Contacts of the helix formed by residues 52 - 66 (chain A) in PDB entry 1J0B
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 GLY 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASP 3.3 14.3 + - - +
44A ASP* 4.1 2.0 - - - +
46A THR* 2.8 19.7 + - - +
51A GLY* 1.3 74.8 - - - -
53A ASN* 1.3 59.5 + - - -
54A LYS* 2.9 13.6 + - - -
55A ILE* 3.2 13.0 + - - +
56A ARG 4.4 0.5 + - - -
308A THR 2.8 19.5 - - - -
309A GLY* 4.1 1.3 - - - -
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Residues in contact with ASN 53 (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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52A GLY* 1.3 71.6 - - - -
54A LYS* 1.3 101.0 + - - +
55A ILE 3.5 0.2 - - - -
56A ARG* 3.6 9.8 + - - +
57A LYS* 3.2 6.9 + - - +
82A ASN* 6.0 0.2 - - - +
167A TYR* 2.8 47.7 + - + +
194A THR* 3.1 13.8 + - - +
308A THR* 2.9 39.8 + - + +
1011A 5PA 3.5 23.7 - - - +
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Residues in contact with LYS 54 (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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52A GLY* 2.9 2.3 + - - -
53A ASN* 1.3 104.3 - - - +
55A ILE* 1.3 67.6 + - + +
56A ARG 3.0 2.7 - - - -
57A LYS* 2.9 30.7 + - + +
58A LEU* 3.0 17.7 + - + +
82A ASN* 4.9 2.2 - - + -
83A HIS* 3.8 36.3 - - - +
86A VAL* 4.1 18.4 - - + -
157A GLY 3.3 16.2 + - - +
1011A 5PA 3.0 58.5 + - - +
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Residues in contact with ILE 55 (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* 4.1 19.3 - - + +
18A ILE* 3.7 25.6 - - + -
46A THR* 4.1 10.1 - - - +
48A LEU* 3.1 52.9 - - + +
51A GLY 3.8 22.4 - - - +
52A GLY 3.2 7.3 + - - +
54A LYS* 1.3 75.9 - - + +
56A ARG* 1.3 63.6 + - - +
58A LEU* 3.2 17.1 + - + +
59A GLU* 3.4 11.3 + - - +
86A VAL* 3.3 22.2 - - + -
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Residues in contact with ARG 56 (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 ILE* 3.5 34.9 - - + +
20A TRP 5.8 0.2 + - - -
22A THR* 3.5 17.4 + - - +
41A LYS* 3.9 5.5 - - - +
43A ASP* 2.4 46.7 + - - +
46A THR* 4.5 5.4 - - + -
53A ASN 3.6 10.7 + - - +
54A LYS 3.0 0.6 - - - -
55A ILE* 1.3 77.9 - - - +
57A LYS* 1.3 62.4 + - - +
59A GLU* 3.2 21.2 + - - +
60A TYR* 4.1 3.5 - - - -
166A GLY* 3.5 35.8 + - - +
167A TYR* 3.6 22.0 - - + +
169A ARG* 5.7 3.0 - - - +
170A ALA* 4.1 12.8 - - - +
173A GLU* 3.7 24.7 + - - -
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Residues in contact with LYS 57 (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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53A ASN* 3.2 17.3 + - - +
54A LYS* 2.9 36.5 + - + +
56A ARG* 1.3 75.1 - - - +
58A LEU* 1.3 59.6 + - + +
59A GLU 3.1 0.2 - - - -
60A TYR* 3.1 7.8 + - - +
61A LEU* 2.9 36.4 + - + +
83A HIS* 6.5 0.4 - - + -
157A GLY 3.8 9.4 - - - +
158A GLY 3.6 17.5 - - - +
159A ALA* 5.1 0.2 - - - -
163A GLY* 3.0 30.8 - - - +
164A THR* 5.4 0.2 - - - +
166A GLY* 4.5 2.5 - - - +
167A TYR* 4.3 8.6 - - + -
193A GLY* 3.8 11.2 - - - -
194A THR* 2.9 42.4 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.9 0.2 - - - +
17A LEU* 4.0 12.0 - - + +
54A LYS* 3.0 17.1 + - + +
55A ILE* 3.2 12.8 + - + +
57A LYS* 1.3 74.7 - - + +
59A GLU* 1.3 63.1 + - - +
61A LEU* 3.9 26.2 - - + -
62A LEU* 3.1 47.4 + - + +
83A HIS* 4.9 4.9 - - + -
86A VAL* 3.3 43.7 - - + +
87A THR* 3.8 30.5 - - + +
90A ALA* 4.1 4.9 - - + -
154A ILE* 4.5 1.1 - - + -
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Residues in contact with GLU 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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14A ARG* 2.5 45.5 + - + -
15A VAL* 2.9 44.3 + - - +
16A GLU* 3.7 2.3 - - - -
17A LEU* 2.7 33.1 + - + -
18A ILE* 2.9 30.6 + - + +
55A ILE 3.4 10.9 + - - +
