Contacts of the helix formed by residues 150 - 166 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C MET* 5.5 1.6 - - - -
148C MET 5.7 0.2 - - - +
149C LEU* 1.3 76.2 - - - +
151C ILE* 1.3 65.8 + - - +
152C GLU* 3.2 15.7 + - - +
153C GLN* 2.6 36.9 + - - +
154C LEU* 3.1 22.6 + - - +
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Residues in contact with ILE 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C MET* 5.9 1.8 - - - -
150C THR* 1.3 75.3 - - - +
152C GLU* 1.3 63.6 + - + +
154C LEU* 3.8 7.3 - - - +
155C SER* 3.0 27.2 + - - -
205C LYS* 3.5 34.9 - - + +
206C MET* 5.3 0.7 - - - -
207C TYR 3.5 24.2 - - - +
208C GLY* 4.2 13.5 - - - +
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Residues in contact with GLU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 3.1 7.6 + - - +
151C ILE* 1.3 81.7 - - + +
153C GLN* 1.3 70.1 + - - +
155C SER* 2.2 30.3 + - - +
156C TYR* 3.0 46.9 + - + +
205C LYS* 5.3 4.3 - - + -
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Residues in contact with GLN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C MET 3.8 5.1 + - - +
149C LEU* 3.3 23.8 - - + -
150C THR* 2.6 47.1 + - - +
152C GLU* 1.3 81.3 - - - +
154C LEU* 1.3 64.1 + - - +
156C TYR* 2.9 27.3 + - + +
157C LEU* 3.0 17.0 + - + +
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Residues in contact with LEU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C MET* 3.6 26.5 - - + -
149C LEU* 3.9 26.1 - - + +
150C THR 3.1 16.1 + - - +
151C ILE* 3.8 4.3 - - - +
153C GLN* 1.3 76.8 - - - +
155C SER* 1.3 58.6 + - - +
157C LEU* 3.2 5.1 + - + +
158C LEU* 2.8 50.8 + - + +
207C TYR 3.8 11.2 - - - +
208C GLY* 3.9 1.3 - - - -
209C CYS* 3.6 28.9 - - - +
210C THR* 4.0 22.7 - - + +
252C ILE* 4.4 7.0 - - + -
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Residues in contact with SER 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE 3.0 14.0 + - - -
152C GLU* 2.2 33.1 + - - +
154C LEU* 1.3 76.6 - - - +
156C TYR* 1.3 71.0 + - - +
158C LEU* 3.1 14.4 + - - +
159C LYS* 2.9 21.7 + - - +
202C ALA* 3.4 29.2 - - - +
203C LYS* 5.3 2.9 + - - -
205C LYS* 4.6 9.3 - - - +
207C TYR 6.0 1.1 - - - -
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Residues in contact with TYR 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLU* 3.0 47.9 + - + -
153C GLN* 2.9 15.9 + - + +
155C SER* 1.3 86.5 + - - +
157C LEU* 1.3 67.3 + - + +
159C LYS* 3.1 17.8 + - - +
160C PHE* 3.2 22.4 + - + -
260C LEU* 6.2 1.3 - - + -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 3.7 29.8 - - + -
153C GLN* 3.0 14.3 + - + +
154C LEU* 3.2 7.6 + - + +
156C TYR* 1.3 77.9 - - + +
158C LEU* 1.3 62.4 + - - +
160C PHE* 3.1 13.4 + - + +
161C ALA* 3.0 17.8 + - - +
252C ILE* 3.8 26.5 - - + -
256C PRO* 4.0 24.5 - - + +
259C TYR* 3.8 18.7 - - + -
260C LEU* 3.9 37.2 - - + -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C LEU* 2.8 40.9 + - + +
155C SER* 3.1 12.5 + - - +
157C LEU* 1.3 73.2 - - - +
159C LYS* 1.3 67.3 + - - +
161C ALA* 2.9 5.7 + - - +
162C ILE* 2.8 26.7 + - - +
202C ALA* 4.2 11.7 - - + -
207C TYR* 3.8 34.1 - - + +
209C CYS 5.2 0.7 - - - +
210C THR* 5.2 0.9 - - + -
213C PHE* 3.8 35.5 - - + -
249C MET* 3.8 25.6 - - + -
