Contacts of the strand formed by residues 87 - 91 (chain B) in PDB entry 5JSJ
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 TYR 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ARG* 5.4 1.4 + - - -
52B ASN* 3.2 22.4 + - - -
53B ILE* 3.4 26.4 - - + +
54B VAL* 4.2 4.9 - - + -
76B VAL* 3.8 20.6 - - + -
78B ASP 3.6 9.2 - - - +
79B GLN* 3.8 25.0 + - + -
84B PRO 4.1 6.0 + - - -
85B SER* 3.5 18.2 - - - -
86B LEU* 1.3 74.2 - - - +
88B LEU* 1.3 64.2 + - - +
89B ILE* 3.9 5.9 - - + +
98B TYR 3.4 0.9 - - - +
99B GLY* 3.2 7.4 - - - -
100B LEU 3.1 39.1 + - - +
102B LEU* 4.0 24.5 - - + -
103B ASN* 3.7 25.5 + - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.6 3.5 - - - -
77B LEU* 2.6 37.5 + - + -
78B ASP* 3.1 34.7 + - + +
80B VAL* 4.3 22.2 - - + -
86B LEU* 4.8 1.6 - - + -
87B TYR* 1.3 79.0 - - - +
89B ILE* 1.3 57.1 + - - +
97B VAL* 3.8 18.2 - - + -
98B TYR 3.3 3.6 - - - +
99B GLY* 4.2 1.8 - - - -
167B TYR* 4.4 9.4 - - + +
176B LEU* 4.9 2.5 - - + -
233B ILE* 4.7 3.4 - - + -
244B PHE* 4.9 19.3 - - + -
253B ILE* 3.8 32.1 - - + -
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 4.8 7.0 - - + -
74B GLY* 4.2 5.2 - - - -
75B THR 3.3 24.2 - - - +
76B VAL* 4.5 4.5 - - + +
77B LEU* 4.4 4.5 - - - -
87B TYR* 3.9 14.4 - - + +
88B LEU* 1.3 78.6 - - - +
90B LYS* 1.3 69.1 + - - +
91B TYR* 3.8 28.0 + - + +
96B CYS 3.9 1.0 - - - +
97B VAL* 3.7 4.6 - - - +
98B TYR* 2.9 32.9 + - - +
100B LEU* 3.7 40.2 - - + +
102B LEU* 4.0 24.7 - - + -
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLY* 3.2 1.6 - - - -
75B THR* 2.8 39.5 + - - +
77B LEU* 4.1 9.5 - - + +
89B ILE* 1.3 74.5 - - - +
91B TYR* 1.3 64.9 + - - +
92B ASP* 3.7 2.0 + - - +
93B GLY 4.7 4.4 - - - +
94B PHE 2.9 33.7 + - - +
95B ASP* 3.0 14.2 + - - -
96B CYS 4.2 6.7 - - - +
162B MET* 3.8 24.4 - - + +
165B TRP* 3.6 33.6 - - - -
178B MET* 3.7 33.4 - - - -
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Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 5.4 1.1 - - + -
60B HIS* 2.8 37.7 + + - -
72B TRP* 3.9 25.8 - + + -
73B LYS 3.4 19.1 - - - +
74B GLY* 4.1 2.5 - - - -
89B ILE* 3.8 28.5 - - + +
90B LYS* 1.3 76.4 + - - +
92B ASP* 1.3 67.0 + - - +
93B GLY 3.1 0.7 + - - -
94B PHE* 3.1 40.3 + - + +
96B CYS 4.7 2.2 + - - -
98B TYR* 3.8 12.5 - + + -
100B LEU* 3.6 33.4 - - + +
102B LEU* 4.3 0.7 - - - +
301B 6PD 3.7 34.5 - + + -
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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