Contacts of the strand formed by residues 49 - 58 (chain F) in PDB entry 1I3R
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F HIS 3.7 1.6 - - - +
43F PHE* 3.7 0.3 - - - -
44F TYR* 2.8 84.4 + - + +
46F GLY 3.9 0.7 - - - +
48F GLN* 1.3 85.1 - - + +
50F VAL* 1.3 71.2 + - - +
51F ARG* 4.3 18.2 - - - +
69F ASP* 4.3 13.1 + - - -
106F ARG* 4.6 0.4 - - - +
67H ASP* 5.5 0.6 + - - -
69H ASP* 3.2 45.6 + - - +
70H VAL* 4.0 3.2 - - - +
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F HIS 3.3 11.4 - - - +
43F PHE* 3.7 24.7 - - + -
47F THR* 3.6 19.1 - - - +
49F ARG* 1.3 90.1 + - - +
51F ARG* 1.3 65.5 + - - +
52F LEU 4.3 0.2 - - - -
68F SER* 4.2 3.8 + - - -
69F ASP* 4.6 6.1 - - - +
101F VAL* 3.9 23.2 - - + +
105F CYS* 3.8 32.8 - - + -
106F ARG* 3.7 20.8 + - + +
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Residues in contact with ARG 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLU 3.5 2.3 - - - +
41F CYS* 3.8 1.0 - - - -
42F HIS* 2.9 55.2 + - + +
44F TYR* 4.8 8.4 + - + -
49F ARG* 4.3 13.5 - - - +
50F VAL* 1.3 78.4 - - - +
52F LEU* 1.3 63.9 + - - +
53F LEU* 4.0 29.9 - - - +
65F ARG* 4.7 4.9 - - - +
67F ASP* 2.5 41.9 + - - +
68F SER* 3.3 4.3 - - - +
69F ASP* 3.1 24.4 + - - +
51H ARG* 3.0 40.6 - - - +
65H ARG* 6.1 0.8 - - - +
67H ASP* 4.4 5.2 + - - -
69H ASP* 5.8 2.9 + - - -
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PHE* 3.3 42.4 - - + -
40F GLU 3.5 19.5 - - - +
50F VAL* 4.3 0.4 - - - +
51F ARG* 1.3 74.1 - - - +
53F LEU* 1.3 62.4 + - - +
54F VAL* 4.3 17.0 - - + -
66F PHE* 3.3 16.3 - - + +
67F ASP* 3.4 4.3 - - - +
68F SER* 2.5 49.2 + - - -
97F LYS* 4.1 20.2 - - - +
100F GLU* 4.2 9.6 - - + +
101F VAL* 4.0 13.9 - - + +
105F CYS* 3.6 11.2 - - - -
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F LYS 3.7 0.2 - - - +
39F SER* 3.7 0.2 - - - -
40F GLU* 2.7 62.6 + - - +
42F HIS* 4.3 11.9 - - + +
51F ARG* 3.9 32.5 + - - +
52F LEU* 1.3 76.1 - - - +
54F VAL* 1.3 62.1 + - - +
55F ARG* 4.1 17.4 + - + +
65F ARG* 4.2 31.4 - - - +
66F PHE 3.4 10.3 - - - +
67F ASP* 4.0 15.9 - - + -
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Residues in contact with VAL 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PHE* 5.5 0.9 - - + -
10F GLU* 4.6 1.6 - - - +
37F CYS* 3.9 9.6 - - - -
38F LYS 3.4 3.1 - - - +
39F SER* 3.9 24.5 - - - +
52F LEU* 4.3 19.3 - - + -
53F LEU* 1.3 74.7 - - - +
55F ARG* 1.3 64.6 + - - +
56F TYR* 3.5 32.1 - - + +
65F ARG* 3.1 12.4 - - - +
66F PHE* 2.9 50.1 + - + +
97F LYS* 4.5 14.1 - - - +
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Residues in contact with ARG 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASP* 2.9 29.7 + - - +
142E ASP* 4.1 4.8 - - - +
37F CYS* 3.4 4.5 - - - -
38F LYS* 2.8 43.1 + - + +
40F GLU* 3.1 40.9 + - - -
53F LEU* 4.1 19.0 - - + +
54F VAL* 1.3 83.3 - - - +
56F TYR* 1.3 63.6 + - - +
57F PHE* 3.5 33.8 - - + -
62F GLU* 3.1 33.3 + - - +
64F LEU 3.8 2.9 - - - -
65F ARG* 4.3 9.0 - - + +
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Residues in contact with TYR 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ASN* 6.1 0.4 - - - -
69E ASN* 5.7 0.9 - - - -
10F GLU* 2.7 39.9 + - + +
11F GLY 4.8 2.4 + - - -
13F LYS* 4.4 12.8 - - - +
35F GLU* 4.3 15.7 - - - +
36F TYR 3.6 2.2 - - - +
37F CYS* 4.0 12.3 - - + -
54F VAL* 3.5 24.7 - - + +
55F ARG* 1.3 76.2 - - - +
57F PHE* 1.3 63.1 + - - +
62F GLU* 3.2 5.6 - - - +
63F ASN* 2.9 41.3 + - - +
64F LEU* 3.0 43.6 + - + +
65F ARG* 5.2 0.7 - - - -
73F PHE* 4.2 15.8 - + - -
87F TRP* 3.9 26.1 - + - -
93F PHE* 5.9 0.3 - - - -
97F LYS* 5.0 3.5 + - - -
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Residues in contact with PHE 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ASP 3.8 2.5 - - - -
143E HIS* 3.5 31.6 - + + -
13F LYS* 6.3 0.2 - - - -
34F LEU 3.7 0.7 - - - +
35F GLU* 3.9 7.0 - - - +
36F TYR* 2.7 67.1 + + + +
37F CYS* 4.9 0.2 - - - -
38F LYS* 3.5 28.0 - - + -
55F ARG* 3.5 50.5 - - + -
56F TYR* 1.3 78.0 - - - +
58F TYR* 1.3 59.1 + - - +
59F ASN 4.0 8.7 - - - +
61F GLU 3.2 6.1 - - - +
62F GLU* 3.6 34.3 - - + -
63F ASN* 4.1 1.8 - - - -
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Residues in contact with TYR 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LEU* 4.1 16.2 - - + -
73E MET* 3.6 38.1 - - + -
74E LYS* 3.9 8.0 - - - -
77E SER* 3.3 32.1 + - - -
79E ASN* 5.0 0.5 - - - -
80E THR 4.1 10.0 + - - -
82E ASP* 4.4 1.7 - - - +
33F PHE* 3.6 23.3 - - + -
34F LEU 3.3 12.8 - - - -
35F GLU* 4.5 2.5 - - - +
57F PHE* 1.3 71.6 - - - +
59F ASN* 1.3 91.3 + - + +
60F LEU 3.1 2.9 + - - -
61F GLU* 2.9 17.9 + - + +
63F ASN* 3.5 19.9 - - - +
79F LEU* 3.8 19.3 - - + -
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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