62.8 - - - +
25A ALA* 3.4 4.3 + - - +
26A GLU* 2.8 36.1 + - + +
80A GLU* 3.0 44.0 + - - +
83A ARG* 4.2 21.0 + - - +
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Residues in contact with ASP 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 GLN* 3.0 39.8 + - - +
20A THR* 3.7 6.0 - - - +
22A ARG* 1.3 80.1 - - - +
24A PHE* 1.3 54.8 + - - +
26A GLU* 3.2 5.5 + - - +
27A LYS* 2.7 39.7 + - - +
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Residues in contact with PHE 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 THR 3.1 15.4 + - - +
21A CYS* 3.5 10.1 - - - +
23A ASP* 1.3 75.9 - - - +
25A ALA* 1.3 56.6 + - - +
27A LYS* 4.6 3.6 - - - -
28A GLU* 2.6 73.1 + - + +
29A LEU* 4.2 14.1 - - + -
46A GLN* 3.9 13.5 - - - -
49A LYS* 3.9 22.2 - - + -
50A MET* 3.5 33.7 - - + -
53A LEU* 4.1 23.3 - - + -
55A LEU* 4.9 2.5 - - + -
81A ILE* 3.8 17.5 - - + -
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Residues in contact with ALA 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 CYS 2.9 16.3 + - - +
22A ARG* 3.8 4.9 - - - +
24A PHE* 1.3 77.4 - - - +
26A GLU* 1.3 57.8 + - - +
29A LEU* 3.0 30.5 + - + +
30A VAL* 2.8 32.9 + - + +
80A GLU 3.4 26.2 - - - +
81A ILE* 4.4 1.1 - - + -
83A ARG* 5.7 3.8 - - + +
84A GLY* 4.3 8.7 - - - -
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Residues in contact with GLU 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 ARG* 2.8 24.3 + - + +
23A ASP* 3.6 7.0 - - - +
25A ALA* 1.3 79.6 - - - +
27A LYS* 1.3 58.2 + - - +
30A VAL* 3.6 24.6 - - - +
31A PRO* 3.7 13.9 - - - +
83A ARG* 3.2 25.4 + - - +
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Residues in contact with LYS 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 ASP* 2.7 22.1 + - + +
24A PHE* 3.9 2.7 - - - +
26A GLU* 1.3 75.8 - - - +
28A GLU* 1.3 87.6 + - + +
29A LEU 3.8 0.2 - - - -
31A PRO* 3.6 16.7 - - - +
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Residues in contact with GLU 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 PHE* 2.6 57.1 + - + +
27A LYS* 1.3 113.0 + - + +
29A LEU* 1.3 60.4 + - + +
31A PRO* 4.3 2.5 - - - +
32A ILE* 3.2 29.1 - - - +
46A GLN* 4.0 15.9 - - + +
49A LYS* 3.9 25.7 + - + +
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Residues in contact with LEU 29 (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 PHE* 4.2 12.3 - - + -
25A ALA* 3.0 27.1 + - + +
28A GLU* 1.3 79.1 - - - +
30A VAL* 1.3 68.4 + - - +
31A PRO 3.4 2.2 - - - -
32A ILE* 3.1 7.3 + - + +
33A ALA* 2.9 26.0 + - - +
36A LEU* 5.7 1.3 - - + -
46A GLN* 3.9 30.1 - - + -
81A ILE* 3.7 45.3 - - + +
84A GLY 4.0 13.9 - - - -
85A CYS* 4.3 6.5 - - + +
88A THR* 4.0 23.1 - - + +
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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