Contacts of the strand formed by residues 88 - 94 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ALA* 4.5 1.1 - - - -
10C THR 3.4 14.1 - - - +
11C THR* 3.9 7.4 - - + -
48C SER 3.8 0.3 - - - +
49C ALA* 3.4 4.7 - - - -
50C THR* 2.8 35.8 + - + +
53C LEU* 4.0 0.2 - - - +
78C GLU* 5.7 0.2 - - - +
85C LEU* 3.7 18.2 - - + +
86C LYS 3.6 9.2 - - - +
87C LYS* 1.3 75.3 - - - +
89C ILE* 1.3 71.6 + - - +
90C ARG* 3.6 36.7 + - - +
115C LEU* 4.3 11.7 - - - -
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ALA* 3.1 3.3 - - - +
10C THR* 2.9 46.5 + - + +
12C VAL* 4.2 22.9 - - + +
20C ILE* 3.7 24.2 - - + -
24C THR* 3.6 28.7 - - + +
27C LEU* 4.5 3.9 - - + +
47C LEU* 4.0 20.6 - - + -
48C SER 3.3 11.7 - - - +
49C ALA* 4.4 0.7 - - + -
53C LEU* 3.8 17.3 - - + -
58C PRO* 4.2 11.0 - - + -
87C LYS 4.3 0.4 + - - +
88C CYS* 1.3 77.1 - - - +
90C ARG* 1.3 65.0 + - - +
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B PHE* 3.7 14.6 - - - -
74B THR* 4.2 9.0 - - + +
7C ARG* 3.6 13.5 - - - +
8C GLY 3.3 6.7 - - - +
9C ALA* 3.9 7.2 - - + +
27C LEU* 5.1 0.4 - - - -
46C LEU 4.0 0.2 - - - +
47C LEU* 3.3 8.0 - - - +
48C SER* 3.0 41.4 + - - +
50C THR* 4.1 11.7 - - - +
78C GLU* 2.8 43.8 + - - +
85C LEU 4.2 7.1 + - - +
88C CYS* 3.6 17.8 + - - -
89C ILE* 1.3 80.2 - - - +
91C VAL* 1.3 62.1 + - - +
115C LEU* 3.2 25.1 - - - +
202C TSA 2.9 43.7 + - - -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B THR* 6.0 0.7 - - - -
7C ARG* 3.2 12.3 + - - -
8C GLY* 2.9 33.3 + - - +
27C LEU* 4.3 10.1 - - + -
28C LEU* 4.0 16.6 - - + -
31C ILE* 3.4 33.4 - - + -
45C MET* 3.8 17.3 - - + -
46C LEU 3.5 6.1 - - - +
47C LEU* 3.5 32.1 - - + -
90C ARG* 1.3 73.5 - - - +
92C MET* 1.3 60.0 + - - +
93C MET* 4.5 9.2 - - + +
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Residues in contact with MET 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN* 3.5 37.7 - - - +
45B MET 4.7 7.0 - - - +
46B LEU* 4.8 11.2 - - + -
72B PRO* 3.6 19.3 - - + +
73B VAL 4.5 3.8 - - - -
74B THR* 4.5 15.2 - - + +
5C GLY* 3.4 30.1 - - - -
6C ILE 3.3 31.0 - - - +
7C ARG* 4.0 15.7 - - - -
45C MET* 3.6 2.6 - - - -
46C LEU* 3.0 43.5 + - + +
91C VAL* 1.3 71.9 - - - +
93C MET* 1.3 56.7 + - - +
94C THR* 3.9 2.6 + - - +
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Residues in contact with MET 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLY* 4.6 0.7 - - - -
6C ILE* 2.8 42.9 + - + +
28C LEU* 3.9 19.7 - - + -
31C ILE* 3.7 31.6 - - + -
32C ILE* 4.5 5.6 - - + -
37C THR* 4.1 16.2 - - - -
42C VAL* 4.0 6.3 - - + -
44C GLN 4.0 3.1 - - - -
45C MET* 3.5 37.7 - - + -
68C TRP* 4.4 11.2 - - + -
91C VAL* 3.8 6.0 - - + -
92C MET* 1.3 70.8 - - - +
94C THR* 1.3 59.0 + - - +
95C VAL* 3.6 24.9 + - + +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 5.0 1.8 - - + -
43B VAL* 4.0 6.5 - - + -
44B GLN* 2.7 33.8 + - - +
94B THR* 6.2 1.1 - - + -
3C ILE* 3.5 30.3 - - + -
4C ARG 3.6 4.3 - - - +
42C VAL* 3.6 0.7 - - - -
43C VAL* 2.8 40.0 + - + -
44C GLN* 3.0 29.1 + - + +
92C MET* 3.9 4.1 + - - +
93C MET* 1.3 69.6 - - - +
95C VAL* 1.3 59.8 + - - +
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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