Contacts of the strand formed by residues 58 - 66 (chain A) in PDB entry 1J5K
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 ASP 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 4.7 12.6 - - + -
20A ILE 3.3 9.4 - - - +
21A PRO* 3.3 16.2 - - - +
22A LYS* 3.9 1.4 - - - +
53A LEU* 3.3 30.6 - - + +
56A SER* 3.3 11.6 + - - +
57A GLU* 1.3 99.9 + - - +
59A ARG* 1.3 67.1 + - - +
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Residues in contact with ARG 59 (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 THR* 3.1 26.9 - - - -
20A ILE* 3.0 23.7 + - + +
22A LYS* 3.5 38.9 - - + +
25A ALA* 3.3 28.3 - - + +
29A ILE* 3.4 4.5 - - - +
49A ILE* 4.8 11.2 - - + -
52A PRO* 4.2 25.9 - - + +
53A LEU* 4.7 5.6 - - - +
58A ASP* 1.3 76.9 - - - +
60A ILE* 1.3 65.6 + - - +
61A ILE* 3.9 1.3 + - + -
106B C 2.8 34.8 + - - +
107B C 2.9 33.5 - - - +
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Residues in contact with ILE 60 (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 GLN* 5.2 12.6 - - + +
18A VAL 3.9 2.2 - - - +
19A THR* 4.1 17.3 - - + -
49A ILE* 3.3 21.0 - - - +
50A ASP* 3.3 40.9 + - + +
51A GLU 5.9 0.4 + - - -
53A LEU* 3.7 35.7 - - + +
59A ARG* 1.3 78.3 - - - +
61A ILE* 1.3 65.7 + - - +
62A THR* 4.5 12.8 - - - +
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Residues in contact with ILE 61 (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 GLN* 3.4 3.3 - - - +
18A VAL* 2.7 49.2 + - + +
20A ILE* 3.7 43.7 - - + -
28A ILE* 5.3 3.1 - - + -
29A ILE* 6.4 1.6 - - + -
36A ILE* 6.2 1.3 - - + -
47A ILE* 3.4 28.3 - - + -
48A LYS 3.8 2.5 - - - -
49A ILE* 4.3 17.0 - - + -
59A ARG* 4.9 1.1 - - + +
60A ILE* 1.3 78.3 - - - +
62A THR* 1.3 62.5 + - - +
63A ILE* 4.1 14.5 + - + -
77A LEU* 4.9 24.5 - - + -
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Residues in contact with THR 62 (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 THR* 4.4 8.3 - - - +
16A THR 3.7 9.4 - - - +
17A GLN* 4.0 21.7 + - + +
47A ILE* 3.4 4.3 - - - +
48A LYS* 2.7 61.1 + - + +
50A ASP* 5.5 4.2 + - - -
60A ILE* 4.5 8.8 + - - +
61A ILE* 1.3 75.3 - - - +
63A ILE* 1.3 68.6 + - - +
64A THR* 4.2 10.3 + - - +
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Residues in contact with ILE 63 (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 ILE 4.3 0.3 - - - +
15A THR* 3.8 3.1 + - - -
16A THR* 2.8 40.1 + - - +
18A VAL* 3.9 19.3 - - + -
45A ALA* 4.7 10.8 - - + -
46A SER 3.6 13.7 - - - +
47A ILE* 4.8 5.4 - - + -
61A ILE* 4.2 13.5 - - + -
62A THR* 1.3 75.4 - - - +
64A THR* 1.3 70.9 + - - +
70A ILE* 3.8 25.6 - - + -
73A ALA* 4.7 4.3 - - + -
74A GLN* 3.7 35.0 - - + +
77A LEU* 4.1 15.0 - - + -
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Residues in contact with THR 64 (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 ILE* 4.9 12.6 - - + -
14A ILE 4.1 8.1 - - - +
15A THR* 4.3 9.6 + - - -
46A SER* 3.2 42.1 + - - -
48A LYS* 6.1 0.2 - - - +
62A THR* 4.2 12.3 + - - +
63A ILE* 1.3 83.3 + - - +
65A GLY* 1.3 61.8 + - - +
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Residues in contact with GLY 65 (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 PRO 4.5 0.4 - - - -
13A ILE* 4.8 9.6 - - - +
14A ILE 3.5 18.5 + - - +
46A SER 5.2 0.2 - - - -
64A THR* 1.3 78.6 - - - +
66A THR* 1.3 69.9 + - - +
69A GLN* 3.3 17.9 - - - -
70A ILE* 3.5 15.4 - - - +
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Residues in contact with THR 66 (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 GLY* 5.5 1.1 - - - -
11A GLY* 3.7 35.4 - - - +
12A PRO 3.3 10.5 - - - -
13A ILE* 4.0 11.7 - - + -
65A GLY* 1.3 74.5 - - - -
67A GLN* 1.3 67.9 + - - +
68A ASP* 3.6 10.4 + - - +
69A GLN* 2.8 39.9 + - - +
70A ILE* 2.9 9.7 + - - +
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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