Contacts of the helix formed by residues 53 - 68 (chain F) 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 ASN 53 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F GLY* 1.3 68.6 - - - -
54F LYS* 1.3 75.2 + - - +
55F ILE 3.2 7.0 + - - -
56F ARG* 3.7 7.8 + - - +
57F LYS* 3.6 5.7 + - - +
167F TYR* 3.0 44.4 - - + +
194F THR* 2.9 19.6 + - - -
308F THR* 3.0 32.0 + - + +
1061F 5PA 3.3 44.6 + - - +
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Residues in contact with LYS 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLY 3.4 1.4 - - - -
53F ASN* 1.3 88.6 + - - +
55F ILE* 1.3 66.1 + - + +
56F ARG 3.4 0.2 - - - -
57F LYS* 3.0 31.8 + - + +
58F LEU* 2.8 36.3 + - + +
82F ASN* 5.8 0.7 - - + -
83F HIS* 3.6 37.0 - - + +
86F VAL* 5.1 4.7 - - + -
157F GLY 3.1 22.8 + - - +
1061F 5PA 2.5 70.1 + - + +
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Residues in contact with ILE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LEU* 3.6 13.3 - - + +
18F ILE* 3.2 33.9 - - + +
46F THR* 3.9 20.9 - - - +
48F LEU* 3.8 31.9 - - + +
51F GLY 3.8 17.3 - - - +
52F GLY 3.9 2.2 - - - +
53F ASN 3.2 1.4 - - - -
54F LYS* 1.3 78.0 - - + +
56F ARG* 1.3 67.1 + - - +
58F LEU* 3.2 8.9 + - + +
59F GLU* 3.2 19.8 + - - +
86F VAL* 3.0 42.2 - - + -
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Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ILE* 3.4 27.4 - - + +
20F TRP 5.7 0.8 + - - -
22F THR* 3.3 19.8 + - - +
41F LYS* 4.1 1.2 - - - +
43F ASP* 2.9 37.1 + - - -
46F THR* 4.5 3.6 - - + +
52F GLY 4.9 0.2 + - - -
53F ASN 3.7 7.5 + - - +
55F ILE* 1.3 78.5 - - - +
57F LYS* 1.3 55.9 + - - +
59F GLU* 2.7 44.1 + - - +
60F TYR* 3.5 2.1 + - - -
166F GLY* 3.6 34.9 + - - +
167F TYR* 3.8 21.1 - - + +
169F ARG* 5.8 5.6 - - - +
170F ALA* 3.9 15.4 - - - +
173F GLU* 3.7 25.4 + - - -
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Residues in contact with LYS 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ASN 3.6 11.8 + - - +
54F LYS* 3.0 38.4 - - + +
56F ARG* 1.3 77.8 - - - +
58F LEU* 1.3 52.7 + - + +
60F TYR* 3.0 6.8 + - - +
61F LEU* 2.8 46.9 + - + +
157F GLY 3.5 17.0 - - - +
158F GLY* 4.0 13.2 - - - +
163F GLY* 3.6 26.0 - - - +
164F THR* 4.9 0.7 - - - +
166F GLY* 4.4 1.1 - - - -
167F TYR* 3.8 11.5 - - + -
193F GLY* 3.9 11.0 - - - -
194F THR* 2.9 40.6 + - - +
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Residues in contact with LEU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL 4.7 0.2 - - - +
17F LEU* 3.5 7.0 - - + +
54F LYS* 2.8 30.3 + - + +
55F ILE* 3.2 9.4 + - - +
56F ARG 3.2 0.6 - - - -
57F LYS* 1.3 81.5 - - + +
59F GLU* 1.3 57.8 + - - +
61F LEU* 3.9 17.3 - - + -
62F LEU* 2.7 54.7 + - + +
83F HIS* 4.5 5.6 - - - +
86F VAL* 3.3 39.0 - - + +
87F THR* 4.0 21.5 - - + +
90F ALA* 4.2 7.9 - - + -
154F ILE* 4.9 4.9 - - + -
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Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ARG* 2.8 55.5 + - - +
15F VAL 2.9 24.3 + - - +
16F GLU* 3.6 2.4 - - - -
17F LEU* 2.8 19.1 + - + -
18F ILE* 2.7 44.6 + - - +
55F ILE 3.2 12.9 + - - +
56F ARG* 2.7 30.1 + - - +
58F LEU* 1.3 75.5 - - - +
60F TYR* 1.3 57.4 + - + +
63F GLY 3.5 2.6 + - - -
169F ARG* 4.5 8.7 + - - -
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Residues in contact with TYR 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 3.9 16.0 + - + +
