Contacts of the helix formed by residues 12 - 23 (chain A) in PDB entry 1JD7
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU 3.5 4.2 + - - +
11A TRP* 1.3 76.6 - - - +
13A TRP* 1.3 64.2 + - - +
14A GLN* 2.8 22.8 + - - +
15A ASP* 2.7 51.1 + - - +
16A VAL* 3.0 18.9 + - - +
60A ARG 4.7 3.1 - - - +
61A GLY* 3.5 23.8 - - - +
319A PRO* 4.2 12.1 - - - +
333A TRP* 5.5 0.6 - - - -
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Residues in contact with TRP 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 TRP 3.7 15.0 - - - -
12A ASN* 1.3 73.9 - - - +
14A GLN* 1.3 61.4 + - + +
16A VAL* 3.5 1.1 + - + +
17A ALA* 3.1 23.7 + - - +
34A VAL* 3.8 22.9 - - + -
35A SER* 3.5 24.5 - - - -
37A PRO* 3.5 24.3 + - + +
49A ARG* 3.6 10.1 - - - -
57A LEU 5.4 0.6 + - - -
59A SER* 3.6 13.9 + - - -
61A GLY* 2.9 29.8 + - - +
62A GLY* 3.5 18.3 + - - +
63A ASN 3.7 2.4 + - - -
66A GLN* 3.6 23.1 - - + +
67A PHE* 3.5 36.4 - + - +
70A MET* 3.5 28.3 - - + +
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Residues in contact with GLN 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 ASN* 2.8 20.9 + - - +
13A TRP* 1.3 72.9 - - + +
15A ASP* 1.3 64.3 + - - +
17A ALA* 3.3 6.2 + - - +
18A GLN* 3.1 39.6 + - - +
61A GLY 4.9 0.2 + - - -
66A GLN* 3.9 31.1 + - + +
73A ARG* 4.8 8.7 - - - +
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Residues in contact with ASP 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 TRP* 4.0 17.6 - - + -
12A ASN* 2.7 33.5 + - - +
14A GLN* 1.3 74.2 - - - +
16A VAL* 1.3 57.1 + - - +
18A GLN* 3.5 3.1 + - - -
19A GLU* 2.9 30.1 + - - +
319A PRO* 3.3 16.1 - - - +
320A VAL* 2.8 32.6 + - + +
321A HIS* 3.1 36.2 + - - +
333A TRP* 5.0 3.3 - - - -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.9 26.0 - - + +
11A TRP* 3.8 25.4 - - + +
12A ASN 3.0 15.3 + - - +
13A TRP* 3.8 2.9 - - + +
15A ASP* 1.3 75.9 - - - +
17A ALA* 1.3 63.8 + - - +
19A GLU* 3.1 2.3 + - - +
20A CYS* 2.8 24.6 + - - -
32A VAL* 4.1 13.5 - - + -
34A VAL* 4.6 6.5 - - + -
70A MET* 3.6 33.4 - - + -
74A CYS* 4.0 11.7 - - - -
81A ILE* 4.4 2.5 - - + -
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Residues in contact with ALA 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 TRP 3.1 15.3 + - - +
14A GLN 3.7 1.1 - - - +
16A VAL* 1.3 78.4 - - - +
18A GLN* 1.3 62.1 + - - +
20A CYS* 3.2 11.4 + - - +
21A GLU* 3.2 22.3 + - - +
69A ASP* 5.2 0.2 - - - +
70A MET* 4.1 16.3 - - - +
73A ARG* 3.4 39.6 - - + +
74A CYS* 4.1 12.1 - - - -
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Residues in contact with GLN 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 GLN* 3.1 27.8 + - - +
15A ASP* 4.2 3.2 + - - -
17A ALA* 1.3 75.7 - - - +
19A GLU* 1.3 58.8 + - - +
20A CYS 3.2 0.2 + - - -
21A GLU* 3.2 8.5 + - - +
22A GLN* 2.9 55.5 + - - +
73A ARG* 4.3 6.7 - - - +
321A HIS* 3.3 44.7 + - + +
901A CL 3.8 26.7 - - + +
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Residues in contact with GLU 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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8A LEU* 4.5 1.6 - - + -
11A TRP* 3.5 25.6 - - + -
15A ASP 2.9 19.4 + - - +
16A VAL* 3.1 7.6 + - - +
18A GLN* 1.3 76.9 - - - +
20A CYS* 1.3 57.3 + - - +
22A GLN* 5.0 0.4 - - - -
23A TYR* 3.0 14.2 + - - +
24A LEU* 2.9 41.7 + - + -
320A VAL* 4.6 1.1 - - - +
321A HIS* 2.8 24.7 + - - -
337A HIS* 2.9 21.5 + - - +
338A ARG* 2.8 40.5 + - - -
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Residues in contact with CYS 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 VAL* 2.8 15.9 + - - -
17A ALA 3.4 5.6 - - - +
19A GLU* 1.3 78.6 - - - +
21A GLU* 1.3 60.6 + - + +
24A LEU* 4.0 14.1 - - - -
25A GLY* 2.9 29.9 + - - +
32A VAL* 4.3 1.8 - - - -
74A CYS* 2.0 60.3 - - - -
77A ALA* 3.6 7.5 - - + +
79A VAL* 3.9 20.2 - - + -
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Residues in contact with GLU 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 ALA 3.2 15.2 + - - +
18A GLN* 3.9 7.0 - - - +
20A CYS* 1.3 78.1 - - - +
22A GLN* 1.3 67.4 + - + +
26A PRO* 3.7 14.0 - - - +
73A ARG* 3.0 64.1 + - - +
76A ALA* 5.9 0.5 - - - +
77A ALA* 4.1 10.6 - - + +
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Residues in contact with GLN 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 GLN* 2.9 45.2 + - - +
19A GLU* 4.8 0.4 - - - +
21A GLU* 1.3 86.5 + - + +
23A TYR* 1.3 60.7 + - - +
26A PRO* 4.0 10.5 - - - +
321A HIS* 4.0 17.5 + - - -
338A ARG* 4.8 10.0 + - - +
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Residues in contact with TYR 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 GLU* 3.0 13.3 + - - +
21A GLU 3.7 0.4 - - - -
22A GLN* 1.3 81.6 - - - +
24A LEU* 1.3 64.7 + - + +
25A GLY 3.3 1.8 - - - -
26A PRO* 3.3 3.7 - - - +
27A LYS* 2.8 74.1 + - + +
29A TYR* 4.1 5.6 - + - -
337A HIS* 3.5 26.5 - + - -
338A ARG* 3.4 66.5 + - + +
343A ALA* 3.0 28.6 - - - +
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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