Contacts of the strand formed by residues 19 - 26 (chain E) in PDB entry 6BA5
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 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E GLY 5.0 0.9 + - - -
18E GLY* 1.3 74.1 + - - -
20E VAL* 1.3 66.4 + - - +
21E THR* 4.1 14.9 + - + +
75E THR* 3.8 22.9 - - + -
76E ILE 3.3 11.3 + - - +
77E SER* 4.1 11.2 + - - +
78E GLY 4.2 1.2 + - - -
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 3.9 17.5 - - - +
13E SER 6.0 0.2 - - - -
14E GLY* 5.4 11.4 - - - +
18E GLY 4.2 0.4 + - - -
19E THR* 1.3 76.0 - - - +
21E THR* 1.3 65.7 + - - +
22E ILE* 4.1 12.8 - - + -
74E LEU 3.7 0.7 - - - +
75E THR* 3.3 5.7 - - - +
76E ILE* 2.9 48.3 + - + +
79E VAL* 4.2 30.5 - - + -
108E VAL* 3.9 33.9 - - + -
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Residues in contact with THR 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E PRO* 4.0 12.6 - - - +
12E THR* 4.6 8.5 - - - +
19E THR* 4.1 17.7 + - + +
20E VAL* 1.3 79.8 - - - +
22E ILE* 1.3 65.3 + - - +
23E ASN* 4.6 10.3 + - - -
73E THR* 4.5 11.0 - - + -
74E LEU 3.5 4.7 - - - -
75E THR* 4.4 11.0 - - + +
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Residues in contact with ILE 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLN* 3.5 17.0 - - + +
8E THR 3.9 5.2 - - - +
9E PRO* 4.5 0.2 - - - -
12E THR* 4.9 0.4 - - - +
20E VAL* 4.1 11.2 - - + -
21E THR* 1.3 78.6 - - - +
23E ASN* 1.3 65.0 + - - +
36E TRP* 3.7 16.2 - - + -
73E THR* 3.3 4.9 - - - +
74E LEU* 2.9 48.9 + - + +
76E ILE* 5.1 1.8 - - + -
87E TYR* 3.8 28.0 - - + -
106E THR* 3.4 34.8 - - + +
108E VAL* 3.9 22.4 - - + -
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Residues in contact with ASN 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E THR 4.5 0.4 - - - -
7E GLN* 3.4 6.2 - - - +
8E THR* 2.8 50.2 + - - +
9E PRO* 5.4 1.6 - - - +
21E THR* 4.6 12.4 + - - -
22E ILE* 1.3 75.4 - - - +
24E CYS* 1.3 65.3 + - - +
36E TRP* 4.3 0.4 - - - -
71E GLU* 3.6 26.5 + - - +
72E TYR 3.4 2.9 - - - -
73E THR* 2.8 34.1 + - - +
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Residues in contact with CYS 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E MET* 4.1 9.4 - - + -
6E THR 3.4 3.4 - - - +
7E GLN* 3.5 24.9 - - - -
23E ASN* 1.3 79.0 - - - +
25E GLN* 1.3 59.7 + - - +
26E ALA 4.1 0.2 - - - -
36E TRP* 3.6 12.8 - - + -
70E THR 3.6 1.7 - - - +
71E GLU* 3.4 6.2 - - - -
72E TYR* 2.8 43.0 + - + +
89E CYS* 2.3 49.1 - - + -
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Residues in contact with GLN 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL 3.6 1.2 - - - +
5E MET* 3.5 5.2 - - - -
6E THR* 2.8 51.2 + - + +
24E CYS* 1.3 71.7 - - - +
26E ALA* 1.3 81.0 + - - +
27E SER* 3.9 0.4 + - - -
70E THR* 2.7 37.8 + - - +
71E GLU* 3.8 20.3 + - - +
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 4.3 1.1 - - + -
5E MET* 3.7 27.2 - - + +
25E GLN* 1.3 92.3 + - - +
27E SER* 1.3 63.2 + - - +
28E GLN 3.2 20.2 + - - +
30E ILE* 3.9 16.6 - - + -
70E THR* 2.9 24.5 + - + +
72E TYR* 4.2 2.7 - - + -
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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