Contacts of the helix formed by residues 162 - 172 (chain B) in PDB entry 3UXA
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 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LYS* 2.5 29.2 + - - -
160B ILE* 4.5 0.3 - - - +
161B ASN* 1.3 83.8 + - - +
163B GLU* 1.3 58.9 + - - +
164B GLU* 2.9 12.6 + - - +
165B ASP* 2.8 26.0 + - - +
166B LEU* 3.0 20.1 + - - +
193B ASN* 4.4 4.7 - - - +
197B LEU* 3.7 13.5 - - - +
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Residues in contact with GLU 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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60A LEU* 3.2 19.7 - - + +
238A ARG* 5.0 4.0 - - - +
162B ASP* 1.3 71.5 - - - +
164B GLU* 1.3 59.8 + - - +
166B LEU 3.3 0.3 + - - -
167B ASP* 2.8 25.2 + - - +
193B ASN* 5.4 0.4 + - - -
196B LYS* 5.8 2.9 - - - +
197B LEU* 3.7 19.6 - - + +
200B MET* 4.1 28.7 - - - +
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Residues in contact with GLU 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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238A ARG* 4.4 20.2 - - - +
3B ARG* 5.6 4.2 + - - -
162B ASP* 2.9 11.2 + - - +
163B GLU* 1.3 74.0 - - - +
165B ASP* 1.3 68.2 + - - +
167B ASP* 3.1 8.1 + - + +
168B ILE* 2.9 40.1 + - + +
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Residues in contact with ASP 165 (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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134B VAL* 3.6 28.9 - - + +
135B LYS* 3.4 24.5 + - - +
159B VAL 4.5 0.9 - - - +
160B ILE* 3.4 25.3 - - + +
161B ASN* 3.1 30.3 + - - +
162B ASP* 2.8 27.4 + - - +
164B GLU* 1.3 71.3 - - - +
166B LEU* 1.3 57.5 + - - +
168B ILE* 3.1 4.0 + - - +
169B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 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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60A LEU* 4.0 19.3 - - + -
160B ILE* 3.5 22.4 - - + +
162B ASP 3.0 11.4 + - - +
163B GLU 3.3 5.6 + - - +
165B ASP* 1.3 73.2 - - - +
167B ASP* 1.3 60.7 + - - +
169B ALA* 3.8 2.4 - - - +
170B LEU* 3.0 44.9 + - + +
177B ILE* 4.4 9.9 - - + -
197B LEU* 3.7 37.0 - - + +
200B MET* 3.7 20.2 - - + +
201B ILE* 3.6 24.0 - - + -
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Residues in contact with ASP 167 (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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58A SER 4.3 0.3 - - - +
60A LEU* 3.1 38.0 + - + +
238A ARG* 3.6 34.9 + - - +
163B GLU 2.8 14.9 + - - +
164B GLU* 3.1 7.9 + - - +
166B LEU* 1.3 76.2 - - - +
168B ILE* 1.3 66.6 + - - +
170B LEU* 3.6 3.1 + - - +
171B ARG* 2.8 61.3 + - - +
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Residues in contact with ILE 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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3B ARG* 5.3 9.2 - - - +
134B VAL* 3.7 20.4 - - + -
137B LEU 5.8 1.3 - - - +
139B GLU* 4.5 37.2 - - + +
142B LEU* 3.5 28.7 - - + -
164B GLU* 2.9 29.8 + - + +
165B ASP 3.6 5.6 - - - +
167B ASP* 1.3 83.3 - - - +
169B ALA* 1.3 66.6 + - - +
170B LEU 3.2 0.2 - - - -
171B ARG* 3.2 16.7 + - + +
172B ILE* 3.3 17.8 + - + +
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Residues in contact with ALA 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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158B ILE* 3.7 24.2 - - + -
160B ILE* 4.0 10.5 - - + -
165B ASP 2.9 16.2 + - - +
166B LEU* 3.3 5.6 + - - +
168B ILE* 1.3 76.2 - - - +
170B LEU* 1.3 61.6 + - - +
172B ILE* 3.2 18.1 - - - +
174B ALA* 3.0 27.7 + - + +
177B ILE* 4.1 18.8 - - + -
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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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57A PRO 4.3 10.5 - - - +
58A SER* 3.2 29.1 - - - +
59A GLY* 3.9 13.9 - - - +
60A LEU* 3.8 26.0 - - + -
187A LEU* 5.5 0.9 - - + +
166B LEU* 3.0 33.8 + - + +
167B ASP 3.9 3.6 - - - +
168B ILE 3.2 0.2 - - - -
169B ALA* 1.3 79.3 - - - +
171B ARG* 1.3 56.8 + - - +
173B GLY* 3.1 18.0 + - - +
174B ALA 4.7 3.4 - - - +
177B ILE* 5.1 4.3 - - + -
200B MET 4.8 2.0 - - - +
202B PRO* 3.7 36.8 - - + -
205B VAL* 4.7 11.9 - - + -
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Residues in contact with ARG 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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58A SER* 3.1 14.1 + - - -
59A GLY* 4.0 7.1 - - - -
60A LEU 5.7 0.2 + - - -
182A ARG* 3.1 32.0 + - - +
189A ILE* 3.4 10.4 - - + +
212A GLY* 5.5 6.1 - - - +
234A SER* 3.1 32.8 + - - -
235A SER* 4.0 24.0 - - - +
238A ARG* 4.7 2.6 - - - +
253A PO4 4.3 14.5 + - - +
139B GLU* 3.0 31.4 + - + +
167B ASP* 2.8 51.1 + - - +
168B ILE* 3.2 16.9 + - + +
170B LEU* 1.3 77.2 - - - +
172B ILE* 1.3 62.7 + - + +
173B GLY 3.2 1.0 + - - -
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Residues in contact with ILE 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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187A LEU 3.8 9.7 - - - +
188A GLU* 4.7 0.2 - - - -
189A ILE* 4.2 16.2 + - + +
139B GLU* 4.9 6.5 - - + +
142B LEU* 3.5 39.7 - - + +
143B GLU* 4.5 22.7 - - + -
146B LEU* 3.8 32.4 - - + +
150B ARG* 4.6 2.6 + - - -
158B ILE* 4.1 16.8 - - + -
168B ILE* 3.3 13.9 + - + +
169B ALA* 3.2 19.7 - - - +
171B ARG* 1.3 82.6 - - + +
173B GLY* 1.3 61.2 + - - +
174B ALA* 3.9 4.9 - - - +
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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