Contacts of the strand formed by residues 55 - 63 (chain A) in PDB entry 2BTU
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 PRO 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU* 4.0 28.7 - - + +
53A GLU 3.3 8.3 - - - +
54A GLU* 1.3 90.6 - - - +
56A VAL* 1.3 64.2 + - - +
160A ILE* 4.2 15.3 - - + -
161A VAL 3.7 5.2 - - - +
46B ASP* 3.3 4.0 - - - +
47B LEU* 3.0 52.0 + - + +
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Residues in contact with VAL 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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54A GLU 3.5 11.7 - - - +
55A PRO* 1.3 79.9 - - - +
57A LEU* 1.3 67.1 + - - +
58A VAL 3.9 0.6 + - - -
160A ILE* 3.3 7.3 - - - +
161A VAL* 2.7 48.8 + - + +
163A LYS* 3.7 22.4 - - + -
166A ILE* 4.8 1.1 - - + -
35B LEU* 3.9 8.5 - - + -
44B MET* 3.3 41.5 - - + -
45B PHE 3.6 9.4 - - - +
46B ASP* 3.6 13.5 - - - +
47B LEU 4.5 0.2 - - - +
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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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47A LEU* 5.1 0.7 - - + -
56A VAL* 1.3 71.4 - - - +
58A VAL* 1.3 61.2 + - - +
59A SER* 4.1 1.8 + - - -
100A LEU* 4.6 2.2 - - + -
158A VAL* 3.8 22.4 - - + -
159A GLY 3.5 6.7 - - - +
160A ILE* 4.0 15.7 - - + -
44B MET* 3.2 5.7 - - - +
45B PHE* 2.6 46.4 + - + +
47B LEU* 3.3 43.7 - - + +
57B LEU* 4.2 27.6 - - + -
100B LEU* 4.7 1.3 - - + -
101B PHE* 3.9 26.8 - - + -
158B VAL* 4.6 2.9 - - + -
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Residues in contact with VAL 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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57A LEU* 1.3 74.0 - - - +
59A SER* 1.3 62.2 + - - +
91A ASP 5.4 1.1 - - - +
92A ILE* 3.7 25.6 - - + +
95A GLN* 5.0 14.6 - - + +
97A ALA* 4.2 18.2 - - + -
158A VAL* 3.5 0.8 - - - -
159A GLY* 2.6 40.5 + - - +
161A VAL* 4.1 20.4 - - + -
166A ILE* 5.8 0.2 - - + -
43B GLY 5.4 0.2 - - - -
44B MET* 3.9 35.2 - - + +
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Residues in contact with SER 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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57A LEU 4.1 1.9 + - - -
58A VAL* 1.3 79.1 - - - +
60A GLY* 1.3 59.5 + - - +
92A ILE* 3.9 10.3 - - - +
156A PHE* 3.9 5.2 - - - -
157A THR 3.0 17.5 - - - -
158A VAL* 3.7 16.8 - - - -
42B GLY 5.7 0.5 - - - +
44B MET* 5.8 0.6 - - - +
101B PHE* 3.4 27.0 - - - -
103B LEU* 4.2 9.6 - - - +
135B ILE* 5.2 4.2 - - - +
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Residues in contact with GLY 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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59A SER* 1.3 79.8 + - - +
61A THR* 1.3 61.0 + - - -
88A CYS* 4.1 10.3 - - - +
91A ASP* 6.6 0.4 - - - -
92A ILE* 4.2 6.5 - - - +
156A PHE* 3.4 4.4 - - - -
157A THR* 3.0 29.7 + - - -
103B LEU* 4.1 10.1 - - - -
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Residues in contact with THR 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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60A GLY* 1.3 74.4 - - - -
62A ASP* 1.3 62.7 + - - +
88A CYS* 4.2 1.8 - - - -
155A GLY 2.6 22.9 + - - -
156A PHE* 4.2 8.3 - - - -
103B LEU* 3.3 26.5 - - + +
104B ASP 4.0 9.0 - - - +
105B TYR* 4.6 8.2 - - + -
137B GLY* 3.8 22.8 - - - +
138B GLU* 3.6 12.6 - - + +
156B PHE* 3.8 15.1 - - - -
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Residues in contact with ASP 62 (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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61A THR* 1.3 75.5 + - - +
63A GLY* 1.3 74.1 + - - +
64A VAL 4.1 1.0 + - - -
84A ALA* 4.9 6.0 - - - +
87A MET* 4.1 34.7 - - + +
88A CYS* 3.5 17.1 - - - +
91A ASP* 4.9 8.1 - - - +
153A LEU 4.2 0.3 - - - +
154A ALA* 3.6 2.4 - - - -
155A GLY* 3.0 26.3 + - - -
105B TYR* 4.6 2.2 - - - -
138B GLU* 2.6 26.4 - - - +
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Residues in contact with GLY 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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62A ASP* 1.3 86.2 + - - +
64A VAL* 1.3 67.4 + - - +
65A GLY* 3.3 4.2 + - - -
152A ASP* 5.6 0.9 - - - -
153A LEU 3.5 10.1 - - - -
154A ALA* 4.1 0.2 - - - -
105B TYR* 3.6 26.0 - - - -
138B GLU* 3.1 9.4 + - - +
140B ALA* 5.9 0.9 - - - -
142B MET* 6.1 1.3 - - - +
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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