Contacts of the strand formed by residues 57 - 64 (chain C) in PDB entry 2B2T
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 GLU 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ARG 3.4 0.2 - - - +
24C ILE* 3.0 6.8 - - - -
25C GLY 2.7 40.6 + - - +
27C LYS* 2.9 63.4 + - + +
28C GLY 3.4 8.5 + - - -
30C THR* 4.3 4.2 + - - +
56C GLY* 1.3 74.3 - - - +
58C ILE* 1.3 62.7 + - - +
59C GLN* 3.5 18.0 + - + +
76C THR* 3.8 24.1 + - + +
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C CYS* 3.8 27.1 - - - -
23C ARG 3.1 8.1 - - - +
24C ILE* 4.3 10.7 - - + +
57C GLU* 1.3 71.4 - - - +
59C GLN* 1.3 59.5 + - - +
60C TYR* 3.5 31.5 - - + +
75C GLU 4.4 0.3 - - - +
76C THR* 3.3 14.9 + - - +
77C GLU 5.4 0.3 + - - -
95C LYS* 5.9 0.7 - - + -
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Residues in contact with GLN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C CYS* 3.5 5.9 - - - -
23C ARG* 2.7 64.0 + - - +
25C GLY* 3.6 14.4 + - - -
26C ARG 3.0 27.0 + - - -
29C ALA* 3.2 11.2 + - - +
30C THR* 3.2 23.5 - - + +
57C GLU* 3.5 16.3 + - + +
58C ILE* 1.3 77.9 - - - +
60C TYR* 1.3 65.7 + - - +
74C TRP* 3.6 13.9 - - + -
75C GLU 3.1 13.9 - - - +
76C THR* 3.9 9.9 - - - +
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.8 28.7 - + + -
21C ASP 3.6 3.8 - - - +
22C CYS* 3.4 31.4 - - + -
58C ILE* 3.5 31.9 - - + +
59C GLN* 1.3 72.7 - - - +
61C LEU* 1.3 60.0 - - - +
62C ILE* 3.1 13.9 + - + +
73C THR 3.4 0.2 - - - +
74C TRP* 3.6 3.4 - - - -
75C GLU 2.7 44.8 + - - +
76C THR* 4.9 2.2 - - - -
77C GLU* 4.6 16.8 + - + -
80C LEU* 5.0 6.3 - - + -
91C LEU* 4.1 14.4 - - + -
94C TYR* 3.8 25.4 - + - -
95C LYS* 3.3 29.2 - - + +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 5.7 3.1 - - + -
106B LYS* 5.2 11.7 - - - +
19C PHE* 3.9 2.1 - - - -
20C MSE 2.9 47.7 + - + +
21C ASP* 3.2 36.9 + - + +
34C THR 5.8 0.2 - - - +
60C TYR* 1.3 67.9 - - - +
62C ILE* 1.3 61.0 + - - +
72C ASN* 4.2 22.9 - - + +
73C THR 3.7 12.6 - - - +
74C TRP* 3.3 39.1 - - + +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 3.3 45.1 - - + -
18C ARG 3.6 5.6 - - - +
19C PHE* 4.5 9.6 - - + -
20C MSE 4.7 0.4 - - - -
60C TYR* 3.7 14.6 - - + +
61C LEU* 1.3 74.4 - - - +
63C LYS* 1.3 69.2 + - - +
64C TRP* 3.5 24.3 - - + -
72C ASN* 3.1 28.4 - - - -
73C THR 2.8 18.9 + - - +
75C GLU* 3.9 10.3 - - + -
80C LEU* 3.3 34.5 - - + -
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.0 56.8 + - + +
18C ARG* 3.0 16.7 + - + +
20C MSE 3.8 24.2 - - + -
61C LEU 4.0 0.6 + - - -
62C ILE* 1.3 72.8 - - - +
64C TRP* 1.3 66.8 + - - +
66C GLY 5.9 0.2 - - - +
67C TRP 2.9 27.1 - - - +
68C SER* 4.3 2.5 - - - +
69C HIS* 3.7 35.3 + - + +
72C ASN* 3.0 26.9 - - - +
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Residues in contact with TRP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 4.2 15.0 - - + +
15C THR 3.3 27.6 - - - +
16C ILE* 3.3 28.3 - - + -
17C GLU* 4.2 1.8 - - - +
62C ILE* 3.5 24.6 + - + +
63C LYS* 1.3 84.5 - - - +
65C LYS* 1.3 61.2 + - - +
66C GLY 3.5 0.9 + - - -
67C TRP* 3.2 43.1 + + + +
71C HIS* 3.7 20.6 + - + -
72C ASN* 3.8 4.0 + - - -
73C THR* 3.1 20.8 + - - +
75C GLU* 3.8 24.9 - - + -
80C LEU* 3.8 8.7 - - + -
83C GLN* 4.9 6.7 - - - -
85C VAL* 3.6 29.4 - - + -
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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