Contacts of the helix formed by residues 162 - 171 (chain A) in PDB entry 2OBD
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 TRP 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A MET* 3.9 41.5 - - + +
50A MET 5.8 0.7 - - - +
52A LEU* 4.1 16.2 - - + -
55A VAL* 3.8 21.8 - - + -
57A TYR* 4.4 7.6 - - + -
97A LEU* 4.9 4.7 - - + -
99A TYR* 3.4 51.4 - + + -
101A TYR* 3.1 31.2 + + - -
160A PRO* 3.2 16.9 - - + +
161A GLY* 1.3 78.5 - - - +
163A ILE* 1.3 79.7 + - + +
164A LYS 3.8 0.7 - - - -
165A GLN* 4.2 5.7 - - - +
166A LEU* 3.2 50.8 + - + +
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.2 20.9 - - + -
99A TYR* 4.3 13.7 - - + +
113A ILE* 4.6 1.8 - - + -
152A LEU* 3.9 23.6 - - + -
154A LEU* 3.8 28.5 - - + -
158A ARG 4.6 0.2 - - - +
159A GLU* 3.0 9.8 + - - +
160A PRO* 3.4 29.2 - - + -
162A TRP* 1.3 103.5 - - + +
164A LYS* 1.3 68.5 + - - +
165A GLN 3.2 1.1 - - - -
166A LEU* 3.2 4.4 + - + +
167A PHE* 3.0 23.7 + - - +
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 6.3 3.8 - - - -
152A LEU* 5.3 6.1 - - - +
159A GLU* 3.1 20.5 + - - +
163A ILE* 1.3 80.2 - - - +
165A GLN* 1.3 68.4 + - - +
167A PHE* 3.6 5.8 + - + +
168A THR* 2.9 43.7 + - - +
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Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLY 4.7 9.4 + - - +
162A TRP* 4.0 10.7 + - - +
163A ILE 3.2 0.4 - - - -
164A LYS* 1.3 90.4 + - - +
166A LEU* 1.3 59.8 + - - +
168A THR* 4.5 7.3 + - - +
169A ASN* 2.9 52.3 + - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 4.2 10.1 - - + -
49A MET* 4.1 19.7 - - + -
57A TYR* 4.1 30.3 - - + +
59A LEU* 6.0 0.9 - - + -
97A LEU* 6.4 0.9 - - + -
162A TRP* 3.2 44.7 + - + +
163A ILE* 3.2 6.3 + - + +
165A GLN* 1.3 74.9 - - - +
167A PHE* 1.3 60.6 + - - +
169A ASN* 5.2 0.2 - - - -
170A PHE* 2.7 54.4 + - + +
171A ILE* 3.2 22.8 + - + -
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Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.7 4.5 - - + -
117A ILE* 4.1 25.8 - - + -
150A LEU* 3.4 39.3 - - + -
151A LEU* 4.5 0.2 - - - -
152A LEU* 3.8 48.7 - - + -
163A ILE 3.0 16.7 + - - +
164A LYS* 3.9 4.0 - - - +
166A LEU* 1.3 76.1 - - - +
168A THR* 1.3 63.3 + - - +
171A ILE* 2.9 43.9 + - + -
172A SER* 2.7 48.3 + - - -
175A LEU* 4.4 2.5 - - + -
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LYS* 2.9 29.0 + - - +
165A GLN* 3.9 12.1 + - - +
167A PHE* 1.3 85.2 - - - +
169A ASN* 1.3 73.4 + - - +
172A SER* 3.5 17.0 + - - +
173A PHE* 5.2 2.4 + - - +
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLN* 2.9 41.6 + - - +
166A LEU* 5.2 0.7 - - - -
168A THR* 1.3 88.5 + - - +
170A PHE* 1.3 62.6 + - + +
172A SER 5.5 0.2 - - - -
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 6.4 2.2 - - + -
44A THR 5.6 2.2 - - - -
45A GLY* 6.2 0.2 - - - -
47A LYS* 3.8 35.2 - - + -
57A TYR* 3.2 28.5 - - - -
166A LEU* 2.7 31.8 + - + +
169A ASN* 1.3 77.9 - - + +
171A ILE* 1.3 64.5 + - + +
173A PHE 5.5 0.7 - - - -
174A THR* 4.1 18.9 + - - +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.2 33.9 - - + -
57A TYR* 4.2 9.0 - - + -
59A LEU* 4.0 27.8 - - + -
166A LEU* 3.2 30.7 + - + +
167A PHE* 2.9 40.9 + - + +
170A PHE* 1.3 91.8 - - + +
172A SER* 1.3 65.4 + - - +
173A PHE 3.4 1.3 + - - -
174A THR* 3.6 6.0 + - - -
175A LEU* 3.0 22.7 + - + +
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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