Contacts of the strand formed by residues 88 - 94 (chain J) in PDB entry 2CHT
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 CYS 88 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9J ALA* 4.4 2.0 - - - -
10J THR 3.3 13.9 - - - -
11J THR* 4.0 0.4 - - - -
49J ALA* 3.4 4.5 - - - +
50J THR* 3.1 32.4 + - + +
53J LEU* 4.3 1.3 - - - +
78J GLU* 5.8 0.2 - - - +
85J LEU* 3.2 44.6 - - + +
87J LYS* 1.3 76.6 - - - +
89J ILE* 1.3 60.4 + - - +
90J ARG* 3.5 42.3 + - - +
115J LEU* 4.2 4.5 - - - -
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Residues in contact with ILE 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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9J ALA* 3.3 2.8 - - - -
10J THR* 2.9 51.5 + - + +
12J VAL* 3.8 28.9 - - + -
20J ILE* 4.7 6.5 - - + +
23J LYS* 5.3 0.7 - - + -
24J THR* 3.9 17.3 - - - +
27J LEU* 4.4 6.8 - - + +
47J LEU* 4.1 15.3 - - + -
48J SER 3.4 15.3 - - - +
49J ALA* 4.9 0.2 - - + -
53J LEU* 4.0 19.1 - - + -
58J PRO* 3.9 29.4 - - + -
87J LYS 4.6 1.8 - - - +
88J CYS* 1.3 73.4 - - - +
90J ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 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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7J ARG* 3.8 13.5 - - - +
8J GLY 3.4 4.3 - - - -
9J ALA* 3.8 5.2 - - + -
46J LEU 4.9 0.2 - - - -
47J LEU* 3.6 0.7 - - - -
48J SER* 2.9 40.7 + - - +
50J THR* 4.2 4.6 - - - +
76J MET* 5.3 1.6 - - - +
78J GLU* 3.3 34.0 + - - +
84J GLY* 4.9 0.2 - - - -
85J LEU 4.0 24.0 + - - +
88J CYS* 3.5 25.5 + - - +
89J ILE* 1.3 75.9 - - - +
91J VAL* 1.3 60.1 + - - +
115J LEU* 3.2 24.9 - - - +
212J TSA 2.6 47.5 + - - -
57L PHE* 3.7 20.4 - - - -
74L THR* 4.6 4.4 + - - +
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Residues in contact with VAL 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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6J ILE 4.7 0.4 - - - +
7J ARG* 2.8 31.5 + - - -
8J GLY* 3.0 23.2 + - - +
27J LEU* 4.0 14.3 - - + +
28J LEU* 3.9 14.1 - - + -
31J ILE* 3.5 31.0 - - + -
45J MET* 3.8 17.3 - - + -
46J LEU 3.7 8.7 - - - +
47J LEU* 3.6 26.7 - - + -
76J MET* 6.5 0.2 - - - -
89J ILE 4.3 0.6 - - - -
90J ARG* 1.3 71.6 - - - +
92J MET* 1.3 69.7 + - - +
93J MET* 4.5 3.4 - - + -
74L THR* 5.3 1.3 - - - +
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Residues in contact with MET 92 (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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5J GLY* 4.3 6.5 - - - -
6J ILE 3.6 4.5 - - - +
7J ARG* 3.9 11.7 - - - -
45J MET* 3.3 4.2 - - - -
46J LEU* 3.0 42.1 + - + +
76J MET* 5.6 0.4 - - + -
91J VAL* 1.3 76.3 - - - +
93J MET* 1.3 59.5 + - - +
94J THR* 3.8 4.0 + - - +
44L GLN* 3.5 37.5 - - + +
45L MET 3.5 24.7 - - - +
46L LEU* 4.3 8.3 - - + -
72L PRO* 3.8 29.4 - - - +
73L VAL 4.0 3.4 - - - -
74L THR* 3.9 26.2 - - + -
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Residues in contact with MET 93 (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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5J GLY* 3.2 2.5 - - - -
6J ILE* 2.7 50.3 + - + +
28J LEU* 3.7 21.5 - - + -
31J ILE* 3.9 32.3 - - + -
32J ILE* 4.8 3.1 - - + -
37J THR* 4.3 11.4 - - - -
42J VAL* 3.8 13.5 - - + -
44J GLN 3.9 2.0 - - - -
45J MET* 3.6 24.5 - - + -
68J TRP* 4.0 25.4 - - + -
91J VAL* 4.5 2.4 - - + +
92J MET* 1.3 72.2 - - - +
94J THR* 1.3 63.8 + - - +
95J VAL* 3.7 16.0 + - + -
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Residues in contact with THR 94 (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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3J ILE* 3.3 29.4 - - + -
4J ARG 3.3 4.5 - - - +
42J VAL* 3.5 3.5 - - - -
43J VAL* 2.7 44.2 + - + -
44J GLN* 2.9 31.9 + - + +
46J LEU* 5.7 1.6 + - - +
92J MET* 4.2 6.4 + - - +
93J MET* 1.3 74.2 - - - +
95J VAL* 1.3 52.6 + - - +
3L ILE* 6.1 0.7 - - + -
43L VAL* 4.2 0.7 - - + -
44L GLN* 2.7 38.9 + - - +
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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