Contacts of the strand formed by residues 26 - 34 (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 ALA 26 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J CYS* 3.0 28.0 - - - +
22J ASP* 4.3 5.0 - - - +
24J THR* 3.4 14.5 + - - +
25J GLY* 1.3 78.9 + - - +
27J ARG* 1.3 60.3 + - - +
29J LEU* 4.3 2.9 - - + -
57J VAL* 3.7 27.8 - - + -
59J LYS 3.7 4.9 - - - -
64J MET* 4.0 6.7 - - + +
97J ILE* 3.8 18.6 - - + -
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Residues in contact with ARG 27 (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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19J THR* 3.8 8.5 - - - +
20J CYS* 2.9 26.3 + - - +
25J GLY 4.7 3.4 - - - +
26J ALA* 1.3 77.0 - - - +
28J GLU* 1.3 57.1 + - + +
59J LYS* 2.8 21.9 + - + +
60J GLY* 4.1 17.8 - - - +
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Residues in contact with GLU 28 (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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17J LEU* 3.5 32.2 - - + +
18J ILE 3.6 9.4 - - - +
19J THR* 5.0 0.2 - - - +
27J ARG* 1.3 80.9 - - + +
29J LEU* 1.3 70.3 + - - +
57J VAL* 3.7 6.4 - - - +
58J THR* 2.9 54.9 + - - +
59J LYS* 3.3 44.7 + - + +
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Residues in contact with LEU 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J SER 3.6 0.5 - - - +
17J LEU* 3.3 4.2 - - - +
18J ILE* 2.8 49.3 + - + +
19J THR 4.4 1.6 - - - +
20J CYS* 3.5 43.1 - - + -
26J ALA* 4.3 3.4 - - + -
28J GLU* 1.3 81.2 - - - +
30J LYS* 1.3 59.3 + - - +
31J VAL 4.1 0.2 - - - -
55J VAL* 3.3 23.8 - - + -
56J SER 3.5 1.6 - - - -
57J VAL* 3.7 29.6 - - + -
58J THR* 4.8 0.2 - - - -
69J LEU* 6.1 0.7 - - + -
71J ALA* 4.7 5.2 - - + -
95J ALA* 4.0 24.5 - - + +
97J ILE* 4.3 12.8 - - + -
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Residues in contact with LYS 30 (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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19920 U 3.2 15.8 + - - -
19930 C 2.8 44.1 + - + +
19940 A 5.7 0.4 - - - +
15J GLY* 4.1 13.9 - - - +
16J SER 3.3 4.5 - - - -
17J LEU* 3.6 21.1 - - + -
29J LEU* 1.3 72.5 - - - +
31J VAL* 1.3 74.1 + - - +
32J ILE* 3.5 2.2 + - + +
55J VAL* 2.9 16.1 - - - +
56J SER* 2.9 31.9 + - - +
58J THR* 3.7 13.9 + - - +
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Residues in contact with VAL 31 (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 5.1 1.4 + - - -
12J LEU* 4.7 9.2 - - + -
13J GLU 3.5 25.1 - - - +
14J LYS* 4.2 5.6 - - - +
15J GLY* 2.7 27.4 + - - -
16J SER* 2.9 22.0 + - - +
18J ILE* 4.2 15.5 - - + -
29J LEU 4.1 0.2 - - - -
30J LYS* 1.3 76.6 - - - +
32J ILE* 1.3 62.1 + - - +
33J SER 4.0 16.4 - - - +
34J VAL* 5.0 1.8 - - + -
47J ALA* 4.9 7.6 - - + -
53J ILE* 4.0 31.0 - - + -
54J THR 4.0 4.0 - - - +
55J VAL* 4.4 2.9 - - + -
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Residues in contact with ILE 32 (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 3.4 66.2 - - + +
25960 A 3.3 24.5 - - - +
14J LYS* 2.6 42.8 + - - +
30J LYS* 3.7 10.3 - - + +
31J VAL* 1.3 79.9 - - - +
33J SER* 1.3 60.5 + - - +
54J THR* 3.0 11.2 + - + +
55J VAL* 4.0 5.6 - - - +
56J SER* 3.6 25.4 - - - +
68J VAL* 4.5 10.1 - - + -
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Residues in contact with SER 33 (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 2.5 32.9 + - - +
25970 U 3.2 29.1 + - - -
85120 CL 3.2 14.5 - - - +
14J LYS* 5.4 1.6 - - - -
31J VAL* 4.0 2.8 - - - +
32J ILE* 1.3 85.8 + - - +
34J VAL* 1.3 65.4 + - - +
45J PRO* 5.8 0.9 - - - -
53J ILE* 3.1 8.3 - - - +
54J THR* 2.7 33.2 + - - -
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Residues in contact with VAL 34 (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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25970 U 2.8 22.9 + - - -
13J GLU 6.3 0.2 - - - -
14J LYS* 6.0 0.7 - - - +
31J VAL* 5.0 4.5 - - + -
33J SER* 1.3 79.7 - - - +
35J HIS* 1.3 69.9 + - - +
37J TYR* 3.2 29.5 + - + +
45J PRO* 4.7 9.7 - - + +
46J LYS 3.3 33.9 - - - +
47J ALA* 3.3 24.0 - - + -
51J ASP* 4.2 23.6 - - + +
52J LYS 4.0 2.5 - - - +
53J ILE* 4.3 1.6 - - + +
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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