Contacts of the helix formed by residues 112 - 119 (chain B) in PDB entry 4OBO
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 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B ALA 4.8 0.9 - - - +
111B GLY* 1.3 74.8 - - - -
113B ILE* 1.3 60.9 + - - +
114B THR* 3.3 8.3 + - - -
115B ASP* 3.0 34.5 + - - +
116B LEU* 3.1 24.3 + - - +
156B GLY 3.5 11.2 - - - -
157B GLN* 3.7 21.7 + - - +
159B VAL 3.3 10.3 - - - -
160B LEU* 3.8 8.8 - - - +
161B LEU* 4.7 3.0 - - - +
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Residues in contact with ILE 113 (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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112B SER* 1.3 67.9 - - - +
114B THR* 1.3 60.0 + - - +
116B LEU* 3.1 18.3 + - + +
117B VAL* 2.9 36.1 + - + +
125B LEU* 4.8 3.1 - - + -
133B ILE* 3.8 21.3 - - + -
137B ILE* 5.6 0.2 - - + -
156B GLY* 3.1 17.4 + - - +
159B VAL* 2.9 39.4 + - + +
161B LEU* 3.9 31.6 - - + -
167B VAL* 5.0 0.7 - - + -
222B THR* 5.1 2.2 - - + -
225B GLU* 6.2 1.1 - - - -
226B MET* 3.6 37.0 - - + -
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Residues in contact with THR 114 (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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112B SER* 3.3 7.8 - - - -
113B ILE* 1.3 76.5 - - - +
115B ASP* 1.4 62.3 + - - +
117B VAL* 3.3 9.1 + - + +
118B LYS* 3.0 26.4 + - + +
156B GLY* 3.0 20.0 + - - -
157B GLN* 3.0 25.4 + - - +
225B GLU* 2.8 27.9 + - + +
229B GLY 6.0 2.0 - - - +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA 5.4 1.6 - - - +
111B GLY* 3.6 10.8 - - - -
112B SER* 3.0 35.9 + - - +
114B THR* 1.4 75.1 - - - +
116B LEU* 1.3 57.4 + - - +
118B LYS* 3.3 20.4 + - - +
119B ASN* 2.9 46.6 + - - +
157B GLN* 5.6 2.3 + - - -
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Residues in contact with LEU 116 (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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112B SER 3.1 12.9 + - - +
113B ILE* 3.1 20.8 + - + +
115B ASP* 1.3 76.1 - - - +
117B VAL* 1.4 55.0 + - - +
119B ASN* 3.5 5.9 + - - +
120B THR* 2.6 33.4 + - - -
125B LEU* 3.9 27.4 - - + -
129B TRP* 4.1 14.1 - - + -
133B ILE* 4.0 10.5 - - + -
161B LEU* 4.0 13.7 - - + -
302B LEU* 3.8 26.5 - - + -
305B HIS* 3.7 31.9 - - + +
306B ILE* 5.6 2.5 - - + -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 2.9 18.7 + - + +
114B THR* 3.3 6.9 + - - +
116B LEU* 1.4 73.8 - - - +
118B LYS* 1.3 62.4 + - - +
120B THR* 3.2 12.1 + - - -
123B ASN* 3.4 48.7 - - + +
124B THR* 3.9 2.0 - - - +
125B LEU* 4.0 22.2 - - + -
225B GLU* 3.9 7.0 - - + +
226B MET* 3.8 34.5 - - + +
229B GLY* 3.8 18.4 - - - +
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Residues in contact with LYS 118 (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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114B THR* 3.0 19.8 + - + +
115B ASP* 3.3 27.6 - - - +
117B VAL* 1.3 77.1 - - - +
119B ASN* 1.3 87.9 + - - +
120B THR 3.2 7.6 + - - +
123B ASN* 3.4 22.2 + - - +
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Residues in contact with ASN 119 (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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115B ASP* 2.9 30.9 + - - +
116B LEU* 3.5 3.7 + - - +
117B VAL 3.3 0.4 - - - -
118B LYS* 1.3 101.7 + - - +
120B THR* 1.3 61.0 + - - +
121B LYS 4.2 0.3 + - - -
305B HIS* 3.8 22.1 + - + -
309B THR* 4.0 24.9 - - + +
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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