Contacts of the strand formed by residues 83 - 90 (chain A) in PDB entry 1JB3
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 THR 83 (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* 4.5 1.9 + - - -
20A GLY 3.3 13.6 + - - -
21A THR* 4.4 11.7 - - - +
81A GLY 3.6 3.5 + - - +
82A ASP* 1.3 74.7 - - - +
84A ARG* 1.3 84.1 + - - +
110A MET 4.3 0.7 - - - +
111A ARG* 4.5 0.7 - - - -
112A ILE* 3.0 35.6 + - + +
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Residues in contact with ARG 84 (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* 3.3 3.6 - - - -
20A GLY 3.1 30.2 + - - -
75A ASP* 5.0 0.8 + - - -
77A GLN 4.6 7.3 + - - -
78A VAL* 4.6 10.0 - - + +
82A ASP* 3.4 29.2 + - + +
83A THR* 1.3 115.7 + - - +
85A ILE* 1.3 66.3 + - - +
86A PHE* 3.3 25.7 - - + -
109A LEU* 4.0 25.5 - - + +
110A MET 3.1 24.0 - - - +
111A ARG* 2.6 51.5 - - - +
112A ILE* 3.4 10.3 - - - +
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Residues in contact with ILE 85 (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 VAL* 3.6 26.2 - - + -
18A LEU 3.3 7.4 - - - +
19A THR* 5.0 1.1 - - - -
45A LEU* 4.2 8.7 - - + -
84A ARG* 1.3 73.2 - - - +
86A PHE* 1.3 61.9 - - - +
87A PHE* 3.7 16.4 + - + -
109A LEU* 3.8 6.4 - - - -
110A MET* 2.8 36.5 + - + +
111A ARG 3.8 7.6 - - - +
112A ILE* 3.6 19.1 - - + -
116A ASN* 3.8 38.8 - - + -
117A LEU* 4.1 18.4 - - + -
120A VAL* 4.2 9.0 - - + -
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Residues in contact with PHE 86 (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 3.8 0.2 - - - +
17A VAL* 3.3 5.9 - - - +
18A LEU* 2.7 50.5 + - + +
20A GLY 3.6 18.4 - - - -
22A VAL* 4.1 15.5 - - + -
39A VAL* 4.0 20.9 - - + -
65A ILE* 3.6 26.7 - - + -
68A PHE* 3.7 26.9 - + - -
78A VAL* 4.7 0.4 - - + -
84A ARG* 3.3 32.5 - - + -
85A ILE* 1.3 72.4 - - - +
87A PHE* 1.3 64.2 + - - +
88A VAL* 3.7 10.1 + - + +
105A LEU* 4.5 2.9 - - + -
109A LEU* 3.4 27.4 - - + -
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Residues in contact with PHE 87 (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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7A LEU* 3.9 9.2 - - + -
10A ARG* 3.7 35.2 - - + -
11A GLU* 4.0 22.0 - - + -
14A ALA* 3.9 14.4 - - + -
16A VAL 3.8 3.6 - - - -
17A VAL* 4.0 12.3 - - + -
85A ILE* 3.7 17.5 - - + -
86A PHE* 1.3 74.4 - - - +
88A VAL* 1.3 63.1 + - - +
105A LEU* 3.6 6.7 - - - +
106A ASN* 2.8 24.2 + - + -
107A SER* 3.2 26.4 + - - +
108A SER 4.0 4.7 + - - -
110A MET* 3.5 34.5 - - + -
120A VAL* 3.9 20.2 - - + -
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Residues in contact with VAL 88 (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 ALA* 3.8 1.7 - - - +
15A ASN 3.4 1.9 + - - -
16A VAL* 2.8 64.1 + - + +
18A LEU* 4.7 4.5 - - + -
65A ILE* 3.9 19.3 - - + -
86A PHE* 4.2 17.5 - - + +
87A PHE* 1.3 80.4 - - - +
89A ASN* 1.3 70.6 + - - +
103A LEU* 3.8 23.3 - - + -
104A MET 3.1 23.1 - - - +
105A LEU* 3.8 6.3 - - + +
106A ASN 4.2 1.1 - - - +
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Residues in contact with ASN 89 (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 GLU 2.9 23.5 + - - +
14A ALA* 3.9 0.2 - - - +
15A ASN* 2.8 44.4 + - - +
88A VAL* 1.3 74.8 + - - +
90A PRO* 1.3 74.7 - - + +
92A PRO* 6.2 0.7 - - + -
103A LEU* 4.2 3.1 - - - -
104A MET* 2.7 35.5 + - + +
106A ASN* 3.4 22.8 - - - +
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Residues in contact with PRO 90 (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 ASN* 5.0 5.4 - - + +
16A VAL* 4.4 5.2 - - + -
50A ILE* 3.6 23.6 - - + -
54A GLU* 3.6 29.8 - - + +
55A ILE* 4.6 10.3 - - + -
89A ASN* 1.3 92.6 - - + +
91A ALA* 1.3 68.4 + - - +
92A PRO* 3.2 10.0 - - - +
102A GLU 3.7 8.3 - - - +
103A LEU* 3.9 17.5 - - + -
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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