Contacts of the strand formed by residues 86 - 94 (chain E) in PDB entry 5J0Z
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 86 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ALA* 5.3 14.3 + - - +
83E ASN* 6.1 1.0 - - - +
84E ALA 3.7 1.9 + - - +
85E ARG* 1.3 70.9 - - - +
87E ALA* 1.3 64.7 + - - +
88E ASP* 5.3 2.6 - - - +
105E ARG 4.2 0.2 - - - +
106E PHE* 3.3 2.2 - - - -
107E SER* 3.0 44.3 + - - +
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Residues in contact with ALA 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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85E ARG* 3.7 14.7 + - - +
86E ASP* 1.3 79.6 + - - +
88E ASP* 1.3 62.9 + - - +
89E VAL* 4.4 1.8 + - + +
104E GLU* 3.4 35.9 - - + +
105E ARG 3.4 7.4 - - - +
106E PHE* 4.1 2.2 - - + -
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Residues in contact with ASP 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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77A ARG* 4.2 20.4 - - - +
84A ALA* 4.6 17.5 - - - +
86E ASP* 5.3 2.9 - - - +
87E ALA* 1.3 76.4 - - - +
89E VAL* 1.3 68.2 + - - +
90E VAL* 5.1 3.4 - - + -
104E GLU* 3.2 6.0 - - - +
105E ARG* 3.0 38.3 + - + +
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Residues in contact with VAL 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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75A GLU* 3.8 8.7 - - - +
68E PRO* 4.0 28.9 - - + -
87E ALA* 5.6 2.0 - - + +
88E ASP* 1.3 77.1 - - - +
90E VAL* 1.3 63.8 + - - +
91E ASP 4.4 2.9 - - - +
92E ILE* 4.1 22.0 - - + -
102E TYR* 3.9 32.8 - - + +
103E LEU 3.9 9.2 - - - +
104E GLU* 4.3 2.2 - - + +
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Residues in contact with VAL 90 (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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75A GLU* 2.7 43.4 - - - +
77A ARG* 3.6 23.8 - - - +
133A ARG* 4.2 13.5 - - - -
42E PHE* 4.5 2.9 - - + -
88E ASP* 3.9 3.4 - - + +
89E VAL* 1.3 75.7 - - - +
91E ASP* 1.3 63.5 + - + +
103E LEU* 2.7 37.8 + - + +
104E GLU 3.7 1.8 - - - -
105E ARG* 3.4 37.7 - - + +
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Residues in contact with ASP 91 (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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133A ARG* 5.8 5.4 - - - +
135A VAL* 4.6 16.1 - - - +
179A ARG* 3.5 19.7 + - - +
65E THR* 3.4 21.0 - - - +
89E VAL* 4.4 1.3 - - - +
90E VAL* 1.3 86.8 - - + +
92E ILE* 1.3 71.0 + - - +
93E SER* 3.1 23.5 + - - -
101E GLN 3.5 3.6 - - - +
103E LEU* 2.9 36.6 + - + +
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Residues in contact with ILE 92 (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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64E LYS 3.9 0.3 - - - +
65E THR* 3.2 30.3 - - - +
66E TYR* 3.4 25.2 + - + +
67E GLU 4.3 1.3 - - - +
68E PRO* 3.5 36.3 - - + +
71E ILE* 3.8 14.4 - - + -
73E ILE* 3.7 17.0 - - + -
89E VAL* 4.1 10.1 - - + +
91E ASP* 1.3 80.1 + - - +
93E SER* 1.3 59.6 + - - +
94E VAL* 4.8 3.4 - - + -
100E VAL* 3.7 28.9 - - + -
101E GLN 3.3 3.8 - - - +
102E TYR* 3.9 16.4 - - + -
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Residues in contact with SER 93 (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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135A VAL* 5.8 0.2 - - - +
136A ASP* 4.5 5.0 - - - +
179A ARG* 3.7 17.5 + - - -
63E VAL* 3.7 20.3 - - - +
64E LYS 3.6 4.6 - - - -
65E THR* 4.9 3.3 + - - +
91E ASP* 3.1 23.9 + - - -
92E ILE* 1.3 72.0 + - - +
94E VAL* 1.3 61.3 + - - +
95E SER 4.0 0.2 - - - -
99E THR 4.0 0.3 - - - +
100E VAL* 3.5 0.9 - - - +
101E GLN* 2.7 54.5 + - - +
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Residues in contact with VAL 94 (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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52E LEU* 3.9 42.0 - - + +
54E PHE* 3.6 6.9 - - + -
63E VAL* 3.5 6.0 - - - +
64E LYS* 2.7 35.5 + - + +
66E TYR* 3.5 35.0 - - + -
71E ILE* 4.9 0.7 - - + -
92E ILE* 4.8 3.1 - - + -
93E SER* 1.3 75.9 - - - +
95E SER* 1.3 74.3 + - - +
98E GLY* 4.4 7.0 - - - -
99E THR 3.5 7.9 - - - +
100E VAL* 4.2 15.3 - - + -
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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