Contacts of the helix formed by residues 158 - 168 (chain D) in PDB entry 2R92
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 GLU 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156D ASP* 2.7 26.4 - - + +
157D GLN* 1.3 79.4 - - + +
159D THR* 1.3 67.8 + - + +
161D GLY* 3.0 3.5 + - - -
162D ALA* 2.9 22.6 + - - +
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Residues in contact with THR 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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154D PHE* 3.8 18.8 - - - +
155D ARG 4.0 0.2 + - - -
156D ASP* 2.4 49.3 + - + +
158D GLU* 1.3 80.8 - - + +
160D VAL* 1.3 59.8 + - - -
161D GLY 2.9 1.7 + - - -
162D ALA* 2.9 15.4 + - - +
163D VAL* 2.8 21.8 + - - +
217D LEU* 4.3 17.2 - - + +
219D THR* 3.8 16.8 - - - +
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ASN* 5.0 2.2 - - - +
53D SER* 4.4 7.4 - - - +
54D GLU* 3.6 36.6 - - + +
57D LEU* 3.8 24.7 - - + -
154D PHE* 3.4 28.3 - - + +
156D ASP 2.8 22.0 + - - +
157D GLN* 4.6 7.4 - - - +
159D THR* 1.3 71.3 - - - +
161D GLY* 1.3 57.6 + - - +
163D VAL* 3.6 11.8 - - + +
164D ILE* 2.9 40.8 + - + +
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Residues in contact with GLY 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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157D GLN* 3.4 13.8 + - - -
158D GLU* 3.0 8.0 + - - -
159D THR 2.9 1.4 - - - -
160D VAL* 1.3 78.9 - - - +
162D ALA* 1.3 59.5 + - - +
164D ILE* 3.3 8.0 + - - +
165D GLN* 2.9 36.2 + - - +
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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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158D GLU 2.9 10.8 + - - +
159D THR* 2.9 9.8 + - - +
161D GLY* 1.3 73.2 - - - +
163D VAL* 1.3 66.6 + - - +
165D GLN* 3.2 14.3 + - - +
166D LEU* 2.9 26.2 + - - +
217D LEU* 4.0 19.9 - - + +
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Residues in contact with VAL 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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51D ASN* 5.1 7.4 - - - +
154D PHE* 3.0 49.6 - - + -
159D THR 2.8 26.0 + - - +
160D VAL* 3.6 10.5 - - + +
162D ALA* 1.3 75.9 - - - +
164D ILE* 1.3 59.9 + - + +
166D LEU* 3.5 4.8 - - - +
167D LEU* 3.1 51.5 + - + +
181D GLY* 5.0 7.6 - - - -
214D LEU* 4.9 9.9 - - + -
217D LEU* 4.1 13.4 - - + +
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Residues in contact with ILE 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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51D ASN* 4.9 5.2 - - - +
54D GLU* 3.3 38.6 - - - +
160D VAL* 2.9 28.9 + - + +
161D GLY* 3.3 7.5 + - - +
162D ALA 3.2 0.2 - - - -
163D VAL* 1.3 77.2 - - + +
165D GLN* 1.3 67.9 + - + +
167D LEU* 4.8 4.5 - - + -
168D LYS* 3.0 57.1 + - + +
177D VAL* 6.4 1.1 - - + -
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Residues in contact with GLN 165 (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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161D GLY 2.9 21.9 + - - +
162D ALA* 3.4 15.1 - - - +
164D ILE* 1.3 78.6 - - + +
166D LEU* 1.3 64.8 + - - +
168D LYS* 3.5 9.5 + - - +
169D SER* 3.9 8.5 + - - -
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Residues in contact with LEU 166 (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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162D ALA 2.9 16.3 + - - +
163D VAL 3.5 3.4 - - - +
165D GLN* 1.3 75.9 - - - +
167D LEU* 1.3 62.3 + - - +
169D SER* 2.4 34.1 + - - +
170D THR* 4.5 0.7 + - - +
210D ILE* 4.2 25.9 - - + +
213D GLU* 4.0 28.5 - - + +
214D LEU* 3.8 28.9 - - + -
217D LEU* 5.1 7.9 - - + -
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Residues in contact with LEU 167 (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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51D ASN* 5.3 2.5 - - - +
163D VAL* 3.1 35.0 + - + +
164D ILE* 4.2 3.6 - - - +
166D LEU* 1.3 81.8 - - + +
168D LYS* 1.3 58.0 + - - +
169D SER 3.0 0.9 + - - -
170D THR* 2.3 35.8 + - + +
172D LEU* 5.3 0.6 + - + -
177D VAL* 3.8 38.8 - - + +
180D LEU* 4.4 20.6 - - + -
181D GLY* 4.3 17.3 - - - +
210D ILE* 3.6 33.4 - - + -
214D LEU* 4.7 9.9 - - + -
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Residues in contact with LYS 168 (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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48D ILE* 6.1 2.6 - - - +
164D ILE* 3.0 43.2 + - + +
165D GLN* 4.0 5.2 - - - +
166D LEU 3.2 0.6 + - - -
167D LEU* 1.3 76.7 - - - +
169D SER* 1.3 59.5 + - - +
170D THR* 3.3 1.0 + - - -
171D GLY* 4.0 7.4 + - - -
177D VAL* 4.7 15.9 - - + -
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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