Contacts of the helix formed by residues 167 - 181 (chain B) in PDB entry 1UPX
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 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B HIS* 1.3 80.4 - - - +
168B ASN* 1.3 66.9 + - - +
169B SER* 4.1 16.0 + - - +
170B LEU* 3.0 25.7 + - + +
171B ASP* 3.2 16.9 + - - +
204B SER* 4.4 20.5 - - - +
208B LEU* 3.7 34.7 - - + +
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Residues in contact with ASN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 5.3 0.9 + - - -
60B HIS* 5.6 0.5 - - - +
63B ASP* 5.2 5.0 - - - +
166B HIS* 4.3 14.4 + - - -
167B GLU* 1.3 72.0 - - - +
169B SER* 1.3 56.8 + - - +
171B ASP* 3.4 6.6 + - - +
172B ALA* 2.8 34.4 + - + +
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B GLU* 4.1 15.4 + - - +
168B ASN* 1.3 78.4 - - - +
170B LEU* 1.3 58.8 + - - +
172B ALA* 3.9 5.6 - - - +
173B PHE* 3.0 29.5 + - - +
201B PHE* 3.7 16.6 - - - -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B MET* 3.7 22.4 - - + -
157B ALA* 4.0 21.1 - - + -
167B GLU* 3.0 24.7 + - + +
169B SER* 1.3 79.3 + - - +
171B ASP* 1.3 67.7 + - - +
173B PHE* 3.3 1.9 + - - +
174B MET* 3.0 25.7 + - + +
201B PHE* 3.7 37.5 - - + +
204B SER* 4.8 2.0 - - - -
205B ALA* 3.8 27.4 - - + +
208B LEU* 4.1 19.5 - - + -
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 4.6 1.3 - - - +
60B HIS* 3.9 13.3 + - - -
63B ASP* 3.5 45.8 - - + +
67B THR* 4.1 17.8 - - - +
157B ALA* 5.1 5.5 - - - +
166B HIS* 4.1 8.3 - - - +
167B GLU 3.2 19.8 + - - +
168B ASN* 4.1 6.2 - - - +
170B LEU* 1.3 78.9 - - - +
172B ALA* 1.3 62.4 + - - +
174B MET* 3.4 9.8 + - - +
175B GLN* 3.1 33.0 + - - +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 4.7 0.2 + - - -
52B ARG* 3.7 38.0 + - - +
168B ASN* 2.8 23.3 + - + +
169B SER* 3.9 5.6 - - - +
171B ASP* 1.3 73.6 - - - +
173B PHE* 1.3 62.3 + - - +
175B GLN* 3.3 3.3 + - - +
176B GLU* 3.0 24.9 + - - +
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LEU* 4.0 2.5 - - + -
153B MET* 3.9 15.3 - - + -
169B SER 3.0 19.7 + - - +
170B LEU 3.7 2.9 - - - +
171B ASP 3.3 0.2 - - - -
172B ALA* 1.3 75.5 - - - +
174B MET* 1.3 67.4 + - - +
176B GLU* 3.1 18.6 + - - +
177B ALA* 2.8 38.6 + - + +
194B LEU* 3.9 9.4 - - + -
197B GLU* 3.4 33.2 - - + -
198B THR* 3.6 44.4 - - - -
201B PHE* 3.4 40.2 - + + -
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Residues in contact with MET 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL* 4.2 9.0 - - + -
67B THR* 3.9 24.7 - - + -
70B LEU* 4.0 18.2 - - + -
150B LEU* 4.1 17.8 - - + +
153B MET* 4.0 18.8 - - + +
154B ALA* 3.4 40.8 - - - +
157B ALA* 4.3 7.4 - - + -
170B LEU* 3.0 20.0 + - + +
171B ASP* 3.6 11.2 - - - +
172B ALA 3.3 0.2 - - - -
173B PHE* 1.3 83.6 - - - +
