Contacts of the strand formed by residues 95 - 99 (chain C) 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 MET 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B LEU* 3.8 19.7 - - + -
72B GLU 3.3 6.1 - - - +
73B PHE* 4.5 0.8 - - - -
51C TRP* 5.2 0.7 - - + -
62C THR* 3.8 29.2 - - + +
73C PHE* 3.5 50.5 - - + -
76C GLU 5.1 0.4 - - - +
77C LEU* 3.9 7.2 - - + -
78C PRO* 3.2 41.4 - - + +
89C LEU* 4.2 9.2 - - + -
91C GLY* 3.4 22.2 - - - -
93C HIS 3.7 3.7 + - - +
94C GLY* 1.3 72.2 - - - +
96C SER* 1.3 66.1 + - - +
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Residues in contact with SER 96 (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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71B LEU* 3.4 12.8 - - - +
72B GLU* 2.9 37.9 + - - -
89C LEU* 3.2 33.3 + - - -
90C ARG* 4.5 0.2 - - - -
91C GLY* 3.6 15.1 + - - -
94C GLY 3.8 2.9 + - - -
95C MET* 1.3 77.9 - - - +
97C GLY* 1.3 62.9 + - - -
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Residues in contact with GLY 97 (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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70B ILE 3.2 10.1 - - - -
71B LEU* 4.7 0.2 - - - -
72B GLU* 3.6 12.6 - - - +
89C LEU* 2.9 31.6 + - - +
96C SER* 1.3 85.2 + - - +
98C HIS* 1.3 80.7 + - - -
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Residues in contact with HIS 98 (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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69B VAL* 3.5 2.4 - - - +
70B ILE* 2.7 62.0 + - + +
72B GLU* 3.8 17.8 + - - -
86C TYR* 3.7 20.7 - + + -
87C PHE 3.4 6.3 - - - +
88C ASN* 2.7 31.6 + - + +
89C LEU* 5.0 0.6 + - - +
97C GLY* 1.3 90.5 + - - -
99C ILE* 1.3 65.0 + - - +
100C LYS 4.1 0.3 + - - -
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Residues in contact with ILE 99 (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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68B ASP 3.9 1.6 - - - -
69B VAL* 3.6 26.2 - - + -
71B LEU* 5.2 4.0 - - + -
47C PHE* 4.5 15.5 - - + -
51C TRP* 4.6 8.7 - - + -
86C TYR* 3.7 2.4 - - - -
87C PHE* 2.8 56.7 + - + +
89C LEU* 4.5 15.7 - - + -
98C HIS* 1.3 74.3 - - - +
100C LYS* 1.3 56.5 + - - +
101C ALA 2.6 20.0 + - - +
124C PHE* 6.3 1.3 - - + -
132C MET* 3.7 23.1 - - + -
133C LEU* 4.0 26.5 - - + -
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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