Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 3BBU
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 THR 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A HIS 3.8 0.5 - - - +
38A TYR* 3.6 1.9 - - - -
39A ASN* 2.7 51.3 + - - -
40A GLY 4.3 3.3 + - - +
52A ASN 3.8 2.3 + - - -
53A ALA* 1.3 71.8 - - - +
55A LEU* 1.3 63.8 + - - +
56A THR* 4.3 4.7 + - - +
65A THR* 3.5 30.1 - - + -
66A VAL 3.4 4.7 - - - +
67A ILE* 3.4 18.2 - - + +
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Residues in contact with LEU 55 (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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11A LEU* 4.2 14.6 - - + -
14A TRP* 3.4 37.7 - - + -
15A LEU* 4.4 6.3 - - + -
36A VAL* 5.2 4.3 - - + -
37A HIS 3.3 10.1 - - - +
38A TYR* 3.3 37.9 - - + -
49A VAL* 5.7 0.2 - - + -
53A ALA* 4.7 0.7 - - + -
54A THR* 1.3 78.9 - - - +
56A THR* 1.3 61.7 + - - +
57A LEU* 4.1 7.2 - - + -
64A ARG 3.7 1.4 - - - +
65A THR* 3.3 2.9 - - - +
66A VAL* 2.8 49.2 + - + +
68A VAL* 3.7 23.6 - - + -
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Residues in contact with THR 56 (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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35A LYS 3.8 0.7 - - - +
36A VAL* 3.2 4.0 - - - +
37A HIS* 2.7 49.5 + - + +
40A GLY* 5.9 1.7 + - - -
54A THR* 4.2 5.4 + - - +
55A LEU* 1.3 73.4 - - - +
57A LEU* 1.3 64.5 + - - +
63A GLU* 3.7 35.7 - - + +
64A ARG 3.4 4.7 - - - +
65A THR* 3.4 17.7 + - - +
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Residues in contact with LEU 57 (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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15A LEU* 3.9 14.6 - - + -
20A PHE* 3.8 44.0 - - + -
21A TYR* 3.6 13.5 - - - +
35A LYS 3.4 5.8 - - - -
36A VAL* 3.9 11.2 - - + -
55A LEU* 4.7 7.0 - - + -
56A THR* 1.3 76.5 - - - +
58A ARG* 1.3 58.2 + - - +
59A GLN* 3.7 37.5 - - + +
63A GLU* 3.5 5.9 - - - -
64A ARG* 2.9 42.5 + - + +
66A VAL* 4.5 12.1 - - + -
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Residues in contact with ARG 58 (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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21A TYR* 2.8 26.9 + - - -
30A MET* 3.8 17.9 - - + +
35A LYS* 3.1 25.0 + - + +
57A LEU* 1.3 72.6 - - - +
59A GLN* 1.3 65.0 + - - +
60A GLY 3.9 9.7 + - - +
62A ASP 3.3 7.6 - - - +
63A GLU* 4.7 1.6 - - - +
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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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19A ARG 4.9 1.4 - - - +
20A PHE* 3.3 40.1 + - - +
21A TYR* 3.8 5.7 - - - -
57A LEU* 3.7 24.2 + - + +
58A ARG* 1.3 77.7 + - - +
60A GLY* 1.3 57.2 + - - +
61A ASN 2.7 1.0 + - - -
62A ASP* 2.6 53.3 + - + +
64A ARG* 3.7 31.1 + - + +
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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