Contacts of the helix formed by residues 161 - 167 (chain B) in PDB entry 4XJO
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 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 4.0 26.7 - - + -
129A GLU* 3.5 26.9 - - + +
161A THR* 4.4 8.5 - - + -
315A HIS* 4.4 4.3 - - + +
125B SER* 3.5 23.2 + - - -
129B GLU* 2.6 33.4 + - - +
160B ASP* 1.3 78.5 - - - +
162B PHE* 1.3 60.0 + - - +
163B LEU 3.4 0.4 - - - -
164B ALA* 3.1 5.5 + - - +
165B MET* 2.8 26.6 + - - +
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Residues in contact with PHE 162 (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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129A GLU* 2.9 54.5 + - + +
132A ALA* 4.4 9.9 - - + -
133A LYS* 3.9 35.7 - - + -
136A LEU* 4.9 4.3 - - + -
163A LEU* 4.1 24.9 - - + +
160B ASP 5.4 0.2 - - - -
161B THR* 1.3 73.9 - - - +
163B LEU* 1.3 60.6 + - - +
165B MET* 3.5 21.4 - - - +
166B SER* 3.5 18.0 + - - -
178B TRP* 4.0 15.9 - + - -
181B VAL* 3.9 25.6 - - + +
182B LEU* 4.0 20.8 - - + +
183B ALA 5.4 0.7 + - - -
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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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162A PHE* 4.1 27.5 - - + +
128B VAL* 4.5 8.1 - - + +
129B GLU* 3.0 31.1 + - - +
132B ALA* 3.7 26.0 - - + -
150B LEU* 4.2 13.9 - - + -
162B PHE* 1.3 73.2 - - - +
164B ALA* 1.3 72.4 + - - +
166B SER* 2.6 36.2 + - - +
167B ILE* 3.8 3.7 + - + +
183B ALA* 5.0 7.0 - - + -
185B GLN* 3.9 14.4 - - - +
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Residues in contact with ALA 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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125B SER 4.6 2.7 - - - +
128B VAL* 4.2 12.6 - - + -
129B GLU* 3.1 6.2 + - - +
158B HIS* 3.3 26.7 - - - +
159B GLY* 3.6 13.9 - - - -
161B THR* 3.1 21.5 + - - +
163B LEU* 1.3 82.8 - - - +
165B MET* 1.3 62.6 + - - +
166B SER 3.3 0.5 + - - -
167B ILE* 3.3 17.2 + - - +
168B CYS* 3.3 13.0 - - - -
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Residues in contact with MET 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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133A LYS* 3.4 20.4 - - - +
314A MET* 5.3 1.8 - - + +
25B TYR* 6.1 0.4 - - - +
159B GLY 4.2 1.6 - - - +
160B ASP* 3.3 28.3 - - - +
161B THR 2.8 17.9 + - - +
162B PHE* 3.5 26.5 - - + +
163B LEU 3.2 0.2 - - - -
164B ALA* 1.3 71.8 - - - +
166B SER* 1.3 60.5 + - - +
168B CYS* 3.1 19.0 + - - +
173B GLY 5.0 4.5 - - - +
175B HIS* 2.8 25.7 + - + +
178B TRP* 3.3 48.0 - - + +
182B LEU* 4.1 13.7 - - + -
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Residues in contact with SER 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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162B PHE 3.5 7.9 + - - -
163B LEU* 2.6 23.9 + - - +
165B MET* 1.3 79.4 - - - +
167B ILE* 1.3 57.8 + - - +
168B CYS 3.6 0.2 - - - -
175B HIS* 3.8 8.8 - - - -
182B LEU* 4.3 5.8 - - - -
183B ALA* 3.5 34.9 - - - +
185B GLN* 3.0 34.8 + - - +
187B PHE* 3.3 19.4 - - - -
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Residues in contact with ILE 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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128B VAL* 4.3 11.7 - - + -
150B LEU* 3.9 29.8 - - + -
152B THR* 3.5 28.6 + - + +
153B TRP 5.1 0.2 - - - +
156B GLY* 4.7 3.1 - - - +
158B HIS* 3.5 41.6 - - + -
163B LEU* 4.1 7.2 - - + +
164B ALA 3.4 13.2 - - - +
166B SER* 1.3 77.7 - - - +
168B CYS* 1.3 65.0 + - - +
169B ASP 3.9 0.7 + - - -
185B GLN* 3.8 21.5 - - + -
187B PHE* 3.8 5.1 - - - -
218B VAL* 3.8 26.9 - - + -
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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