Contacts of the helix formed by residues 150 - 166 (chain D) in PDB entry 5Y1Z
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 THR 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D LEU* 1.3 77.5 - - - +
151D ILE* 1.3 64.8 + - - +
152D GLU* 3.1 26.8 + - - +
153D GLN* 3.0 31.6 + - - +
154D LEU* 2.9 21.9 + - - +
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Residues in contact with ILE 151 (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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150D THR* 1.3 73.1 - - - +
152D GLU* 1.3 79.5 + - - +
154D LEU* 3.5 8.1 + - + +
155D SER* 2.6 36.8 + - - +
205D LYS* 4.1 27.1 - - + +
207D TYR 3.0 29.6 - - - +
208D GLY* 3.5 19.7 - - - +
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Residues in contact with GLU 152 (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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150D THR* 3.1 17.4 + - - +
151D ILE* 1.3 91.5 - - - +
153D GLN* 1.3 63.4 + - + +
155D SER* 3.2 8.8 + - - -
156D TYR* 3.1 20.8 + - - +
205D LYS* 3.4 34.6 + - + +
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Residues in contact with GLN 153 (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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148D MET 4.0 5.5 - - - +
149D LEU* 3.5 22.1 - - + -
150D THR* 3.0 44.6 + - + +
152D GLU* 1.3 73.8 - - + +
154D LEU* 1.3 67.6 + - - +
156D TYR* 2.9 19.0 + - - +
157D LEU* 3.0 18.2 + - + +
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Residues in contact with LEU 154 (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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146D MET* 4.1 24.9 - - + -
149D LEU* 4.5 17.5 - - + +
150D THR 2.9 12.0 + - - +
151D ILE* 3.7 11.0 - - + +
153D GLN* 1.3 75.8 - - - +
155D SER* 1.3 64.2 + - - +
157D LEU* 3.2 4.8 + - + +
158D LEU* 2.9 42.5 + - + +
207D TYR 3.3 25.6 - - - +
208D GLY* 3.6 5.6 - - - +
209D CYS* 3.4 30.3 - - - +
210D THR* 4.1 14.8 - - + -
252D ILE* 4.7 5.8 - - + -
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Residues in contact with SER 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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151D ILE* 2.6 23.3 + - - +
152D GLU* 3.3 10.5 - - - -
154D LEU* 1.3 75.9 - - - +
156D TYR* 1.3 64.7 + - - +
158D LEU* 3.1 12.3 + - - +
159D LYS* 2.9 21.5 + - - +
202D ALA* 3.4 29.9 + - - +
203D LYS* 5.2 2.2 - - - -
205D LYS* 3.9 17.4 - - - +
207D TYR 4.9 2.9 + - - -
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Residues in contact with TYR 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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152D GLU 3.1 11.0 + - - +
153D GLN* 2.9 12.4 + - - +
155D SER* 1.3 75.5 - - - +
157D LEU* 1.3 64.7 + - + +
159D LYS* 3.0 35.4 + - + +
160D PHE* 3.2 43.9 + + - -
260D LEU* 4.1 14.4 - - + -
264D GLN* 3.5 33.2 + - - -
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Residues in contact with LEU 157 (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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149D LEU* 4.1 16.6 - - + -
153D GLN* 3.0 12.6 + - + +
154D LEU* 3.7 6.1 - - - +
156D TYR* 1.3 77.0 - - + +
158D LEU* 1.3 64.3 + - - +
160D PHE* 3.1 11.2 + - + +
161D ALA* 3.0 20.3 + - - +
252D ILE* 3.9 33.4 - - + -
256D PRO* 3.9 31.2 - - + +
259D TYR* 3.9 16.7 - - + -
260D LEU* 3.8 39.9 - - + -
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Residues in contact with LEU 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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154D LEU* 2.9 37.4 + - + +
155D SER* 3.1 11.0 + - - +
157D LEU* 1.3 75.0 - - - +
159D LYS* 1.3 62.7 + - - +
161D ALA* 3.1 4.2 + - - +
162D ILE* 3.0 30.0 + - - +
202D ALA* 4.2 11.2 - - + -
207D TYR* 3.7 34.1 - - + +
209D CYS 4.8 0.9 - - - +
