Contacts of the helix formed by residues 143 - 151 (chain C) in PDB entry 2OB1
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 SER 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C SER* 2.6 29.7 + - - -
51C THR* 3.4 13.0 - - - +
139C ILE 2.9 10.9 + - - -
140C LEU 3.4 0.3 - - - +
142C GLU* 1.3 74.5 - - - +
144C GLU* 1.3 55.2 + - - +
145C ILE* 3.4 1.6 - - - +
146C LEU* 3.1 37.9 + - - +
147C ARG* 2.8 35.9 + - - +
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Residues in contact with GLU 144 (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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98B LYS* 5.8 2.1 + - - -
47C SER* 5.1 0.2 + - - -
142C GLU 3.2 5.2 + - - +
143C SER* 1.3 71.1 + - - +
145C ILE* 1.3 59.3 + - - +
147C ARG* 3.5 27.3 - - - +
148C ILE* 2.8 61.0 + - + +
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Residues in contact with ILE 145 (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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40C LYS* 5.1 2.5 - - + +
43C GLU* 3.6 42.2 - - + +
44C TRP* 3.6 24.0 - - + +
47C SER* 3.4 35.4 - - - +
143C SER* 3.4 0.2 - - - +
144C GLU* 1.3 80.1 - - - +
146C LEU* 1.3 61.1 + - + +
148C ILE* 4.1 4.9 - - - +
149C SER* 3.1 27.7 + - - -
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Residues in contact with LEU 146 (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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44C TRP* 3.6 27.4 - - + +
47C SER* 4.3 0.2 - - - +
48C TYR* 3.9 37.2 - - + +
110C LEU* 4.2 5.8 - - + -
113C LEU* 3.5 29.2 - - + -
139C ILE* 4.1 5.4 - - + +
140C LEU* 3.8 23.6 - - + +
143C SER* 3.1 30.9 + - - +
145C ILE* 1.3 75.1 - - + +
147C ARG* 1.3 66.2 + - - +
149C SER* 2.7 18.7 + - - -
150C LEU* 3.1 17.3 + - + +
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Residues in contact with ARG 147 (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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140C LEU 3.1 13.3 + - - +
141C ARG 3.1 17.5 + - - +
142C GLU 3.2 26.7 + - - -
143C SER 2.8 22.3 + - - +
144C GLU* 3.5 32.6 + - - +
146C LEU* 1.3 72.3 - - - +
148C ILE* 1.3 62.1 + - - +
150C LEU 3.3 0.3 + - - -
151C GLY 2.9 9.4 + - - -
152C LEU* 2.9 59.6 + - + +
154C LYS* 3.5 45.1 - - - +
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Residues in contact with ILE 148 (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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144C GLU* 2.8 56.7 + - + +
145C ILE* 4.1 5.8 - - - +
147C ARG* 1.3 78.4 - - + +
149C SER* 1.3 58.2 + - - +
151C GLY* 3.1 18.1 + - - -
152C LEU 5.6 0.7 - - - -
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Residues in contact with SER 149 (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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44C TRP* 3.5 31.0 + - - -
113C LEU* 3.6 16.0 - - - +
116C LEU* 6.0 1.7 - - - +
117C GLN* 4.4 13.3 - - - +
145C ILE 3.1 17.6 + - - -
146C LEU* 2.7 24.1 + - - -
148C ILE* 1.3 76.6 - - - +
150C LEU* 1.3 59.9 + - - +
151C GLY 3.5 0.4 - - - -
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Residues in contact with LEU 150 (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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112C MET* 4.4 2.7 - - + -
113C LEU* 3.6 30.1 - - + -
116C LEU* 3.9 20.9 - - + -
140C LEU* 3.8 30.3 - - + -
146C LEU 3.1 13.8 + - - +
149C SER* 1.3 76.0 - - - +
151C GLY* 1.3 62.5 + - - +
152C LEU* 3.4 32.9 + - + -
166C GLN* 3.3 21.9 - - + +
169C TYR* 3.7 29.8 - - + -
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Residues in contact with GLY 151 (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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147C ARG 2.9 5.0 + - - -
148C ILE* 3.1 12.6 + - - -
149C SER 3.5 0.4 - - - -
150C LEU* 1.3 78.6 - - - +
152C LEU* 1.3 62.3 + - - +
166C GLN* 3.3 23.8 + - - -
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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