Contacts of the strand formed by residues 52 - 60 (chain J) 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 LYS 52 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1J MET* 4.9 11.5 - - + +
34J VAL* 3.8 1.9 - - - +
35J HIS* 2.8 68.0 + - + +
50J GLY 3.9 1.6 + - - -
51J ASP* 1.3 72.5 - - - +
53J ILE* 1.3 60.1 + - - +
70J GLU* 4.1 31.6 + - + -
71J ALA 3.3 15.3 - - - +
72J VAL* 4.3 11.9 - - + -
98J VAL* 4.5 13.2 - - + -
99J ASP 5.6 0.4 + - - -
100J GLU 5.0 5.3 + - - -
102J GLU* 3.1 32.8 + - + +
121J PHE* 4.5 7.4 - - + -
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Residues in contact with ILE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J LEU* 5.5 0.4 - - + -
18J ILE* 4.1 12.1 - - + -
31J VAL* 4.0 24.2 - - + -
33J SER 3.1 13.9 - - - +
34J VAL* 4.4 2.5 - - + -
35J HIS* 4.4 0.9 - - - +
47J ALA* 3.7 28.9 - - + -
51J ASP* 4.1 5.6 - - + +
52J LYS* 1.3 79.0 - - - +
54J THR* 1.3 61.2 + - - +
55J VAL* 3.4 23.8 - - + -
70J GLU* 3.6 5.2 - - - +
71J ALA 2.9 37.0 + - - +
73J VAL* 3.8 26.7 - - + -
95J ALA* 4.6 4.5 - - + -
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Residues in contact with THR 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25960 A 3.7 32.3 - - - +
25970 U 2.9 27.1 + - - +
31J VAL* 3.9 1.0 - - - -
32J ILE* 3.0 27.1 + - + -
33J SER* 2.7 15.1 + - - +
35J HIS 5.1 0.8 + - - +
53J ILE* 1.3 70.9 - - - +
55J VAL* 1.3 73.2 + - - +
68J VAL* 3.7 19.5 - - + -
69J LEU 3.5 11.7 - - - +
70J GLU* 4.4 10.4 + - - +
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Residues in contact with VAL 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J LEU* 3.3 39.9 - - + -
30J LYS 2.9 21.3 - - - +
31J VAL* 4.5 1.1 - - + -
32J ILE* 4.0 5.2 - - - -
53J ILE* 3.4 35.9 - - + +
54J THR* 1.3 83.8 - - - +
56J SER* 1.3 72.0 + - - +
57J VAL* 6.0 0.4 - - - -
68J VAL* 3.2 6.9 - - - +
69J LEU* 2.6 42.2 + - + +
71J ALA* 4.1 13.7 - - + -
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Residues in contact with SER 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19930 C 2.8 39.2 + - - -
29J LEU* 3.5 0.9 - - - -
30J LYS* 2.9 44.3 + - - +
32J ILE* 3.6 16.6 - - - -
55J VAL* 1.3 81.4 - - - +
57J VAL* 1.3 63.2 + - - +
58J THR* 3.5 1.4 + - - -
66J ARG 5.0 0.9 - - - -
67J GLN 3.3 9.2 - - - -
68J VAL* 4.5 2.0 - - - -
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Residues in contact with VAL 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19930 C 5.0 3.9 + - - -
26J ALA* 3.7 22.4 - - + -
28J GLU 3.7 4.7 - - - +
29J LEU* 3.7 19.1 - - + -
55J VAL 6.0 0.2 - - - -
56J SER* 1.3 72.9 + - - +
58J THR* 1.3 60.5 + - - +
59J LYS 3.2 29.2 - - - +
64J MET* 3.3 29.2 - - + +
65J ARG* 3.9 7.8 - - - +
66J ARG* 3.0 25.1 + - - +
67J GLN 3.1 13.0 + - - +
69J LEU* 4.2 18.2 - - + -
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Residues in contact with THR 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19930 C 4.7 1.7 + - - -
17J LEU* 4.1 5.6 - - + +
28J GLU* 2.9 41.5 + - - +
30J LYS* 3.7 33.8 + - - +
56J SER* 3.5 2.7 + - - -
57J VAL* 1.3 74.5 - - - +
59J LYS* 1.3 68.8 + - + +
65J ARG* 3.9 14.2 - - - +
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Residues in contact with LYS 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ARG* 2.8 31.4 + - + -
28J GLU* 3.3 47.6 + - + +
57J VAL* 3.2 14.3 - - - +
58J THR* 1.3 89.7 - - + +
60J GLY* 1.3 59.2 + - - +
65J ARG* 4.4 3.4 - - - +
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Residues in contact with GLY 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J GLY 3.3 12.3 - - - -
26J ALA* 4.4 0.7 - - - -
27J ARG* 4.0 18.0 - - - +
57J VAL* 4.9 1.3 - - - -
59J LYS* 1.3 76.3 - - - +
61J THR* 1.3 66.8 + - - -
62J PRO* 3.5 2.9 - - - +
65J ARG* 3.4 19.5 + - - +
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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