Contacts of the strand formed by residues 72 - 77 (chain C) in PDB entry 2PJY
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 THR 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C SER* 5.0 5.1 - - - -
34C VAL 3.4 15.3 - - - -
35C THR* 3.3 33.9 - - + +
36C GLU 5.4 0.2 - - - +
65C SER* 3.4 20.2 - - - -
68C THR* 4.0 12.4 - - - +
71C VAL* 1.3 91.9 - - + +
73C THR* 1.3 60.6 + - - +
74C THR* 4.1 12.6 + - - +
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL 4.1 0.2 - - - +
33C SER* 3.4 3.5 - - - -
34C VAL* 2.9 53.1 + - + +
36C GLU* 4.0 13.7 - - - +
64C PRO* 5.2 1.9 - - - +
65C SER* 3.9 22.7 + - - -
72C THR* 1.3 73.9 - - - +
74C THR* 1.3 67.6 + - - +
75C TYR* 5.5 0.5 - - - +
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Residues in contact with THR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 3.8 28.3 - - + -
32C VAL 3.4 5.6 - - - -
33C SER* 4.3 7.0 - - - -
61C VAL 4.2 6.7 - - - +
62C CYS 3.7 8.9 + - - +
63C ALA 2.7 33.3 + - - +
64C PRO* 3.5 16.2 - - - +
68C THR* 5.7 3.4 - - + -
72C THR* 4.1 12.9 + - - +
73C THR* 1.3 83.2 + - - +
75C TYR* 1.3 61.1 + - - +
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA* 3.5 29.3 + - + +
21B ALA* 3.3 28.2 - - + +
31C PHE* 3.5 3.6 - - - -
32C VAL* 2.7 68.4 + - + +
73C THR 5.5 0.2 - - - +
74C THR* 1.3 76.2 - - - +
76C CYS* 1.3 69.5 + - - +
77C CYS* 3.9 20.9 - - + -
82C CYS 5.1 4.9 - - - -
85C ILE* 6.4 0.7 - - + -
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Residues in contact with CYS 76 (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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21B ALA* 3.7 8.3 - - - +
22B VAL* 3.3 20.5 + - - +
24B PHE* 3.7 15.9 - - + -
29C LEU* 4.8 6.1 - - + -
30C CYS 3.4 6.3 - - - +
31C PHE* 3.7 24.2 - - - -
48C ILE* 5.0 2.2 - - - -
62C CYS* 2.0 59.0 + - + +
75C TYR* 1.3 74.8 - - - +
77C CYS* 1.3 64.5 + - - +
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Residues in contact with CYS 77 (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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20B GLY 3.4 17.3 - - - +
22B VAL* 3.8 9.9 - - - +
29C LEU* 3.5 5.7 - - - +
30C CYS* 2.7 41.6 + - + +
75C TYR* 3.9 16.6 - - + -
76C CYS* 1.3 78.3 - - - +
78C ASN* 1.3 61.6 + - - +
79C GLN* 3.2 10.8 - - - -
82C CYS* 2.0 52.7 - - - -
83C ASN* 5.6 0.7 - - + -
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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
------------------------------------------------------------
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