252C ILE* 4.4 4.0 - - + -
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C SER 2.9 12.7 + - - +
156C TYR* 3.1 12.8 + - + +
158C LEU* 1.3 73.8 - - - +
160C PHE* 1.3 64.2 + - + +
162C ILE* 3.2 10.0 + - - +
163C GLN* 3.0 28.0 + - + +
199C GLU* 5.7 10.6 - - + +
202C ALA* 4.9 5.0 - - + +
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Residues in contact with PHE 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C TYR* 3.2 24.3 + - + -
157C LEU* 3.1 17.5 + - + +
159C LYS* 1.3 78.3 - - - +
161C ALA* 1.3 61.7 + - - +
163C GLN* 3.2 13.1 + - + +
164C LYS* 3.1 26.0 + - + +
259C TYR* 4.0 3.1 - - + +
260C LEU* 3.9 22.2 - - + -
263C CYS* 3.7 46.2 - - + -
264C GLN* 4.3 18.6 - - + -
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Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LEU 3.0 9.1 + - - +
158C LEU* 2.9 10.8 + - - +
160C PHE* 1.3 73.8 - - - +
162C ILE* 1.3 66.1 + - - +
164C LYS* 3.1 4.4 + - - +
165C MET* 2.9 29.3 + - - +
213C PHE* 4.7 5.2 - - + -
248C GLU* 3.9 12.4 - - + +
249C MET* 3.7 29.8 - - + -
252C ILE* 4.8 1.1 - - + -
259C TYR* 3.6 16.3 + - - +
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C LEU 2.8 15.7 + - - +
159C LYS* 3.2 11.0 + - - +
161C ALA* 1.3 72.3 - - - +
163C GLN* 1.3 66.9 + - - +
165C MET* 2.9 22.2 + - - +
166C LYS* 3.1 23.5 + - + +
195C LEU* 3.9 14.1 - - + +
198C LEU* 3.6 34.3 - - + -
199C GLU* 3.4 44.4 - - + +
202C ALA* 5.6 0.9 - - + -
213C PHE* 3.7 23.8 - - + -
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Residues in contact with GLN 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C LYS* 3.0 18.4 + - + +
160C PHE* 3.4 15.0 - - + +
162C ILE* 1.3 78.6 - - + +
164C LYS* 1.3 62.3 + - + +
166C LYS* 3.0 49.2 + - - +
167C GLN* 4.9 1.6 + - - -
199C GLU* 4.9 10.2 + - - +
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Residues in contact with LYS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER* 5.0 1.1 - - - -
103A ALA* 5.8 5.7 - - - +
160C PHE* 3.1 21.6 + - + +
161C ALA 3.1 6.5 + - - +
163C GLN* 1.3 77.5 - - + +
165C MET* 1.3 60.0 + - - +
167C GLN* 3.1 32.0 + - - +
244C ILE* 3.6 12.0 - - + +
248C GLU* 3.0 41.5 - - + +
259C TYR* 4.1 5.2 - - - +
262C ALA 5.9 0.4 + - - -
263C CYS* 4.6 17.0 - - - +
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Residues in contact with MET 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ALA* 2.9 20.1 + - + +
162C ILE* 2.9 23.3 + - - +
164C LYS* 1.3 74.7 - - - +
166C LYS* 1.3 56.7 + - - +
167C GLN* 2.8 15.9 + - - +
170C THR* 3.9 12.3 - - - +
195C LEU* 3.9 28.6 - - + +
198C LEU* 4.1 13.0 - - + -
213C PHE* 4.1 7.2 - - - -
217C ALA* 4.1 6.7 - - + -
220C ILE* 5.6 0.2 - - + -
241C VAL* 3.8 30.1 - - + +
242C ILE* 5.1 0.7 - - + -
244C ILE* 3.9 21.6 - - + +
245C CYS* 3.6 39.0 - - + +
248C GLU* 5.8 0.2 - - + -
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ILE* 3.1 22.1 + - + +
163C GLN* 3.0 41.1 + - - +
165C MET* 1.3 71.7 - - - +
167C GLN* 1.3 66.4 + - - +
168C PRO* 3.8 2.3 - - - +
170C THR* 3.6 7.2 - - - -
174C GLN* 4.0 26.6 + - + +
195C LEU* 3.7 28.9 - - + -
199C GLU* 3.9 18.8 + - - +
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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