Contacts of the strand formed by residues 83 - 89 (chain E) in PDB entry 4B3E
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 ASP 83 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46E HIS* 4.3 5.2 - - - -
63E HIS* 3.2 15.8 + - - -
71E HIS* 3.0 25.5 + - + -
72E GLY 3.0 35.5 + - - +
74E PRO* 3.5 11.5 - - - +
79E ARG* 3.3 24.8 + - + +
80E HIS* 2.9 40.5 + - - +
81E VAL 3.2 3.4 - - - -
82E GLY* 1.3 73.4 - - - +
84E LEU* 1.3 58.8 + - - +
85E GLY 3.4 4.5 - - - +
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Residues in contact with LEU 84 (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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20E PHE* 5.1 3.4 - - + -
31E VAL* 5.0 7.2 - - + -
45E PHE* 3.2 40.6 + - + +
47E VAL* 4.1 23.8 - - + +
74E PRO* 4.0 11.7 - - + +
79E ARG* 4.3 1.1 - - - +
82E GLY 3.0 13.6 + - - +
83E ASP* 1.3 74.2 - - - +
85E GLY* 1.3 62.0 + - - +
86E ASN 3.5 2.6 + - - +
99E ILE* 3.8 27.0 - - + +
101E ASP* 3.7 38.6 - - + +
104E ILE* 4.2 21.5 - - + -
117E LEU* 4.6 6.3 - - + -
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Residues in contact with GLY 85 (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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44E GLY* 3.5 5.7 - - - -
45E PHE* 2.9 27.3 + - - +
73E GLY* 5.1 0.2 - - - -
74E PRO* 3.6 19.8 - - - +
83E ASP* 3.4 5.1 - - - +
84E LEU* 1.3 77.1 - - - +
86E ASN* 1.3 63.2 + - - +
124E ASP* 3.9 11.0 + - - +
126E LEU* 4.0 13.9 - - - -
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Residues in contact with ASN 86 (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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42E LEU* 4.1 20.6 - - + +
43E HIS 3.2 5.1 - - - +
44E GLY 3.4 11.8 + - - -
45E PHE* 4.6 0.7 - - - -
84E LEU 3.5 4.9 + - - +
85E GLY* 1.3 74.1 - - - -
87E VAL* 1.3 70.1 + - - +
99E ILE* 5.1 4.0 - - - +
123E ALA* 3.5 2.1 - - - -
124E ASP* 2.8 47.2 + - - +
126E LEU* 3.7 16.6 - - - +
153F GLN* 3.9 43.9 + - - +
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Residues in contact with VAL 87 (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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35E ILE* 4.7 3.4 - - + -
38E LEU* 5.1 0.4 - - + -
41E GLY 3.8 0.7 - - - +
42E LEU* 3.4 3.8 - - - -
43E HIS* 2.8 54.8 + - + +
45E PHE* 3.7 30.3 - - + +
86E ASN* 1.3 76.9 - - - +
88E THR* 1.3 61.4 + - - +
95E ALA* 4.2 14.6 - - + -
96E ASP 5.9 0.4 - - - +
97E VAL* 3.5 34.8 - - + -
99E ILE* 4.6 4.0 - - + -
119E VAL* 4.1 15.3 - - + -
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Residues in contact with THR 88 (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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52A ASP* 3.7 17.0 + - - +
54A THR* 4.1 6.1 + - - +
59A SER* 3.5 34.9 + - - +
41E GLY 3.6 6.3 - - - +
42E LEU* 4.0 6.5 - - + +
87E VAL* 1.3 78.2 + - - +
89E ALA* 1.3 66.6 + - - +
90E ASP 3.9 0.3 + - - -
94E VAL 3.8 1.6 - - - +
95E ALA* 3.3 18.2 - - - +
96E ASP 4.3 6.3 + - - +
153F GLN* 3.9 30.5 + - - +
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Residues in contact with ALA 89 (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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55A ALA* 3.4 7.6 - - - +
38E LEU* 3.7 28.7 - - + -
39E THR 3.5 23.6 - - - +
40E GLU* 4.2 0.2 - - - -
41E GLY* 2.9 32.2 + - - +
43E HIS* 4.2 1.0 - - + -
87E VAL 4.2 0.4 - - - -
88E THR* 1.3 75.7 - - - +
90E ASP* 1.3 64.4 + - - +
93E GLY 4.0 11.4 - - - -
94E VAL 3.4 7.6 - - - +
95E ALA* 3.9 1.2 - - - +
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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