Contacts of the helix formed by residues 158 - 174 (chain B) in PDB entry 1UJ2
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 ASP 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B ASP* 5.3 3.9 - - - +
157B THR* 1.3 77.2 - - - +
159B ALA* 1.3 59.1 + - - +
160B ASP* 3.3 16.5 - - - +
161B THR* 3.1 14.8 + - - +
162B ARG* 2.9 25.5 + - - +
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Residues in contact with ALA 159 (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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157B THR 3.5 2.0 + - - -
158B ASP* 1.3 71.7 - - - +
160B ASP* 1.3 57.4 + - - +
162B ARG* 3.3 28.3 + - - +
163B LEU* 2.9 28.4 + - - +
185B TYR* 3.9 13.8 + - - +
190B LYS* 5.8 6.5 - - - +
193B PHE* 5.7 2.5 - - + -
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Residues in contact with ASP 160 (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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158B ASP* 3.5 17.5 - - - +
159B ALA* 1.3 72.8 + - - +
161B THR* 1.3 75.6 + - - +
163B LEU* 3.2 9.6 + - + +
164B SER* 3.0 22.9 + - - -
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Residues in contact with THR 161 (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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157B THR* 3.7 21.8 - - + -
158B ASP* 3.1 18.1 + - - +
160B ASP* 1.3 87.8 + - - +
162B ARG* 1.3 63.0 + - - +
164B SER* 3.2 8.8 + - - -
165B ARG* 3.1 41.0 + - + +
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY* 3.7 10.8 - - - +
29B THR* 3.1 54.8 + - + +
30B ALA* 3.5 16.4 - - - +
31B SER* 3.6 20.6 - - - +
157B THR* 2.9 34.7 + - + +
158B ASP 2.9 14.3 + - - +
159B ALA* 3.5 27.1 - - - +
161B THR* 1.3 73.4 - - - +
163B LEU* 1.3 60.7 + - - +
165B ARG* 3.2 2.2 + - - +
166B ARG* 2.8 31.0 + - - +
185B TYR* 4.6 8.9 + - - +
193B PHE* 3.6 37.5 - - - +
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Residues in contact with LEU 163 (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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159B ALA 2.9 17.1 + - - +
160B ASP* 3.2 9.1 + - - +
162B ARG* 1.3 75.8 - - - +
164B SER* 1.3 64.8 + - - +
166B ARG* 3.2 7.5 + - + +
167B VAL* 2.9 45.7 + - + +
181B ILE* 5.2 2.5 - - + -
182B LEU* 4.1 18.8 - - + -
185B TYR* 3.6 54.7 + - + -
186B ILE* 5.7 3.8 - - + -
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Residues in contact with SER 164 (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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160B ASP 3.0 12.7 + - - -
161B THR* 3.4 11.7 - - - -
162B ARG 3.2 0.2 - - - -
163B LEU* 1.3 78.3 - - - +
165B ARG* 1.3 63.6 + - - +
167B VAL* 3.3 7.3 + - - +
168B LEU* 3.3 30.8 + - - +
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.3 21.1 + - + -
31B SER 3.0 28.9 + - - -
32B GLY* 4.4 0.2 - - - -
157B THR* 3.7 15.0 - - - +
161B THR* 3.1 26.9 + - + +
162B ARG* 3.2 6.9 + - - +
164B SER* 1.3 81.8 - - - +
166B ARG* 1.3 57.3 + - - +
168B LEU* 3.5 6.4 + - - +
169B ARG* 3.0 29.3 + - - +
210B ARG* 2.9 24.2 + - - +
1302B ADP 3.2 78.1 + - + +
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Residues in contact with ARG 166 (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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29B THR* 3.1 31.0 + - + +
30B ALA* 3.9 12.3 - - + +
162B ARG 2.8 19.9 + - - +
163B LEU* 3.7 8.1 - - + +
165B ARG* 1.3 71.2 - - - +
