Contacts of the strand formed by residues 69 - 76 (chain B) in PDB entry 2OVI
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 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 3.7 2.6 - - + +
65B HIS* 3.5 1.4 - - - -
66B THR* 2.7 43.9 + - + +
68B ASP* 1.3 86.5 - - + +
70B ILE* 1.3 73.7 + - - +
71B LEU* 3.9 16.4 - - + +
64C VAL* 4.7 6.5 - - + -
86C TYR* 6.2 1.8 - - - -
98C HIS 3.5 11.9 - - - +
99C ILE* 3.6 34.5 - - + -
132C MET* 3.6 32.3 - - + +
133C LEU* 4.6 3.8 - - + -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.9 18.4 - - + -
64B VAL 3.4 7.9 - - - +
65B HIS* 4.4 24.5 - - + +
69B VAL* 1.3 76.1 - - - +
71B LEU* 1.3 58.5 + - - +
72B GLU* 2.9 37.5 - - + +
86C TYR* 5.1 7.0 - - + -
97C GLY* 3.2 2.1 - - - -
98C HIS* 2.7 76.0 + - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 2.9 24.2 - - - +
64B VAL* 3.0 23.6 + - + +
69B VAL* 3.9 11.4 - - + +
70B ILE* 1.3 74.6 - - - +
72B GLU* 1.3 60.2 + - - +
62C THR* 4.7 1.3 - - + -
63C LEU 4.7 0.9 - - - -
64C VAL* 3.4 32.8 - - + +
71C LEU* 5.1 0.2 - - - +
73C PHE* 3.4 33.3 - - + -
89C LEU* 4.6 8.5 - - + -
95C MET* 3.8 25.1 - - + -
96C SER 3.4 17.3 - - - +
99C ILE* 5.2 3.4 - - + -
133C LEU* 4.0 13.9 - - + -
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Residues in contact with GLU 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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61B THR* 3.6 27.5 - - + +
62B THR 3.3 3.4 - - - -
63B LEU* 3.9 9.3 - - + +
70B ILE* 2.9 24.1 - - + +
71B LEU* 1.3 74.5 - - - +
73B PHE* 1.3 61.8 + - - +
74B SER* 4.1 3.1 + - - +
73C PHE* 3.9 5.0 - - - -
94C GLY 3.4 0.7 - - - +
95C MET* 3.3 5.5 - - - -
96C SER* 2.9 52.4 + - - +
97C GLY* 3.6 13.0 - - - -
98C HIS* 3.8 15.3 - - - -
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Residues in contact with PHE 73 (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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60B VAL 3.5 1.4 - - - +
61B THR* 3.4 1.4 - - - -
62B THR* 2.6 40.2 + - - +
72B GLU* 1.3 73.7 - - - +
74B SER* 1.3 73.9 + - - +
75B GLY* 3.7 23.8 - - - -
76B GLU 3.7 15.9 - - - -
92B LYS* 3.5 20.2 - - + -
93B HIS* 3.8 13.7 - - + -
94B GLY* 4.5 1.8 - - - -
95B MET* 3.2 58.8 - - + -
73C PHE* 3.2 24.9 - + + -
93C HIS 5.2 0.4 - - - -
94C GLY* 3.4 20.6 - - - -
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Residues in contact with SER 74 (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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59B ASN* 5.4 1.8 - - - -
60B VAL 3.3 5.6 - - - -
61B THR* 3.2 22.3 + - - +
72B GLU* 4.1 2.6 + - - +
73B PHE* 1.3 87.4 - - - +
75B GLY* 1.3 58.8 + - - +
94C GLY* 3.0 22.1 + - - -
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Residues in contact with GLY 75 (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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59B ASN* 3.6 20.4 - - - +
60B VAL* 3.0 31.9 + - - +
73B PHE* 3.7 13.9 - - - -
74B SER* 1.3 75.4 - - - +
76B GLU* 1.3 67.5 + - - -
77B LEU 3.5 1.7 + - - -
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Residues in contact with GLU 76 (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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55B CYS 4.8 8.8 - - - +
57B TRP 4.7 3.8 - - - +
58B GLY* 3.7 30.6 - - - +
59B ASN* 3.7 8.3 + - - +
73B PHE* 3.7 3.6 - - - -
75B GLY* 1.3 73.8 - - - -
77B LEU* 1.3 68.8 + - - +
78B PRO* 3.3 8.8 - - - +
92B LYS* 3.4 15.8 - - + +
93B HIS* 6.4 0.2 - - - +
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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