Contacts of the helix formed by residues 154 - 164 (chain D) in PDB entry 2OX6
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 154 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D TYR* 3.5 1.4 + - - -
152D SER* 3.4 6.9 + - - -
153D GLU* 1.3 84.8 - - - +
155D ARG* 1.3 64.4 + - - +
156D GLU* 3.6 11.7 + - - +
157D SER* 3.2 21.8 + - - -
158D ARG* 3.1 31.0 + - - +
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Residues in contact with ARG 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D VAL* 5.8 0.2 - - - +
90D TYR* 3.2 9.5 + - - -
99D TYR 3.7 0.6 + - - -
100D ASN* 2.5 37.0 + - - +
102D GLU* 2.7 40.2 + - - +
103D PHE* 3.2 18.7 - - - -
113D TYR* 3.9 12.6 + - - -
154D SER* 1.3 74.5 - - - +
156D GLU* 1.3 56.7 + - - +
158D ARG* 3.2 38.0 - - - +
159D ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D SER* 3.6 10.2 + - - +
155D ARG* 1.3 78.3 - - - +
157D SER* 1.3 58.4 + - - +
159D ALA* 3.3 7.5 + - - +
160D LYS* 2.8 58.5 + - + +
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D TYR* 3.6 18.1 - - - -
145D TYR* 4.5 2.9 - - - -
146D ARG* 4.3 4.9 - - - -
151D LEU* 3.7 21.4 - - - +
152D SER 2.7 29.6 + - - -
154D SER* 3.2 8.5 + - - -
156D GLU* 1.3 76.3 - - - +
158D ARG* 1.3 65.3 + - - +
160D LYS* 3.7 9.7 + - - +
161D TRP* 3.0 24.3 + - - +
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Residues in contact with ARG 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D VAL* 3.8 13.9 - - + +
90D TYR* 2.8 43.6 + - - -
99D TYR* 2.9 40.9 + - - +
137D LEU* 4.2 11.2 - - + -
142D TYR* 3.6 28.2 + - + -
153D GLU* 2.9 32.6 + - - -
154D SER* 3.1 9.5 + - - +
155D ARG* 3.2 45.8 - - - +
156D GLU 3.3 0.2 - - - -
157D SER* 1.3 77.2 - - - +
159D ALA* 1.3 57.4 + - - +
161D TRP* 3.2 7.0 + - - +
162D ALA* 2.8 29.5 + - - +
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ALA* 4.9 10.5 - - - +
88D VAL* 4.4 5.1 - - + +
155D ARG 3.0 17.5 + - - +
156D GLU* 3.5 7.4 - - - +
158D ARG* 1.3 73.4 - - - +
160D LYS* 1.3 64.9 + - - +
162D ALA* 3.3 7.7 + - - +
163D ALA* 3.1 22.7 + - - +
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Residues in contact with LYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TYR* 3.7 19.0 + - + +
151D LEU* 4.6 18.8 - - + -
156D GLU* 2.8 54.7 + - + +
157D SER* 3.7 9.3 + - - +
158D ARG 3.3 0.4 - - - -
159D ALA* 1.3 74.0 - - + +
161D TRP* 1.3 63.8 + - - +
163D ALA* 3.5 18.0 + - - +
164D THR* 3.6 10.4 - - - +
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Residues in contact with TRP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D VAL* 5.2 2.2 - - + -
135D ILE* 4.1 12.1 - - + -
136D ASN 3.5 11.0 - - - -
137D LEU* 3.8 31.0 - - + -
138D ASN* 3.4 37.5 - - + -
141D ALA* 3.7 10.1 + - + +
142D TYR* 3.7 27.7 - + + +
145D TYR* 3.5 48.4 - + + -
157D SER 3.0 14.9 + - - +
158D ARG 3.6 7.4 - - - +
160D LYS* 1.3 76.7 - - - +
162D ALA* 1.3 72.0 + - + +
164D THR* 2.7 36.3 + - - -
165D GLN* 3.3 38.5 + - + +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ALA* 3.5 26.6 - - + +
88D VAL* 3.5 22.9 - - + -
135D ILE* 4.1 11.9 - - + +
158D ARG 2.8 16.6 + - - +
159D ALA* 3.7 4.9 - - - +
160D LYS 3.3 0.4 - - - -
161D TRP* 1.3 85.2 - - + +
163D ALA* 1.3 57.0 + - - +
165D GLN* 2.9 28.9 + - - +
166D LEU 3.8 1.9 + - - -
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ARG* 6.0 3.6 - - - +
86D ALA* 3.8 10.4 - - + +
159D ALA 3.1 12.7 + - - +
160D LYS* 3.5 13.5 - - - +
161D TRP 3.2 0.2 - - - -
162D ALA* 1.3 75.1 - - - +
164D THR* 1.3 60.4 + - + +
165D GLN 3.3 1.2 + - - -
166D LEU* 3.4 28.8 + - + +
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Residues in contact with THR 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TYR* 3.8 26.9 - - + +
160D LYS 3.6 12.1 - - - +
161D TRP* 2.7 25.9 + - - +
163D ALA* 1.3 77.7 - - + +
165D GLN* 1.3 71.2 + - - +
166D LEU 3.4 4.1 + - - +
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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