167B VAL* 1.3 61.8 + - - +
169B ARG* 3.8 10.3 - - - +
170B ASP* 2.8 53.5 + - - +
176B ARG* 5.0 0.2 - - - +
181B ILE* 4.5 13.9 + - + +
184B GLN* 3.3 16.0 + - - +
185B TYR* 4.7 11.0 - - - +
189B VAL* 3.7 14.5 - - - +
1301B C5P 2.8 66.5 + - - -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 2.9 29.3 + - + +
164B SER* 3.7 7.0 - - - +
165B ARG 3.3 0.2 - - - -
166B ARG* 1.3 75.8 - - - +
168B LEU* 1.3 69.4 + - + +
171B ILE* 3.1 40.0 + - + +
178B LEU* 3.7 24.9 - - + -
181B ILE* 3.8 16.6 - - + +
182B LEU* 3.9 27.6 - - + -
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Residues in contact with LEU 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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164B SER* 3.3 18.7 + - - +
165B ARG* 4.0 8.3 - - - +
166B ARG 3.3 0.2 - - - -
167B VAL* 1.3 87.3 - - + +
169B ARG* 1.3 61.2 + - - +
171B ILE* 3.6 8.4 + - + +
172B SER* 3.1 25.7 + - - -
1302B ADP 6.0 0.2 - - - +
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Residues in contact with ARG 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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29B THR* 3.5 9.8 + - - -
30B ALA* 4.0 12.7 - - - +
165B ARG 3.0 17.6 + - - +
166B ARG* 3.8 14.0 - - - +
168B LEU* 1.3 76.2 - - - +
170B ASP* 1.3 80.5 + - - +
172B SER* 3.8 5.6 - - - -
173B GLU* 2.7 64.3 + - + +
174B ARG* 3.2 26.6 - - - +
1301B C5P 3.1 24.4 + - - -
1302B ADP 2.9 66.6 + - - +
1303B MG 4.0 1.6 - - - -
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 2.8 54.1 + - - +
169B ARG* 1.3 100.1 + - - +
171B ILE* 1.3 61.7 + - - +
174B ARG* 3.1 36.4 + - - -
175B GLY 3.3 0.2 + - - -
176B ARG* 3.1 32.8 + - + +
181B ILE* 3.6 21.5 - - + +
1301B C5P 4.7 0.7 - - - +
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Residues in contact with ILE 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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167B VAL* 3.1 35.8 + - + +
168B LEU* 3.9 9.6 - - + +
170B ASP* 1.3 76.7 - - - +
172B SER* 1.3 64.2 + - - +
175B GLY* 4.3 8.8 + - - -
176B ARG 3.4 18.2 - - - +
177B ASP* 4.9 0.7 - - - -
178B LEU* 4.4 20.9 - - + +
181B ILE* 3.6 14.4 - - + -
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Residues in contact with SER 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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168B LEU 3.1 19.3 + - - -
169B ARG* 3.4 6.6 + - - -
171B ILE* 1.3 80.7 - - - +
173B GLU* 1.3 71.8 + - - +
175B GLY 5.1 0.4 - - - -
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Residues in contact with GLU 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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114B PHE* 5.4 0.7 - - - +
115B VAL* 4.0 11.4 - - - +
169B ARG* 2.7 41.0 + - - +
172B SER* 1.3 87.3 + - - +
174B ARG* 1.3 68.2 + - + +
175B GLY 3.5 2.4 + - - -
1302B ADP 4.3 7.8 + - - -
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Residues in contact with ARG 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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62B ASP* 4.2 0.8 + - - -
114B PHE* 3.6 59.7 - - + -
115B VAL* 3.7 22.0 - - - +
169B ARG* 3.2 34.0 + - - +
170B ASP* 3.1 30.0 + - - +
173B GLU* 1.3 88.6 + - + +
175B GLY* 1.3 59.2 + - - +
176B ARG* 2.9 36.2 + - + +
1301B C5P 3.1 51.5 + - - -
1303B MG 4.2 3.2 - - - -
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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