175B GLN* 1.3 59.8 + - + +
177B ALA* 3.5 1.9 + - - +
178B LEU* 3.0 35.3 + - + +
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Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU 6.3 0.2 - - - -
45B GLY* 3.5 21.3 - - - +
48B ALA* 3.2 14.2 - - - +
49B THR* 3.3 9.1 + - - +
52B ARG* 2.8 37.3 + - - +
62B ILE* 4.4 3.6 - - - +
63B ASP* 2.8 42.1 + - - +
66B VAL* 4.1 30.9 - - + +
171B ASP* 3.1 19.4 + - - +
174B MET* 1.3 77.9 - - + +
176B GLU* 1.3 60.3 + - - +
178B LEU* 3.6 5.7 - - - +
179B ALA 3.1 21.1 + - - -
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 3.3 28.6 + - + +
172B ALA 3.0 17.1 + - - +
173B PHE* 3.1 21.5 + - - +
175B GLN* 1.3 74.1 - - - +
177B ALA* 1.3 59.7 + - - +
179B ALA* 3.2 3.7 + - - +
180B LYS* 2.9 60.9 + - + +
197B GLU* 5.2 3.8 - - - +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 4.7 2.2 - - + -
150B LEU* 3.7 22.2 - - + -
173B PHE* 2.8 43.4 + - + +
174B MET 3.9 1.1 - - - +
176B GLU* 1.3 70.2 - - - +
178B LEU* 1.3 66.1 + - - +
180B LYS* 3.1 8.8 + - - +
181B THR* 3.1 25.5 + - - +
194B LEU* 4.1 17.5 - - + +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 5.8 0.2 - - + -
41B THR* 4.0 19.5 - - + +
42B LYS* 3.8 42.2 - - + +
45B GLY* 4.9 1.1 - - - -
66B VAL* 3.8 28.7 - - + -
70B LEU* 4.2 26.5 - - + -
147B THR* 5.0 3.6 - - + +
150B LEU* 3.8 19.7 - - + +
174B MET 3.0 22.9 + - - +
175B GLN* 3.6 10.8 - - + +
177B ALA* 1.3 76.3 - - - +
179B ALA* 1.3 62.1 + - - +
181B THR* 2.7 23.8 + - - -
182B LEU 3.8 1.4 + - - -
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LYS 4.3 9.1 + - - -
45B GLY 4.0 1.3 - - - +
46B GLN* 3.6 35.7 - - + +
49B THR* 4.3 8.3 - - + +
175B GLN 3.1 14.5 + - - +
176B GLU* 3.2 10.1 + - - +
178B LEU* 1.3 75.1 - - - +
180B LYS* 1.3 63.0 + - + +
182B LEU* 3.0 19.2 + - - +
183B ASP* 3.6 8.4 + - - +
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Residues in contact with LYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ARG* 4.9 0.7 + - - -
176B GLU* 2.9 48.8 + - + +
177B ALA 3.1 8.5 + - - +
179B ALA* 1.3 78.2 - - + +
181B THR* 1.3 56.8 + - - +
182B LEU 3.0 0.2 - - - -
183B ASP* 3.1 31.5 + - + +
186B LEU* 3.7 28.9 - - + +
191B LEU* 4.8 2.8 - - - +
194B LEU* 3.7 32.7 - - + +
197B GLU* 4.9 9.5 + - - -
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LYS* 3.1 28.6 + - - +
143B ARG* 2.9 60.1 + - - +
146B ILE* 3.9 24.0 - - + -
147B THR* 4.1 4.5 - - - +
150B LEU* 5.0 1.1 - - + -
177B ALA 3.1 15.2 + - - +
178B LEU* 2.7 18.7 + - - -
180B LYS* 1.3 75.6 - - - +
182B LEU* 1.3 60.5 + - - +
183B ASP 3.5 0.2 - - - -
191B LEU* 5.3 2.2 - - + -
194B LEU* 5.1 1.6 - - + -
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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