210D THR* 5.0 0.9 - - + -
213D PHE* 3.9 26.2 - - + -
249D MET* 3.9 32.3 - - + -
252D ILE* 4.2 9.9 - - + -
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Residues in contact with LYS 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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155D SER 2.9 12.0 + - - +
156D TYR* 3.2 30.7 - - + +
158D LEU* 1.3 76.1 - - - +
160D PHE* 1.3 66.7 + - + +
162D ILE* 3.3 14.1 + - - +
163D GLN* 3.1 28.1 + - + +
199D GLU* 3.8 26.7 - - + +
202D ALA* 4.9 4.4 - - + +
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Residues in contact with PHE 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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156D TYR* 3.2 67.9 + + - -
157D LEU* 3.1 12.1 + - + +
159D LYS* 1.3 81.9 - - + +
161D ALA* 1.3 63.2 + - - +
163D GLN* 2.9 25.0 + - + +
164D LYS* 3.0 18.4 + - - +
259D TYR* 3.9 2.5 - - + +
260D LEU* 3.9 11.9 - - + -
263D CYS* 3.6 48.2 - - + -
264D GLN* 3.8 18.2 - - - -
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Residues in contact with ALA 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 LEU 3.0 10.9 + - - +
158D LEU* 3.1 10.7 + - - +
160D PHE* 1.3 76.7 - - - +
162D ILE* 1.3 62.7 + - - +
164D LYS* 2.9 14.2 + - - +
165D MET* 3.0 24.4 + - + +
213D PHE* 4.6 0.2 - - + -
248D GLU* 3.8 10.8 - - + +
249D MET* 3.7 30.7 - - + -
252D ILE* 4.9 0.9 - - + -
259D TYR* 3.5 16.5 + - + +
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Residues in contact with ILE 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 LEU 3.0 23.2 + - - +
159D LYS* 3.6 11.0 - - - +
160D PHE 3.3 0.2 - - - -
161D ALA* 1.3 74.4 - - - +
163D GLN* 1.3 67.2 + - - +
165D MET* 3.2 11.0 + - + +
166D LYS* 3.1 33.1 + - + +
195D LEU* 4.2 21.1 - - + +
198D LEU* 4.0 8.7 - - + +
199D GLU* 3.5 49.4 - - + +
202D ALA* 4.4 4.5 - - + -
213D PHE* 3.6 26.2 - - + -
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Residues in contact with GLN 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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159D LYS* 3.1 23.6 + - + +
160D PHE* 2.9 24.2 + - + +
162D ILE* 1.3 83.9 + - - +
164D LYS* 1.3 64.8 + - + +
165D MET 3.3 0.5 + - - -
166D LYS* 3.4 33.0 + - - +
167D GLN* 4.4 2.3 + - - -
199D GLU* 4.0 23.2 + - - -
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Residues in contact with LYS 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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100B SER* 4.9 1.5 - - - -
160D PHE* 3.0 13.2 + - - +
161D ALA 2.9 6.9 + - - +
163D GLN* 1.3 79.5 - - + +
165D MET* 1.3 59.6 + - - +
167D GLN* 2.8 32.6 + - - +
244D ILE* 3.6 11.7 - - + +
248D GLU* 3.2 43.4 + - + +
259D TYR* 4.2 3.8 + - - +
262D ALA* 5.6 2.4 + - - +
263D CYS* 3.8 31.0 - - - +
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Residues in contact with MET 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 ALA* 3.0 34.4 + - + +
162D ILE* 3.5 12.3 - - + +
163D GLN 3.2 0.4 - - - -
164D LYS* 1.3 74.7 - - - +
166D LYS* 1.3 56.9 + - - +
167D GLN* 2.7 15.9 + - - +
170D THR* 3.8 13.7 - - - +
195D LEU* 4.4 16.8 - - + +
198D LEU* 4.9 4.9 - - - -
213D PHE* 3.2 37.7 - - + -
217D ALA* 5.1 1.8 - - - -
241D VAL* 4.0 32.4 - - + +
244D ILE* 4.0 21.5 - - + +
245D CYS* 3.5 28.5 - - + +
248D GLU* 5.4 0.2 - - + -
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Residues in contact with LYS 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 ILE* 3.1 23.7 + - + +
163D GLN* 3.4 33.1 + - - +
165D MET* 1.3 72.6 - - - +
167D GLN* 1.3 64.2 + - - +
168D PRO* 3.7 2.6 - - - +
170D THR* 3.5 7.9 - - - -
174D GLN* 3.6 36.0 + - - +
195D LEU* 3.5 23.8 - - + -
199D GLU* 5.1 5.7 + - - +
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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