Contacts of the strand formed by residues 58 - 64 (chain A) 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 ILE 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A CYS* 5.2 8.3 - - - -
23A ARG 3.2 9.6 - - - +
24A ILE* 4.2 17.5 - - + -
57A GLU* 1.3 73.7 - - - +
59A GLN* 1.3 58.2 + - - +
60A TYR* 2.9 38.6 - - + +
76A THR* 3.8 18.4 - - - +
77A GLU* 4.7 2.5 + - + +
95A LYS* 5.9 1.8 - - + -
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Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A CYS* 3.5 5.5 - - - -
23A ARG* 2.7 76.4 + - + +
25A GLY* 3.6 10.4 + - - -
26A ARG 3.1 25.6 + - - -
29A ALA 3.2 18.6 + - - +
30A THR* 3.4 10.0 - - + +
57A GLU* 3.2 25.9 + - - +
58A ILE* 1.3 77.4 - - - +
60A TYR* 1.3 64.3 + - - +
74A TRP* 4.0 11.0 - - + -
75A GLU 3.1 11.4 - - - +
76A THR* 3.9 10.3 - - + -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.8 23.8 - + + -
21A ASP 3.6 4.3 - - - +
22A CYS* 4.1 16.2 - - - -
58A ILE* 2.9 39.0 - - + +
59A GLN* 1.3 77.2 - - - +
61A LEU* 1.3 62.2 + - - +
62A ILE* 3.5 8.1 + - + +
73A THR 3.5 0.2 - - - +
74A TRP* 3.1 7.0 - - - -
75A GLU 2.7 44.4 + - - +
76A THR* 4.6 1.1 - - - -
77A GLU* 4.2 21.3 + - + -
80A LEU* 5.1 2.2 - - + -
91A LEU* 3.6 24.0 - - + -
94A TYR* 4.0 30.5 - + - -
95A LYS* 3.6 25.6 - - + +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.8 2.9 - - - -
20A MSE 2.9 49.1 + - + +
21A ASP* 3.0 25.8 + - + +
60A TYR* 1.3 71.6 - - - +
62A ILE* 1.3 64.2 + - - +
72A ASN* 3.7 29.4 - - + +
73A THR 3.7 14.4 - - - +
74A TRP* 3.3 39.9 - - + +
131A GLN* 6.0 1.6 - - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.5 24.2 - - + -
18A ARG 3.9 4.7 - - - +
19A PHE* 4.2 14.1 - - + -
60A TYR* 3.7 15.7 - - + +
61A LEU* 1.3 77.6 - - - +
63A LYS* 1.3 71.6 + - - +
64A TRP* 3.5 30.7 - - + -
72A ASN* 3.2 29.2 - - - -
73A THR 2.8 17.6 + - - +
75A GLU* 3.6 35.9 - - + -
80A LEU* 3.7 21.3 - - + -
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 2.9 59.1 + - + +
18A ARG* 2.9 26.0 + - + +
20A MSE 4.1 18.3 - - + +
61A LEU 4.1 0.4 + - - -
62A ILE* 1.3 73.3 - - - +
64A TRP* 1.3 74.8 + - - +
66A GLY 4.7 0.6 - - - +
67A TRP 2.7 29.7 + - - +
68A SER* 4.4 1.3 - - - +
69A HIS* 3.5 40.4 - - + +
72A ASN* 3.4 18.4 - - - +
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Residues in contact with TRP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.9 16.2 - - + +
15A THR 3.3 24.0 - - - +
16A ILE* 3.7 24.5 - - + -
17A GLU* 3.9 0.9 - - - -
62A ILE* 3.5 26.4 + - + -
63A LYS* 1.3 100.4 + - - +
65A LYS* 1.3 66.4 + - - +
67A TRP* 3.1 31.5 + - + +
71A HIS 3.7 13.5 - - - -
72A ASN* 4.4 1.4 + - - -
73A THR* 3.0 27.9 + - - -
75A GLU* 3.8 16.4 - - + -
80A LEU* 4.1 8.1 - - + -
83A GLN* 4.2 7.2 - - - -
85A VAL* 3.9 28.7 - - + -
4D M3L 3.4 30.1 - - - -
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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