12F PHE* 3.2 39.7 + - + -
13F PRO 3.8 10.0 - - - +
14F ARG* 3.3 33.8 + - + -
56F ARG 3.5 3.1 + - - +
57F LYS 3.0 5.3 + - - +
59F GLU* 1.3 78.4 - - + +
61F LEU* 1.3 60.7 + - - +
63F GLY 4.0 1.3 - - - -
64F ASP 3.6 10.4 + - - -
162F ILE* 3.0 46.2 - - + +
165F LEU* 4.1 22.0 - - + -
166F GLY* 4.1 14.4 - - - +
169F ARG* 2.7 49.0 + - + -
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F LYS* 2.8 23.7 + - + +
58F LEU* 3.9 11.0 - - + -
60F TYR* 1.3 75.8 - - - +
62F LEU* 1.3 64.4 + - - +
63F GLY 2.9 3.1 - - - -
64F ASP* 2.9 14.8 + - - +
65F ALA* 2.9 14.0 + - - +
152F TYR* 3.7 32.9 - - + +
154F ILE* 3.7 37.2 - - + -
155F PRO* 5.1 0.4 - - + -
158F GLY* 3.9 14.8 - - - +
160F SER* 4.2 4.9 - - - +
162F ILE* 4.1 12.3 - - + -
163F GLY* 3.7 29.2 - - - +
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 4.1 7.6 - - + -
17F LEU* 4.0 7.0 - - + -
58F LEU* 2.7 45.9 + - + +
61F LEU* 1.3 75.5 - - + +
63F GLY* 1.3 54.3 + - - +
65F ALA* 4.0 6.2 - - + +
66F LEU* 2.9 35.3 + - - +
73F VAL* 4.2 16.4 - - + -
87F THR* 5.0 2.5 - - + +
90F ALA* 3.5 29.4 - - + +
91F ALA* 3.8 23.8 - - + +
94F LEU* 3.6 24.9 - - + +
96F LEU* 4.9 4.3 - - + -
154F ILE* 5.5 4.9 - - + -
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Residues in contact with GLY 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PRO* 3.9 14.5 - - - +
14F ARG* 3.9 1.6 - - - -
15F VAL* 3.8 24.2 - - - +
59F GLU 3.5 10.1 + - - -
61F LEU 2.9 1.6 - - - -
62F LEU* 1.3 77.9 - - - +
64F ASP* 1.3 58.5 + - - +
66F LEU* 3.6 2.4 - - - +
67F SER* 2.8 35.1 + - - -
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Residues in contact with ASP 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PRO* 4.2 7.9 + - + +
60F TYR 3.6 14.4 + - - +
61F LEU 2.9 4.6 + - - +
63F GLY* 1.3 72.8 - - - +
65F ALA* 1.3 66.8 + - - +
67F SER* 2.8 9.3 + - - -
68F LYS* 2.8 53.3 + - - +
152F TYR* 2.4 32.9 + - - +
162F ILE* 4.2 15.7 - - + +
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F LEU 2.9 10.4 + - - +
62F LEU* 4.0 14.6 - - + +
64F ASP* 1.3 77.7 + - - +
66F LEU* 1.3 66.3 + - - +
67F SER 2.8 1.6 + - - -
68F LYS 2.9 10.3 + - - +
69F GLY 3.5 6.6 + - - -
70F ALA* 3.5 15.3 + - + +
73F VAL* 5.1 2.7 - - + -
96F LEU* 5.0 5.8 - - + -
152F TYR* 3.3 49.3 - - + -
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 3.3 15.0 - - + -
62F LEU 2.9 18.1 + - - +
63F GLY* 3.6 5.4 - - - +
65F ALA* 1.3 78.6 - - - +
67F SER* 1.3 61.7 + - - +
69F GLY* 3.5 9.2 + - - -
70F ALA 5.2 2.0 - - - +
94F LEU* 3.2 42.0 - - + +
96F LEU* 3.7 36.5 - - + +
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Residues in contact with SER 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PRO* 3.9 21.0 - - - +
63F GLY 2.8 17.3 + - - -
64F ASP* 2.8 14.6 + - - -
65F ALA 2.8 1.2 + - - -
66F LEU* 1.3 73.5 - - - +
68F LYS* 1.3 53.8 + - - -
69F GLY* 2.7 17.5 + - - -
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Residues in contact with LYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ASP* 2.8 45.6 + - - +
65F ALA* 2.9 5.5 + - - +
67F SER* 1.3 69.4 - - - +
69F GLY* 1.3 63.9 + - - +
70F ALA* 3.0 5.5 + - + +
150F LYS* 4.4 9.2 + - - +
152F TYR* 4.3 16.2 - - + -
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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