Contacts of the strand formed by residues 49 - 56 (chain R) in PDB entry 1JJ2
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 VAL 49 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38R ALA* 3.5 20.8 - - + +
41R VAL* 3.8 13.9 - - + -
42R GLU* 2.7 38.7 + - + +
47R VAL* 4.5 0.9 - - + -
48R THR* 1.3 73.9 - - - +
50R GLU* 1.3 66.9 + - - +
51R GLN* 3.8 6.1 - - - +
52R VAL* 3.7 20.2 - - + -
66R VAL* 3.5 35.0 - - + -
67R ARG 3.8 2.9 - - - -
68R LEU* 4.2 4.7 - - + -
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Residues in contact with GLU 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48R THR* 3.4 26.0 + - - +
49R VAL* 1.3 75.3 - - - +
51R GLN* 1.3 61.3 + - - +
67R ARG* 2.8 41.3 + - - +
68R LEU 3.9 1.1 - - - +
69R SER* 3.4 32.8 - - - -
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Residues in contact with GLN 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15070 C 3.8 17.1 + - - -
15080 C 4.2 11.8 + - - -
23R LYS* 5.9 1.6 - - - +
49R VAL* 3.7 2.1 - - - -
50R GLU* 1.3 82.5 - - - +
52R VAL* 1.3 71.0 + - - +
53R ASN* 2.8 26.4 - - - +
65R VAL 3.6 1.0 - - - +
66R VAL* 3.4 3.1 - - - +
67R ARG* 2.8 68.9 + - + +
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Residues in contact with VAL 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R LYS* 3.3 53.0 + - + +
37R VAL* 3.8 23.6 - - + -
38R ALA* 3.9 11.0 - - + +
49R VAL* 3.7 21.1 - - + -
51R GLN* 1.3 84.5 - - - +
53R ASN* 1.3 76.5 + - - +
54R THR* 4.2 2.0 - - + -
64R ALA* 4.1 9.2 - - + -
65R VAL 3.5 2.5 - - - -
66R VAL* 4.1 11.0 - - + -
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Residues in contact with ASN 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14470 U 3.1 50.7 + - - +
14480 A 3.4 9.5 - - - +
15070 C 3.2 19.3 + - - +
34R LYS* 5.4 0.4 - - - -
51R GLN* 2.8 33.0 - - - +
52R VAL* 1.3 81.7 + - - +
54R THR* 1.3 61.6 + - - +
63R LYS 3.8 0.2 - - - +
64R ALA* 3.2 3.8 - - - +
65R VAL* 2.7 46.8 + - + +
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Residues in contact with THR 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14470 U 3.4 18.6 - - - +
14480 A 3.5 12.4 + - - -
16740 C 4.2 10.3 + - - +
16750 C 4.3 9.5 + - - -
16770 U 6.1 0.2 - - - -
80280 MG 4.2 2.8 - - - -
32R ALA 5.2 0.4 - - - +
34R LYS* 3.6 34.7 - - + +
37R VAL* 5.1 4.5 - - + -
52R VAL* 4.2 8.7 - - + -
53R ASN* 1.3 79.5 - - - +
55R GLN* 1.3 64.7 + - - +
56R ASN* 6.3 0.2 - - - -
62R LYS* 4.1 23.6 - - + -
63R LYS 3.2 7.6 - - - +
64R ALA* 4.3 7.0 - - + -
65R VAL* 6.4 0.4 - - - -
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Residues in contact with GLN 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14460 U 3.1 71.4 + - - +
14470 U 4.4 14.0 - - - +
16770 U 6.1 3.1 - - + +
81 LYS* 5.3 1.2 - - - +
54R THR* 1.3 79.5 - - - +
56R ASN* 1.3 70.2 + - - +
57R THR* 3.3 29.8 + - - +
58R MET 5.1 0.6 - - - +
62R LYS* 3.3 5.2 - - - +
63R LYS* 2.8 52.9 + - + +
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Residues in contact with ASN 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16750 C 2.9 33.3 + - - -
16760 G 2.7 41.9 + - - +
16770 U 4.4 0.5 + - - -
51 LYS* 3.6 19.1 - - + -
81 LYS* 2.8 32.0 + - + -
30R ASP* 3.9 9.0 - - - +
54R THR* 6.3 0.2 - - - -
55R GLN* 1.3 74.4 - - - +
57R THR* 1.3 60.4 + - - +
61R GLU 3.9 4.0 - - - +
62R LYS* 3.5 21.8 - - - +
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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