Contacts of the helix formed by residues 167 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A HIS* 1.3 80.1 - - - +
168A ASN* 1.3 66.2 + - - +
169A SER* 4.2 15.0 + - - +
170A LEU* 3.0 27.5 + - + +
171A ASP* 3.2 16.7 + - - +
204A SER* 4.6 17.0 - - - +
208A LEU* 3.8 34.0 - - + +
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 4.5 16.3 + - - -
58A VAL 5.5 2.9 - - - +
63A ASP* 5.2 6.0 - - - +
166A HIS* 4.2 9.6 + - - -
167A GLU* 1.3 71.1 - - - +
169A SER* 1.3 58.3 + - - +
171A ASP* 3.4 5.0 + - - +
172A ALA* 2.9 34.5 + - + +
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 4.2 15.6 + - - +
168A ASN* 1.3 78.8 - - - +
170A LEU* 1.3 59.2 + - - +
172A ALA* 4.0 5.0 - - - +
173A PHE* 3.0 27.9 + - - +
201A PHE* 3.7 15.6 - - - -
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A MET* 4.7 9.0 - - + -
157A ALA* 3.8 14.4 - - + -
167A GLU* 3.0 22.5 + - + +
169A SER* 1.3 80.2 + - - +
171A ASP* 1.3 69.8 + - - +
173A PHE* 3.3 4.0 + - - +
174A MET* 3.0 56.1 + - + +
201A PHE* 4.3 14.4 - - + +
204A SER* 4.7 3.8 - - - -
205A ALA* 3.7 36.3 - - + +
208A LEU* 4.1 22.2 - - + -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 4.6 1.8 - - - +
60A HIS* 4.1 12.1 + - - -
63A ASP* 3.4 46.8 - - + +
67A THR* 4.2 6.8 - - - +
157A ALA* 5.1 1.9 - - - +
166A HIS* 4.1 8.7 - - - +
167A GLU 3.2 19.9 + - - +
168A ASN* 4.1 6.2 - - - +
170A LEU* 1.3 79.4 - - - +
172A ALA* 1.3 62.9 + - - +
174A MET* 3.3 24.1 + - - +
175A GLN* 3.1 33.7 + - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 4.7 0.3 + - - -
52A ARG* 3.9 38.4 + - - +
168A ASN* 2.9 20.4 + - - +
169A SER* 4.0 6.1 - - - +
171A ASP* 1.3 76.4 - - - +
173A PHE* 1.3 62.2 + - - +
175A GLN* 3.4 1.9 + - - +
176A GLU* 3.0 24.7 + - - +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.0 2.5 - - + -
153A MET* 4.0 13.0 - - + -
169A SER 3.0 20.2 + - - +
170A LEU 3.7 3.1 - - - +
172A ALA* 1.3 77.0 - - - +
174A MET* 1.3 68.2 + - - +
176A GLU* 3.2 16.3 + - - -
177A ALA* 2.8 40.9 + - + +
194A LEU* 4.0 9.2 - - + -
197A GLU* 3.5 31.2 - - + -
198A THR* 3.7 37.9 - - - -
201A PHE* 3.4 49.6 - + + -
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 5.2 4.3 - - + -
67A THR* 3.5 21.1 - - + -
70A LEU* 4.6 17.5 - - + -
150A LEU* 4.2 18.4 - - + +
153A MET* 3.8 20.6 - - - +
154A ALA* 3.8 17.9 - - - -
157A ALA* 4.1 2.7 - - + -
170A LEU* 3.0 44.9 + - + +
171A ASP* 3.4 24.9 - - - +
173A PHE* 1.3 82.5 - - - +
175A GLN* 1.3 62.5 + - + +
177A ALA* 3.4 1.9 + - - +
178A LEU* 3.0 34.8 + - - +
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Residues in contact with GLN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY* 3.5 30.4 - - - +
48A ALA* 3.3 14.2 - - - +
49A THR* 3.5 3.1 - - - +
52A ARG* 2.9 30.8 + - - +
62A ILE* 4.4 3.4 - - - +
63A ASP* 2.9 41.7 + - - +
66A VAL* 4.2 29.8 - - + +
171A ASP* 3.1 21.0 + - - +
172A ALA 3.9 2.7 - - - +
174A MET* 1.3 76.8 - - + +
176A GLU* 1.3 64.4 + - - +
178A LEU* 3.6 4.1 + - - +
179A ALA* 3.2 16.5 + - - +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 3.3 29.2 + - + +
172A ALA 3.0 18.6 + - - +
173A PHE* 3.7 18.0 - - - +
175A GLN* 1.3 74.6 - - - +
177A ALA* 1.3 60.2 + - - +
179A ALA* 3.2 5.1 + - - +
180A LYS* 3.0 57.7 + - + +
197A GLU* 5.5 2.4 - - - +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 4.8 0.2 - - + -
150A LEU* 3.8 20.2 - - + -
173A PHE* 2.8 45.0 + - + +
174A MET 3.8 3.6 - - - +
176A GLU* 1.3 68.7 - - - +
178A LEU* 1.3 66.7 + - - +
180A LYS* 3.1 18.0 + - - +
181A THR* 3.2 18.4 + - - +
194A LEU* 4.1 16.7 - - + +
198A THR* 4.8 0.9 - - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 5.8 0.4 - - + -
41A THR* 4.1 17.7 - - + +
42A LYS* 3.6 43.1 - - + +
45A GLY* 5.0 1.6 - - - -
66A VAL* 3.8 30.3 - - + -
70A LEU* 4.1 27.4 - - + -
147A THR* 5.0 4.0 - - + +
150A LEU* 3.7 21.3 - - + +
174A MET 3.0 23.2 + - - +
175A GLN* 3.7 7.4 - - + +
177A ALA* 1.3 77.2 - - - +
179A ALA* 1.3 61.3 + - - +
181A THR* 2.7 24.4 + - - -
182A LEU 3.9 0.5 + - - -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 4.0 9.6 + - - -
45A GLY 4.3 0.7 - - - +
46A GLN* 3.5 38.8 - - + +
49A THR* 4.7 4.0 - - + +
175A GLN 3.2 9.9 + - - +
176A GLU* 3.5 11.0 - - + +
177A ALA 3.2 0.2 - - - -
178A LEU* 1.3 78.6 - - - +
180A LYS* 1.3 63.1 + - + +
182A LEU* 3.0 16.7 + - - +
183A ASP* 3.6 8.7 + - - +
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG* 5.0 0.7 + - - -
176A GLU* 3.0 47.1 + - + +
177A ALA* 3.1 9.3 + - - +
179A ALA* 1.3 78.1 - - + +
181A THR* 1.3 57.4 + - - +
183A ASP* 3.1 31.7 + - + +
186A LEU* 3.7 29.3 - - + +
191A LEU* 4.8 2.6 - - - +
194A LEU* 3.7 32.2 - - + +
197A GLU* 4.9 10.5 + - - -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 3.1 28.1 + - - +
143A ARG* 3.0 53.4 + - + +
146A ILE* 3.8 29.2 - - + -
147A THR* 4.0 5.2 - - - +
150A LEU* 5.0 0.9 - - + -
177A ALA 3.3 15.5 - - - +
178A LEU* 2.7 18.7 + - - +
179A ALA 3.2 0.6 - - - -
180A LYS* 1.3 75.6 - - - +
182A LEU* 1.3 62.2 + - - +
183A ASP 3.5 0.2 - - - -
191A LEU* 5.2 2.0 - - + -
194A LEU* 4.9 2.0 - - + -
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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