Contacts of the helix formed by residues 138 - 149 (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 ASN 138 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ASN 3.3 4.6 + - - +
137D LEU* 1.3 70.8 - - - +
139D VAL* 1.3 58.2 + - - +
140D GLU* 3.3 10.6 + - - +
141D ALA* 3.0 27.7 + - + +
142D TYR* 2.9 29.3 + - - +
161D TRP* 3.4 19.1 - - + -
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Residues in contact with VAL 139 (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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95D ILE* 4.0 32.2 - - + +
98D GLN* 5.4 3.4 - - - +
99D TYR* 3.6 34.5 - - + +
137D LEU* 4.0 7.8 + - + -
138D ASN* 1.3 73.0 + - - +
140D GLU* 1.3 64.8 + - + +
142D TYR* 3.4 6.9 + - - +
143D LYS* 2.9 55.5 + - + +
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Residues in contact with GLU 140 (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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138D ASN* 3.3 7.9 + - - +
139D VAL* 1.3 89.4 - - + +
141D ALA* 1.3 62.6 + - - +
143D LYS* 3.4 16.3 + - - +
144D ALA* 3.1 24.1 + - - +
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Residues in contact with ALA 141 (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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138D ASN* 3.0 25.3 + - + +
140D GLU* 1.3 73.6 - - - +
142D TYR* 1.3 61.1 + - - +
144D ALA* 3.3 6.2 + - - +
145D TYR* 2.9 30.5 + - - +
161D TRP* 3.7 19.3 + - + +
165D GLN* 5.1 3.6 - - - +
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Residues in contact with TYR 142 (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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99D TYR* 4.1 18.6 - + - -
137D LEU* 3.9 22.0 - - + -
138D ASN 2.9 18.4 + - - +
139D VAL* 3.7 5.4 - - - +
141D ALA* 1.3 77.4 - - - +
143D LYS* 1.3 57.6 + - + +
145D TYR* 3.4 3.4 + + - +
146D ARG* 3.0 63.9 + - + +
153D GLU* 2.8 30.4 + - - -
154D SER 3.5 13.2 + - - -
157D SER* 3.6 23.8 - - - -
158D ARG* 3.6 16.4 - - + -
161D TRP* 3.7 31.3 - + + +
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Residues in contact with LYS 143 (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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99D TYR* 3.8 16.1 + - - +
139D VAL* 2.9 39.1 + - + +
140D GLU* 3.7 18.4 - - - +
142D TYR* 1.3 79.1 - - + +
144D ALA* 1.3 57.7 + - - +
146D ARG* 3.1 28.8 + - - +
147D GLU* 2.9 38.4 + - - +
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Residues in contact with ALA 144 (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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140D GLU 3.1 17.7 + - - +
141D ALA* 3.7 7.0 - - - +
143D LYS* 1.3 76.4 - - - +
145D TYR* 1.3 56.8 + - - +
147D GLU* 3.6 7.6 + - - +
148D GLN* 3.1 28.6 + - - +
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Residues in contact with TYR 145 (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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141D ALA 2.9 17.5 + - - +
142D TYR* 3.6 4.7 - + - +
144D ALA* 1.3 75.2 - - - +
146D ARG* 1.3 62.2 + - + +
148D GLN* 3.3 5.0 + - + -
149D ASN* 3.0 62.5 + - - +
151D LEU* 3.7 25.1 - - + +
157D SER 4.5 1.8 - - - -
160D LYS* 3.7 20.3 + - + +
161D TRP* 3.5 48.2 - + + -
164D THR* 3.8 20.2 - - + +
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Residues in contact with ARG 146 (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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99D TYR* 5.5 1.8 + - - -
142D TYR* 3.0 57.2 + - + +
143D LYS* 3.4 32.1 - - - +
145D TYR* 1.3 79.3 - - + +
147D GLU* 1.3 59.0 + - - +
150D GLY* 2.9 9.0 + - - -
151D LEU* 2.9 69.4 + - + +
152D SER* 3.9 10.6 - - - +
153D GLU* 3.2 34.8 - - - +
157D SER* 4.3 2.9 - - - -
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Residues in contact with GLU 147 (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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143D LYS* 2.9 23.0 + - - +
144D ALA* 3.7 8.7 - - - +
146D ARG* 1.3 76.3 - - - +
148D GLN* 1.3 62.8 + - - +
149D ASN 3.3 1.0 + - - -
150D GLY* 3.3 10.1 + - - -
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Residues in contact with GLN 148 (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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144D ALA 3.1 19.3 + - - +
145D TYR* 3.3 8.7 + - + +
147D GLU* 1.3 77.4 - - - +
149D ASN* 1.3 66.7 + - - +
150D GLY 3.5 0.6 + - - -
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Residues in contact with ASN 149 (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* 3.0 49.1 + - - +
148D GLN* 1.3 91.4 - - - +
150D GLY* 1.3 65.9 + - - +
151D LEU* 3.2 32.3 + - + +
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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