Contacts of the strand formed by residues 87 - 90 (chain J) in PDB entry 1JJ2
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 ARG 87 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27200 C 2.5 37.0 + - - +
27210 U 2.8 50.7 + - - +
27630 G 2.9 28.9 + - - +
27640 C 3.9 0.8 + - - -
79J PRO* 4.3 13.0 - - + -
80J ILE 3.1 15.0 - - - +
81J ARG* 2.8 51.8 - - - +
85J GLY 4.3 2.2 - - - +
86J THR* 1.3 77.8 - - - +
88J VAL* 1.3 59.2 + - - +
18T GLY 3.1 9.5 + - - +
19T THR* 3.9 15.9 - - + +
20T MET 2.7 31.7 + - - -
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Residues in contact with VAL 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J LYS 4.3 0.3 - - - +
79J PRO* 3.4 2.5 - - - +
80J ILE* 2.8 47.5 + - + +
82J ARG* 3.8 46.7 - - + +
86J THR* 4.8 4.3 - - + +
87J ARG* 1.3 81.6 - - - +
89J LYS* 1.3 63.2 + - - +
90J PHE* 4.1 23.8 - - + -
132J VAL* 5.4 1.1 - - + +
20T MET* 3.4 24.0 - - + +
22T VAL* 4.1 13.5 - - + -
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Residues in contact with LYS 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27220 G 5.2 5.3 + - - -
76J GLN 4.2 2.0 - - - -
77J ARG 3.2 22.9 - - - +
79J PRO* 4.0 21.0 - - + +
88J VAL* 1.3 75.8 - - - +
90J PHE* 1.3 68.3 + - - +
19T THR* 3.8 19.0 - - + +
20T MET 3.1 5.1 + - - +
21T PHE* 3.5 24.1 - - + -
22T VAL* 2.9 25.6 + - - +
31T PHE* 6.0 0.7 - - - -
37T GLU* 3.5 30.8 + - - +
41T ASP* 6.0 0.2 + - - -
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Residues in contact with PHE 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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49J LEU* 4.1 19.5 - - + -
74J VAL 4.6 0.2 - - - -
75J ARG* 3.3 35.7 - - + -
76J GLN* 3.1 26.4 + - + +
77J ARG* 3.5 19.2 - - - +
80J ILE* 5.0 0.7 - - + -
88J VAL* 4.1 22.4 - - + -
89J LYS* 1.3 79.3 - - - +
91J GLU* 1.3 64.6 + - - +
92J ASP 3.2 13.8 + - - +
112J PRO* 4.8 0.9 - - + -
113J ILE* 4.5 5.8 - - - -
114J ALA* 3.7 31.6 - - + -
132J VAL* 5.2 4.0 - - + -
21T PHE* 3.9 8.7 - - - -
22T VAL* 3.7 37.7 - - + -
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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