Contacts of the helix formed by residues 138 - 149 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E ARG* 3.6 7.2 - - - +
136E PRO 4.1 7.9 - - - +
137E ILE* 1.3 81.3 - - - +
139E TYR* 1.3 65.9 + - - +
140E PRO* 3.4 12.9 - - - +
141E GLN* 3.1 35.3 + - - +
142E GLY* 3.1 18.4 + - - -
156E GLU* 4.4 0.9 - - - +
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Residues in contact with TYR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ARG* 3.4 10.0 - - - +
138E THR* 1.3 70.5 - - - +
140E PRO* 1.4 77.1 - - + +
142E GLY 3.2 2.1 + - - -
143E LEU* 3.0 48.2 + - + +
154E TYR* 3.5 41.3 + + - -
156E GLU* 3.6 29.4 - - + +
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Residues in contact with PRO 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E THR* 3.4 14.4 - - - +
139E TYR* 1.4 102.8 - - + +
141E GLN* 1.3 55.7 + - + +
143E LEU* 3.4 8.0 + - + +
144E ALA* 3.0 27.4 + - - +
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Residues in contact with GLN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E PHE* 3.3 18.2 - - + -
136E PRO 4.0 2.6 - - - +
137E ILE* 3.5 23.7 - - + +
138E THR* 3.1 41.9 + - - +
140E PRO* 1.3 74.6 - - + +
142E GLY* 1.3 61.4 + - - +
144E ALA* 3.4 6.7 + - - +
145E MET 2.9 23.4 + - - -
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Residues in contact with GLY 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E PHE* 4.7 0.2 - - - -
90E PHE* 4.0 14.6 - - - -
112E LEU* 3.6 7.4 - - - +
137E ILE* 4.0 2.1 - - - +
138E THR 3.1 8.7 + - - -
139E TYR 3.2 0.2 + - - -
141E GLN* 1.3 79.5 - - - +
143E LEU* 1.3 55.7 + - - +
145E MET* 3.2 3.8 + - - +
146E ALA* 2.8 25.3 + - - +
154E TYR* 3.6 32.3 - - - -
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Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E TYR* 3.0 44.6 + - + +
140E PRO* 3.6 8.3 - - + +
142E GLY* 1.3 73.1 - - - +
144E ALA* 1.3 65.6 + - - +
146E ALA* 3.1 8.5 + - + +
147E ARG* 3.0 64.2 + - + +
154E TYR* 3.7 25.9 - - + +
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Residues in contact with ALA 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PRO 3.0 18.0 + - - +
141E GLN* 3.6 8.1 - - - +
143E LEU* 1.3 74.5 - - - +
145E MET* 1.3 63.3 + - - +
147E ARG* 3.3 12.1 + - - +
148E GLU* 3.1 23.9 + - - +
26J ASP* 6.6 0.2 - - - -
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Residues in contact with MET 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E PHE* 3.4 60.6 - - + +
93E VAL* 4.1 18.2 - - + -
94E ARG* 3.6 55.2 - - + +
112E LEU* 3.7 15.0 - - + -
141E GLN 2.9 6.9 + - - -
142E GLY 3.5 6.1 - - - +
144E ALA* 1.3 74.8 - - - +
146E ALA* 1.3 63.6 + - - +
148E GLU* 3.2 19.6 + - - +
149E ILE* 3.2 19.7 + - - +
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E LEU* 3.6 12.0 - - + +
142E GLY 2.8 14.8 + - - +
143E LEU* 3.1 12.5 + - + +
145E MET* 1.3 75.2 - - - +
147E ARG* 1.3 62.4 + - + +
149E ILE* 3.5 2.0 + - - +
150E GLY 3.2 3.6 + - - -
151E SER* 2.9 47.1 + - - +
154E TYR* 3.6 27.1 - - + +
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Residues in contact with ARG 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 4.6 2.8 - - - +
30A GLY* 3.5 11.8 - - - -
143E LEU* 3.0 51.3 + - + +
144E ALA* 3.6 11.7 - - - +
145E MET 3.2 0.2 - - - -
146E ALA* 1.3 74.8 - - + +
148E GLU* 1.3 66.1 + - - +
150E GLY* 3.2 12.6 + - - +
151E SER 5.8 1.1 - - - -
26J ASP* 4.0 21.2 + - - +
28J HIS* 3.5 58.0 + - + +
29J GLU* 5.6 3.4 - - - +
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY* 3.5 21.2 - - - +
31A GLU* 4.5 3.1 + - - +
94E ARG* 2.9 54.6 + - - +
98E TYR* 4.8 6.4 - - - -
144E ALA 3.1 13.6 + - - +
145E MET* 3.4 17.2 - - - +
147E ARG* 1.3 76.4 - - - +
149E ILE* 1.3 61.0 + - + +
33J THR* 5.5 11.4 + - + +
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Residues in contact with ILE 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 4.4 2.5 - - - -
80E ILE* 4.2 9.2 - - + -
93E VAL* 4.0 29.4 - - + +
94E ARG* 5.0 3.8 - - - -
98E TYR* 3.4 52.4 - - + -
102E ARG* 4.7 2.9 + - - -
110E ILE* 4.1 32.4 - - + +
112E LEU* 4.2 17.3 - - + -
145E MET* 3.2 21.3 + - - +
146E ALA 3.5 13.2 - - - +
147E ARG 3.2 0.2 - - - -
148E GLU* 1.3 82.8 - - + +
150E GLY* 1.3 60.3 + - - +
151E SER* 4.1 3.6 - - - -
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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