Contacts of the helix formed by residues 138 - 149 (chain G) in PDB entry 2OV2
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 138 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120G ARG* 3.8 8.1 - - - +
136G PRO 4.0 8.5 - - - +
137G ILE* 1.3 80.8 - - - +
139G TYR* 1.3 65.6 + - - +
140G PRO* 3.4 18.1 - - - +
141G GLN* 2.9 32.6 + - - +
142G GLY* 3.0 18.7 + - - -
154G TYR* 4.4 1.0 + - - -
156G GLU* 4.3 0.4 - - - -
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Residues in contact with TYR 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G ARG* 3.7 10.3 - - - +
138G THR* 1.3 71.3 - - - +
140G PRO* 1.4 75.5 - - + +
142G GLY 3.2 1.7 + - - -
143G LEU* 3.0 52.2 + - + +
154G TYR* 3.6 30.6 + + - -
156G GLU* 3.5 35.7 - - + +
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Residues in contact with PRO 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G THR* 3.4 14.8 - - - +
139G TYR* 1.4 100.8 - - + +
141G GLN* 1.3 56.6 + - + +
143G LEU* 3.5 8.1 + - + +
144G ALA* 3.0 27.4 + - - +
147G ARG* 5.3 1.2 + - - -
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Residues in contact with GLN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G PHE* 3.5 18.4 - - + -
136G PRO 4.0 2.6 - - - +
137G ILE* 3.6 23.7 - - + +
138G THR* 2.9 46.1 + - - +
140G PRO* 1.3 76.3 - - + +
142G GLY* 1.3 67.1 + - - +
144G ALA* 3.2 7.2 + - - +
145G MET 3.0 19.6 + - - -
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Residues in contact with GLY 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G PHE* 4.1 14.4 - - - -
112G LEU* 3.4 8.5 - - - +
137G ILE* 4.1 1.9 - - - +
138G THR 3.0 10.9 + - - -
139G TYR 3.2 0.4 + - - -
141G GLN* 1.3 76.8 - - - +
143G LEU* 1.3 56.6 + - - +
145G MET* 3.4 0.9 + - - +
146G ALA* 2.9 27.7 + - - +
154G TYR* 3.5 32.7 - - - -
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Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G TYR* 3.0 49.3 + - + +
140G PRO* 3.6 8.3 - - + +
142G GLY* 1.3 75.4 - - - +
144G ALA* 1.3 64.3 + - - +
146G ALA* 3.2 8.1 + - + +
147G ARG* 3.0 46.5 + - + +
154G TYR* 3.6 23.9 - - + +
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Residues in contact with ALA 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G PRO 3.0 18.4 + - - +
141G GLN* 3.2 7.8 + - - +
143G LEU* 1.3 73.2 - - - +
145G MET* 1.3 65.0 + - - +
147G ARG* 3.2 29.6 + - - +
148G GLU* 2.9 24.7 + - - +
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Residues in contact with MET 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G PHE* 3.5 69.1 - - + +
91G GLU* 4.9 0.4 - - - -
93G VAL* 4.1 14.8 - - + -
94G ARG* 3.5 54.5 - - + +
112G LEU* 3.9 10.1 - - + -
141G GLN 3.0 5.7 + - - -
142G GLY 3.6 4.7 - - - +
144G ALA* 1.3 77.2 - - - +
146G ALA* 1.3 63.2 + - - +
148G GLU* 3.1 11.2 + - - +
149G ILE* 3.1 33.6 + - - +
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G LEU* 3.6 12.1 - - + +
142G GLY 2.9 15.2 + - - +
143G LEU* 3.3 14.1 - - + +
144G ALA 3.2 0.2 - - - -
145G MET* 1.3 77.2 - - - +
147G ARG* 1.3 59.4 + - + +
149G ILE* 3.5 1.6 + - - -
150G GLY 3.3 3.1 + - - -
151G SER* 2.9 45.0 + - - +
153G LYS 4.9 0.2 - - - -
154G TYR* 3.6 26.5 - - + +
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Residues in contact with ARG 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 4.6 2.6 - - - +
30C GLY* 3.6 10.9 - - - -
140G PRO 5.3 1.2 + - - -
143G LEU* 3.0 42.7 + - + +
144G ALA* 3.2 27.2 + - - +
146G ALA* 1.3 73.0 - - + +
148G GLU* 1.3 65.7 + - - +
150G GLY* 3.2 11.9 + - - +
151G SER 5.1 1.6 - - - +
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Residues in contact with GLU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY* 3.4 23.9 - - - +
31C GLU* 5.4 1.4 - - - +
94G ARG* 2.7 55.8 + - - +
98G TYR* 4.8 5.7 - - - -
144G ALA 2.9 13.2 + - - +
145G MET* 3.4 18.5 - - - +
147G ARG* 1.3 77.7 - - - +
149G ILE* 1.3 60.4 + - + +
150G GLY 3.3 0.2 - - - -
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Residues in contact with ILE 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY 4.5 1.6 - - - -
80G ILE* 4.2 19.1 - - + -
93G VAL* 3.8 23.8 - - + +
94G ARG* 5.0 3.6 - - + -
98G TYR* 3.4 51.8 - - + -
102G ARG* 4.7 2.4 + - - -
110G ILE* 4.3 18.9 - - + +
112G LEU* 4.4 13.5 - - + -
145G MET* 3.1 34.7 + - - +
146G ALA* 3.6 8.1 - - - +
147G ARG 3.2 0.2 - - - -
148G GLU* 1.3 82.4 - - + +
150G GLY* 1.3 61.9 + - - +
151G SER* 4.1 9.4 - - - -
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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