Contacts of the strand formed by residues 68 - 72 (chain B) in PDB entry 2O07
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 VAL 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU* 3.5 11.7 - - - +
24B THR 5.5 0.7 - - - +
25B CYS* 4.6 13.2 - - + -
28B TRP* 3.9 18.8 - - + -
64B VAL* 3.7 2.4 - - - +
65B LEU 2.9 34.1 + - - +
66B ASP* 4.2 7.0 - - + +
67B GLY* 1.3 80.1 - - - +
69B ILE* 1.3 75.2 + - - +
70B GLN* 3.0 16.4 - - - +
175B SER* 4.2 4.3 - - - +
176B ASP* 3.3 25.4 - - + +
601B SPD 3.6 9.0 - - - +
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.8 22.4 - - + -
23B GLU* 2.7 36.5 + - + +
33B LEU* 3.8 30.5 - - + +
35B LEU* 4.1 13.9 - - + -
62B VAL* 4.2 14.8 - - + -
63B LEU 3.7 4.7 - - - -
64B VAL* 4.4 2.0 - - + +
67B GLY 4.0 0.2 + - - -
68B VAL* 1.3 80.0 - - - +
70B GLN* 1.3 60.9 + - - +
71B CYS* 3.9 19.5 - - - +
72B THR* 4.2 10.8 - - + -
240B THR* 3.8 16.8 - - - +
241B TYR* 3.4 19.8 - - + -
601B SPD 3.9 0.9 - - - +
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 2.7 29.2 + - + +
65B LEU* 3.5 40.0 - - + +
68B VAL* 3.0 27.3 - - - +
69B ILE* 1.3 73.3 - - - +
71B CYS* 1.3 60.3 + - - +
175B SER* 3.1 37.2 + - - +
241B TYR* 2.7 31.2 + - - -
501B MTA 3.7 11.1 - - + +
601B SPD 3.3 34.1 - - + +
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Residues in contact with CYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN 4.0 0.6 - - - +
62B VAL* 3.4 4.7 - - - +
63B LEU* 3.0 36.2 + - - +
69B ILE* 3.7 3.5 - - - -
70B GLN* 1.3 82.0 - - - +
72B THR* 1.3 65.5 + - - +
75B ASP* 5.4 1.1 - - - -
76B GLU* 4.1 10.1 - - + +
80B GLN* 5.0 0.9 - - - +
104B ASP* 4.0 13.0 - - - -
137B LEU* 3.8 20.4 - - - -
140B MET* 3.6 39.0 - - + -
238B ILE* 6.5 1.1 - - - -
240B THR* 5.5 0.9 - - - -
241B TYR* 5.2 2.0 - - - +
601B SPD 4.7 2.9 - - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.2 6.3 - - + -
59B TYR* 3.4 26.5 + - + -
61B ASN 3.2 8.5 - - - -
62B VAL* 3.9 15.3 - - + -
69B ILE* 4.2 5.2 - - + -
71B CYS* 1.3 79.9 - - - +
73B GLU* 1.3 65.7 + - - +
74B ARG 3.5 2.8 + - - -
75B ASP* 2.9 26.1 + - - -
76B GLU* 3.0 24.9 + - - +
137B LEU* 5.5 1.3 - - - -
140B MET* 5.6 0.2 - - - -
240B THR* 3.4 31.4 - - + +
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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