Contacts of the helix formed by residues 49 - 63 (chain I) 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 ARG 49 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11180 A 4.3 15.1 + - - +
11190 G 2.7 48.2 + - - +
12440 U 4.5 2.8 + - - -
48I GLY* 1.3 68.9 - - - -
50I GLU* 1.3 67.7 + - - +
51I GLU* 2.8 45.5 + - - +
52I GLN* 2.9 29.2 + - + +
53I ILE* 3.1 12.4 + - - +
55I GLU* 4.6 8.9 + - - -
128I LYS* 4.1 22.2 - - - +
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Residues in contact with GLU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I GLY 3.4 6.5 + - - -
49I ARG* 1.3 70.8 - - - +
51I GLU* 1.3 72.2 + - - +
53I ILE* 3.7 2.4 - - - +
54I VAL* 2.9 42.3 + - + +
129I PHE 5.1 2.1 - - - +
130I VAL* 3.4 40.9 - - + +
134I GLU* 4.8 13.6 - - - +
138I THR* 4.8 9.0 + - - -
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Residues in contact with GLU 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ARG* 2.8 47.5 + - - +
50I GLU* 1.3 91.6 + - - +
52I GLN* 1.3 60.7 + - - +
54I VAL* 4.0 3.7 - - - +
55I GLU* 3.1 30.7 + - - +
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Residues in contact with GLN 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11190 G 2.8 77.5 + - - +
12440 U 4.5 2.4 + - - -
85160 CL 3.9 8.9 - - - +
49I ARG* 2.9 38.4 + - + +
51I GLU* 1.3 73.3 - - - +
53I ILE* 1.3 82.2 + - + +
55I GLU* 3.1 21.5 + - - +
56I LYS* 3.1 14.6 + - - +
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Residues in contact with ILE 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11190 G 5.7 0.9 - - + +
46I ILE* 3.3 40.4 - - + +
47I THR 3.4 24.7 - - - +
48I GLY* 3.7 17.9 - - - +
49I ARG 3.1 10.9 + - - +
50I GLU* 3.7 6.7 - - - +
52I GLN* 1.3 100.7 - - - +
54I VAL* 1.3 64.5 + - + +
56I LYS* 3.2 10.2 + - - +
57I TYR* 3.1 33.4 - - + -
130I VAL* 4.2 11.2 - - + -
135I ILE* 4.1 16.2 - - + -
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Residues in contact with VAL 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU* 2.9 33.6 + - + +
51I GLU* 4.0 4.9 - - - +
53I ILE* 1.3 76.1 - - + +
55I GLU* 1.3 62.0 + - + +
57I TYR* 3.4 6.0 + - - +
58I GLU* 2.9 49.0 + - + +
130I VAL* 5.7 0.4 - - + -
135I ILE* 4.7 21.3 - - + -
138I THR* 3.6 36.6 - - + +
139I LEU* 5.5 1.8 - - + -
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Residues in contact with GLU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ARG* 4.6 10.4 + - - -
51I GLU* 3.1 25.6 + - - +
52I GLN* 3.1 14.1 + - - +
54I VAL* 1.3 75.8 - - + +
56I LYS* 1.3 58.3 + - - +
58I GLU* 3.3 12.1 + - - +
59I LYS* 2.8 30.8 + - - +
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Residues in contact with LYS 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12360 A 4.0 21.2 - - + +
12370 U 4.4 9.4 + - - -
12410 G 4.9 0.2 + - - -
12420 A 3.1 38.4 + - - +
85160 CL 3.3 29.9 - - + +
52I GLN* 3.1 14.5 + - - +
53I ILE* 3.4 11.0 - - - +
55I GLU* 1.3 76.3 - - - +
57I TYR* 1.3 73.9 + - + +
59I LYS* 3.1 9.1 + - - +
60I ARG* 3.1 47.0 + - - +
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Residues in contact with TYR 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12420 A 4.1 19.3 + - - -
12430 C 5.0 2.4 + - - -
19I MET* 4.6 11.2 - - - -
46I ILE* 4.3 14.9 - - + +
53I ILE* 3.1 41.4 + - + +
54I VAL 4.1 4.7 - - - +
56I LYS* 1.3 91.9 + - + +
58I GLU* 1.3 62.7 + - - +
60I ARG* 3.1 27.3 + - - +
61I VAL* 3.2 17.0 + - - +
71I TYR* 3.1 35.6 - + + -
78I ILE* 3.8 22.7 - - + -
132I LEU* 6.1 0.4 - - + -
135I ILE* 4.3 21.8 - - + -
139I LEU* 4.2 15.5 - - + -
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Residues in contact with GLU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28020 C 3.6 19.6 + - - -
28030 C 5.1 3.5 - - - +
54I VAL* 2.9 42.4 + - + +
55I GLU* 3.6 10.8 - - - +
57I TYR* 1.3 74.2 - - - +
59I LYS* 1.3 66.6 + - - +
61I VAL* 3.2 5.7 + - - +
62I ASP* 2.9 33.6 + - - +
138I THR* 4.3 15.0 - - + +
139I LEU* 3.6 22.5 - - + -
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Residues in contact with LYS 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12350 G 5.5 0.2 - - - -
12360 A 3.0 77.3 + - + +
55I GLU 2.8 13.8 + - - +
56I LYS* 3.3 12.6 - - - +
58I GLU* 1.3 77.4 - - - +
60I ARG* 1.3 57.2 + - - +
62I ASP* 3.1 11.8 + - + +
63I ILE* 2.9 42.1 + - + +
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Residues in contact with ARG 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12360 A 2.9 35.3 + - + +
12410 G 3.0 25.6 + - - -
12420 A 2.4 38.2 + - - -
56I LYS* 3.1 35.8 + - - +
57I TYR* 3.1 20.2 + - - +
59I LYS* 1.3 76.2 - - - +
61I VAL* 1.3 57.7 + - - +
63I ILE* 3.6 14.7 + - - +
69I TYR* 4.0 6.5 - - + -
71I TYR* 3.1 59.9 + - + +
8346I NA 2.8 18.5 - - - -
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Residues in contact with VAL 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26770 A 4.2 10.6 + - - +
57I TYR 3.2 13.9 + - - +
58I GLU* 3.2 8.7 + - - +
60I ARG* 1.3 75.5 - - - +
62I ASP* 1.3 69.6 + - - +
63I ILE 3.4 0.7 - - - +
71I TYR* 4.4 17.0 - - + +
73I LYS* 3.9 41.5 - - + +
139I LEU* 4.3 20.6 - - + +
8346I NA 2.8 18.5 - - - -
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Residues in contact with ASP 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12350 G 5.7 1.6 - - - +
26780 A 5.7 0.7 + - - -
28020 C 5.5 0.3 - - - +
28030 C 4.6 11.1 + - - -
58I GLU* 2.9 24.9 + - - +
59I LYS* 3.8 12.0 - - + +
61I VAL* 1.3 83.4 - - - +
63I ILE* 1.3 63.2 + - - +
64I GLY* 3.7 1.4 + - - +
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Residues in contact with ILE 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12350 G 3.2 49.1 - - + +
12360 A 3.0 53.8 - - + +
59I LYS* 2.9 33.5 + - + +
60I ARG* 3.8 12.6 - - - +
61I VAL 3.3 1.3 - - - +
62I ASP* 1.3 78.9 - - - +
64I GLY* 1.3 63.4 + - - +
69I TYR* 3.8 12.7 - - + +
8346I NA 2.5 27.6 - - - -
8521I CL 4.2 1.9 - - - +
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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