56A ARG* 3.4 14.9 - - - +
57A LYS 3.1 0.8 - - - -
58A LEU* 1.3 77.0 - - - +
60A TYR* 1.3 59.7 + - + +
63A GLY 3.3 15.2 + - - -
169A ARG* 4.7 4.2 - - - -
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Residues in contact with TYR 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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9A LEU* 3.6 16.3 + - - +
12A PHE* 3.7 35.4 + - + -
13A PRO 4.0 13.3 - - - +
14A ARG* 3.3 27.3 + - + -
56A ARG 4.1 9.2 - - - -
57A LYS 3.1 5.0 + - - +
59A GLU* 1.3 78.0 - - - +
61A LEU* 1.3 66.4 + - - +
63A GLY 3.3 3.1 + - - -
64A ASP* 3.1 19.8 + - - +
162A ILE* 2.9 35.3 - - + +
165A LEU* 3.6 32.5 - - + -
166A GLY* 4.0 13.5 - - - -
169A ARG* 3.5 28.4 + - - -
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Residues in contact with LEU 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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57A LYS* 2.9 24.8 + - + +
58A LEU* 3.9 20.6 - - + -
60A TYR* 1.3 74.8 - - - +
62A LEU* 1.3 55.4 + - - +
64A ASP* 2.6 33.9 + - - +
65A ALA* 2.9 8.2 + - - +
83A HIS* 5.1 0.7 - - + -
152A TYR* 4.1 12.1 + - + +
154A ILE* 3.6 43.1 - - + -
155A PRO* 5.4 0.9 - - + -
158A GLY* 3.8 17.0 - - - +
160A SER* 3.2 27.6 - - - +
162A ILE* 3.5 12.6 - - + -
163A GLY* 3.9 5.6 - - - -
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Residues in contact with LEU 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 VAL* 4.0 4.9 - - + -
17A LEU* 4.6 4.9 - - + -
58A LEU* 3.1 32.5 + - + +
61A LEU* 1.3 79.8 - - - +
63A GLY* 1.3 55.8 + - - +
64A ASP 3.1 0.7 - - - -
65A ALA* 3.8 6.1 - - + +
66A LEU* 3.0 35.7 + - - +
73A VAL* 4.3 28.7 - - + -
87A THR 4.8 1.8 - - - +
90A ALA* 3.8 34.1 - - + +
91A ALA* 4.4 11.4 - - + -
94A LEU* 3.3 31.9 - - + -
96A LEU* 4.5 3.8 - - + -
154A ILE* 4.7 7.4 - - + -
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Residues in contact with GLY 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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13A PRO* 3.4 29.2 - - - +
14A ARG 4.8 0.2 - - - -
15A VAL* 3.6 19.9 - - - +
59A GLU 3.3 10.4 + - - -
60A TYR 3.3 10.3 + - - -
61A LEU 3.0 1.4 - - - -
62A LEU* 1.3 76.0 - - - +
64A ASP* 1.3 57.6 + - - +
66A LEU* 4.5 3.6 - - - -
67A SER* 3.5 16.7 + - - -
13R PRO* 5.7 0.5 - - - +
67R SER* 4.4 0.2 + - - -
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Residues in contact with ASP 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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60A TYR 3.1 11.0 + - - +
61A LEU* 2.8 14.8 - - - +
63A GLY* 1.3 80.5 - - - +
65A ALA* 1.3 57.6 + - - +
66A LEU 3.3 0.7 - - - -
67A SER* 3.0 9.7 + - - -
68A LYS* 3.0 52.8 + - - +
152A TYR* 2.4 29.7 + - - +
162A ILE* 3.6 22.4 - - + +
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Residues in contact with ALA 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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61A LEU 2.9 9.4 + - - +
62A LEU* 3.9 11.7 - - + +
64A ASP* 1.3 77.5 - - - +
66A LEU* 1.3 62.4 + - - +
68A LYS* 3.2 5.7 + - - +
69A GLY 3.1 15.8 + - - -
70A ALA* 3.5 17.0 + - + +
73A VAL* 4.8 4.3 - - + -
96A LEU* 4.6 12.3 - - + -
152A TYR* 3.6 42.1 - - + -
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Residues in contact with LEU 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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15A VAL* 3.9 20.4 - - + -
62A LEU 3.0 22.8 + - - +
63A GLY* 4.5 2.7 - - - -
65A ALA* 1.3 75.0 - - - +
67A SER* 1.3 54.1 + - - +
68A LYS 2.4 18.3 + - - -
69A GLY* 2.5 17.7 + - - +
70A ALA 5.0 1.8 - - - +
94A LEU* 4.1 22.9 - - + +
96A LEU* 4.1 30.3 - - + -
11R LYS* 4.1 23.8 - - + +
13R PRO* 6.6 0.4 - - + -
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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