Contacts of the strand formed by residues 86 - 91 (chain J) in PDB entry 3EO1
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 VAL 86 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J GLN* 3.2 5.2 - - - -
39J GLN* 2.7 46.1 + - + +
41J PRO* 5.9 4.5 - - + -
85J ALA* 1.3 78.7 - - - +
87J TYR* 1.3 66.8 + - - +
88J TYR* 3.7 31.1 - - + +
102J GLY* 4.6 2.0 - - - -
103J THR 3.3 23.3 - - - +
104J ARG* 4.6 17.3 - - + +
166J GLU* 6.2 0.2 - - - +
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Residues in contact with TYR 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J GLN* 2.9 18.8 + - - +
21J LEU* 3.4 27.8 - - + -
36J TRP* 5.0 1.8 - - + -
37J TYR 3.1 17.7 - - - +
38J GLN* 3.5 16.5 + - + -
48J LEU* 3.6 6.3 - - + -
63J PHE* 3.4 33.8 - + - -
74J LEU* 3.7 20.9 - - + -
76J ILE* 3.3 20.9 - - + +
83J ASP 3.0 19.0 + - - -
85J ALA 3.6 17.9 - - - -
86J VAL* 1.3 79.4 - - - +
88J TYR* 1.3 64.7 + - - +
102J GLY* 3.2 2.3 - - - -
103J THR 2.9 22.6 + - - -
105J LEU* 3.6 20.2 - - + -
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Residues in contact with TYR 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J GLN* 3.5 7.6 - - - +
35J ALA 3.8 0.2 - - - +
36J TRP* 3.5 6.4 - - - -
37J TYR* 2.7 47.6 + - + +
39J GLN* 2.9 41.4 + - + -
45J PRO* 5.7 0.7 - - + -
86J VAL* 3.7 27.6 - - + +
87J TYR* 1.3 80.1 - - - +
89J CYS* 1.3 63.2 + - - +
99J PHE* 4.7 7.6 - - + -
100J GLY 3.7 18.8 - - - +
101J GLN 4.9 2.2 - - - -
102J GLY* 4.0 11.4 - - - -
39K GLN* 3.2 11.0 + - - -
43K GLN 4.1 5.5 + - - -
44K GLY* 4.3 18.2 - - - -
45K LEU* 3.8 28.0 - - + -
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Residues in contact with CYS 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 3.4 9.6 - - - +
6J GLN* 3.5 10.2 + - - -
23J CYS* 2.0 53.2 - - + -
34J LEU* 4.1 6.5 - - + -
35J ALA 3.1 9.4 - - - +
36J TRP* 4.0 15.3 - - + -
88J TYR* 1.3 75.4 - - - +
90J GLN* 1.3 59.9 + - - +
99J PHE* 3.4 2.3 - - - -
100J GLY* 2.7 38.8 + - - -
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Residues in contact with GLN 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J LEU* 3.0 8.5 - - - +
35J ALA* 2.5 56.7 + - - +
37J TYR* 2.8 44.1 + - + -
88J TYR 4.1 0.2 - - - -
89J CYS* 1.3 73.8 - - - +
91J GLN* 1.3 62.1 - - - +
92J TYR* 4.2 6.0 - - - -
97J ILE* 3.2 29.0 - - + +
98J THR 3.5 4.9 - - - +
99J PHE* 3.6 18.3 - - + -
105K ASP 3.1 21.3 - - - +
106K ALA* 3.7 6.3 - - - +
107K MET* 3.6 9.5 - - - +
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Residues in contact with GLN 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR* 4.2 6.7 - - + -
4J LEU* 3.8 13.2 - - + +
29J LEU* 3.8 29.1 - - + +
33J TYR 3.5 5.4 - - - +
34J LEU* 4.1 2.7 - - + -
89J CYS 4.4 0.2 + - - -
90J GLN* 1.3 75.8 - - - +
92J TYR* 1.3 60.3 + - - +
93J ALA* 3.0 25.0 + - - +
94J ASP* 3.0 31.6 + - - +
96J PRO 3.0 24.2 + - - -
97J ILE* 3.2 19.9 - - - +
98J THR* 2.9 37.6 + - - +
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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