Contacts of the strand formed by residues 88 - 94 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9I ALA* 4.3 8.7 - - - -
10I THR 3.2 19.3 - - - -
11I THR* 3.6 15.5 - - + -
48I SER* 3.9 0.5 + - - +
49I ALA* 3.5 2.8 - - - -
50I THR* 2.9 31.3 + - - +
53I LEU* 4.1 0.5 - - - +
78I GLU* 5.8 0.2 - - - +
85I LEU* 3.7 22.9 - - + +
87I LYS* 1.3 76.5 - - - +
89I ILE* 1.3 64.8 + - - +
90I ARG* 2.8 46.8 + - - +
115I LEU* 4.4 0.2 - - - -
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Residues in contact with ILE 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ALA* 3.2 2.4 - - - -
10I THR* 3.0 40.4 + - + +
12I VAL* 3.7 24.7 - - + -
20I ILE* 3.7 22.7 - - + -
24I THR* 3.3 32.1 - - + +
27I LEU* 4.3 5.1 - - + +
47I LEU* 4.7 6.3 - - + -
48I SER 3.2 9.9 - - - +
49I ALA* 4.6 0.7 - - + -
53I LEU* 3.8 16.6 - - + -
58I PRO* 3.9 24.7 - - + -
88I CYS* 1.3 78.0 - - - +
90I ARG* 1.3 66.7 + - - +
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Residues in contact with ARG 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H PHE* 4.3 12.5 - - - -
74H THR* 4.4 6.7 - - - +
7I ARG* 3.6 11.4 - - - +
8I GLY 3.4 3.8 - - - -
9I ALA* 4.1 3.6 - - + -
46I LEU 4.5 0.3 - - - -
47I LEU* 3.3 2.6 - - - +
48I SER* 2.9 46.4 + - - +
50I THR* 4.0 15.4 - - - +
76I MET* 5.7 0.5 - - - +
78I GLU* 3.3 25.7 + - - +
85I LEU* 4.3 7.9 + - - +
88I CYS* 2.8 44.1 - - - +
89I ILE* 1.3 77.6 - - - +
91I VAL* 1.3 61.5 + - - +
115I LEU* 3.5 20.6 - - - +
208I TSA 2.8 50.8 + - - +
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Residues in contact with VAL 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H THR* 5.6 1.6 - - - -
6I ILE 4.1 0.2 - - - -
7I ARG* 3.2 12.4 + - - -
8I GLY* 3.1 38.4 + - - -
27I LEU* 3.7 29.4 - - + -
28I LEU* 3.8 19.5 - - + -
31I ILE* 3.8 12.1 - - + -
45I MET* 3.7 20.4 - - + -
46I LEU 3.3 12.3 - - - +
47I LEU* 4.6 9.4 - - + -
89I ILE* 5.9 0.2 - - + -
90I ARG* 1.3 73.8 - - - +
92I MET* 1.3 65.8 + - - +
93I MET* 4.0 7.0 - - + +
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Residues in contact with MET 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H GLN* 3.5 39.9 - - + +
45H MET 3.6 24.7 - - - +
46H LEU* 4.9 1.3 - - + -
72H PRO* 3.6 33.2 - - - +
74H THR* 3.9 25.4 - - + +
5I GLY* 4.4 3.8 - - - -
6I ILE 3.4 9.0 - - - +
7I ARG* 3.6 19.3 - - - -
44I GLN 4.2 0.2 - - - +
45I MET* 3.4 2.9 - - - -
46I LEU* 3.0 44.1 + - + +
91I VAL* 1.3 75.8 - - - +
93I MET* 1.3 56.0 + - - +
94I THR* 4.0 2.4 + - - +
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Residues in contact with MET 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ARG 3.9 0.5 - - - +
5I GLY* 3.2 3.6 - - - -
6I ILE* 2.8 43.1 + - + +
28I LEU* 3.7 30.3 - - + +
31I ILE* 3.8 32.8 - - + -
32I ILE* 4.6 5.6 - - + -
37I THR* 4.4 14.6 - - - -
42I VAL* 4.0 7.0 - - + -
44I GLN 3.7 3.1 - - - -
45I MET* 3.8 28.7 - - + -
68I TRP* 4.4 13.5 - - + -
91I VAL* 4.0 2.7 - - + -
92I MET* 1.3 72.1 - - - +
94I THR* 1.3 62.5 + - - +
95I VAL* 3.9 22.1 + - + -
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Residues in contact with THR 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ILE* 6.2 0.2 - - + -
94G THR* 6.3 0.7 - - + -
3H ILE* 5.8 2.5 - - + -
43H VAL* 3.8 11.2 - - + -
44H GLN* 2.6 35.5 + - - +
94H THR* 6.4 0.4 - - + -
3I ILE* 3.6 24.0 - - + -
4I ARG 3.7 2.9 - - - -
42I VAL* 3.6 3.1 - - - -
43I VAL* 2.7 40.9 + - + -
44I GLN* 2.9 31.8 + - + +
92I MET* 4.4 4.5 + - - +
93I MET* 1.3 71.9 - - - +
95I VAL* 1.3 52.7 + - - +
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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