Contacts of the helix formed by residues 151 - 157 (chain A) in PDB entry 2O7R
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 ASP 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LYS* 2.6 29.9 + - - -
58A LEU* 3.7 21.7 - - + +
70A LEU* 3.5 6.5 - - - +
145A TRP* 6.0 0.2 - - + -
149A SER* 2.9 17.3 + - - +
150A ARG* 1.3 75.8 - - - +
152A GLU* 1.3 67.3 + - - +
153A TRP* 2.8 29.6 + - - +
154A LEU* 3.3 17.7 + - + +
155A THR* 2.8 30.1 + - - +
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Residues in contact with GLU 152 (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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56A LYS* 4.0 7.1 + - - -
150A ARG 4.0 8.9 - - - +
151A ASP* 1.3 83.5 - - - +
153A TRP* 1.3 71.7 + - + +
155A THR* 3.7 9.0 - - - +
156A ASN* 3.0 36.5 + - - +
157A PHE* 4.2 1.7 - - - -
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Residues in contact with TRP 153 (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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45A PRO* 3.8 24.0 - - + -
54A LEU* 3.6 35.2 - - + -
55A THR* 3.6 22.4 - - - -
56A LYS* 3.7 44.5 - - + +
70A LEU* 3.9 25.6 - - + -
72A LEU* 3.8 34.0 - - + +
118A VAL* 5.5 5.3 - - + +
151A ASP* 2.8 8.0 + - - +
152A GLU* 1.3 84.7 - - + +
154A LEU* 1.3 58.9 + - + +
157A PHE* 2.9 44.2 + + - +
158A ALA* 3.7 1.0 + - - +
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Residues in contact with LEU 154 (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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70A LEU* 4.0 28.0 - - + -
85A LEU* 4.2 17.5 - - + -
118A VAL* 4.5 6.1 - - + -
120A ALA* 5.4 0.7 - - + -
145A TRP* 4.6 16.4 - - + -
146A ILE* 4.7 8.7 - - + -
149A SER* 3.6 29.2 - - - +
151A ASP* 3.3 17.6 + - + +
152A GLU 3.4 0.2 - - - -
153A TRP* 1.3 77.3 - - - +
155A THR* 1.3 64.6 + - + +
158A ALA* 3.1 45.2 + - + +
160A PHE* 3.7 23.1 - - + -
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Residues in contact with THR 155 (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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82A LYS* 3.0 26.9 + - - -
149A SER 4.1 7.4 - - - +
150A ARG* 3.7 29.5 + - + +
151A ASP 2.8 25.8 + - - +
152A GLU* 3.6 9.5 + - - +
153A TRP 3.4 0.2 - - - -
154A LEU* 1.3 74.3 - - + +
156A ASN* 1.3 70.5 + - - +
158A ALA 4.8 0.3 - - - +
160A PHE* 5.0 5.2 - - + -
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Residues in contact with ASN 156 (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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80A SER 5.6 2.1 - - - +
81A ALA 5.3 1.2 - - - +
82A LYS* 3.8 16.8 - - - +
152A GLU* 3.0 27.7 + - - +
155A THR* 1.3 87.9 + - - +
157A PHE* 1.4 82.9 + - + +
158A ALA 4.0 0.2 - - - -
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Residues in contact with PHE 157 (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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72A LEU* 3.7 30.1 - - + -
76A ALA* 3.7 35.7 - - + -
77A LEU* 3.9 25.8 - - + -
79A ASN 5.1 3.6 - - - -
81A ALA 4.6 5.1 - - - +
82A LYS* 3.4 8.7 - - - +
83A LEU* 2.9 24.9 + - - +
118A VAL* 3.8 8.4 - - + +
152A GLU 4.5 2.2 - - - -
153A TRP* 2.9 29.5 + + - +
156A ASN* 1.4 103.7 - - + +
158A ALA* 1.3 59.8 + - - +
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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