Contacts of the helix formed by residues 161 - 172 (chain B) in PDB entry 2R8J
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 LEU 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B CYS* 3.1 20.5 + - - +
27B ALA* 4.1 7.6 - - + -
146B CYS* 4.4 7.4 - - + -
159B LEU* 3.3 41.3 - - + +
160B ASP* 1.3 71.2 - - - +
162B GLY* 1.3 67.0 + - - +
163B ARG 3.4 1.3 - - - -
164B ILE* 3.3 14.9 + - + +
165B CYS* 3.0 31.7 + - - -
241B GLY* 3.5 35.7 - - - +
244B VAL* 4.5 13.2 - - + -
245B CYS* 4.3 15.9 - - + +
248B ILE* 5.6 2.0 - - + -
264B LEU* 4.7 3.6 - - + -
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Residues in contact with GLY 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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12B LEU* 3.2 32.8 - - - +
18B ALA* 5.3 1.8 - - - -
25B CYS* 4.1 7.1 + - - -
160B ASP* 3.1 19.4 + - - -
161B LEU* 1.3 77.8 - - - +
163B ARG* 1.3 61.9 + - - +
165B CYS* 3.5 4.3 + - - +
166B PHE* 3.1 22.2 + - - +
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Residues in contact with ARG 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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147A ASP* 6.4 1.6 - - + -
12B LEU 3.3 9.4 + - - +
13B GLY* 3.1 28.3 - - - +
14B SER 3.6 7.3 + - - -
15B PRO* 3.4 30.4 - - + +
18B ALA* 3.7 9.3 - - - +
147B ASP* 2.7 42.6 + - - +
148B LEU* 3.3 30.5 - - - +
160B ASP* 2.7 31.7 + - - -
161B LEU 3.4 0.6 - - - -
162B GLY* 1.3 70.0 - - - +
164B ILE* 1.3 67.9 + - + +
166B PHE* 3.2 5.1 + - + +
167B ASN* 2.8 42.0 + - - +
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Residues in contact with ILE 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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145B ALA 3.2 28.0 - - - +
146B CYS* 4.5 10.5 - - + -
147B ASP* 4.9 9.0 - - - +
161B LEU* 3.3 18.7 + - + +
163B ARG* 1.3 75.7 - - + +
165B CYS* 1.3 58.1 + - - +
167B ASN* 3.8 5.3 - - - +
168B MET* 2.8 38.5 + - + +
244B VAL* 3.6 46.2 - - + -
248B ILE* 5.4 0.9 - - + -
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Residues in contact with CYS 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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12B LEU* 5.1 0.4 - - + -
25B CYS* 4.0 4.3 - - - -
161B LEU* 3.0 35.1 + - - +
162B GLY* 3.7 3.4 - - - +
164B ILE* 1.3 80.8 - - - +
166B PHE* 1.3 53.6 + - - +
168B MET* 3.1 7.8 + - - +
169B LEU* 2.7 37.4 + - - +
237B ILE* 3.7 48.2 - - + +
240B LEU* 4.1 8.4 - - + +
241B GLY* 3.9 16.4 - - - -
244B VAL* 5.8 0.2 - - - -
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Residues in contact with PHE 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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9B LEU* 3.8 47.6 - - + -
10B ILE* 4.1 17.5 - - + -
12B LEU* 4.1 14.3 - - + +
13B GLY* 4.8 11.9 - - - -
162B GLY 3.1 15.4 + - - +
163B ARG* 3.5 5.6 - - - +
165B CYS* 1.3 79.9 - - - +
167B ASN* 1.3 71.8 + - - +
169B LEU* 3.0 8.6 + - + +
170B MET* 2.8 48.5 + - + +
171B PHE* 4.7 5.4 - + - -
194B PHE* 3.8 33.9 - + - -
237B ILE* 5.0 1.1 - - - -
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Residues in contact with ASN 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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143A LYS 4.7 1.9 + - - +
144A SER* 3.5 39.1 + - - +
163B ARG* 2.8 43.4 + - - +
164B ILE* 3.8 4.7 - - - +
166B PHE* 1.3 83.7 - - - +
168B MET* 1.3 68.2 + - - +
170B MET 4.4 0.2 - - - +
171B PHE* 2.8 32.3 + - + +
172B ASP 3.3 4.5 + - - -
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Residues in contact with MET 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 ILE* 2.8 24.4 + - + +
165B CYS* 3.3 9.4 - - - +
167B ASN* 1.3 73.1 - - - +
169B LEU* 1.3 63.9 + - - +
170B MET 3.3 0.2 + - - -
172B ASP* 3.0 45.4 + - - +
175B TYR* 3.7 37.9 - - + -
183B LEU* 4.0 9.1 - - + +
191B ARG* 3.3 5.2 + - - -
240B LEU* 4.0 31.9 - - + +
243B GLN* 5.9 1.6 - - + -
244B VAL* 3.7 27.8 - - - -
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Residues in contact with LEU 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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9B LEU* 4.0 23.3 - - + -
165B CYS 2.7 17.7 + - - +
166B PHE* 3.2 11.2 - - + +
168B MET* 1.3 75.2 - - - +
170B MET* 1.3 78.3 + - + +
183B LEU* 5.3 0.7 - - - -
187B LEU* 3.3 34.4 - - + +
191B ARG* 2.9 20.8 + - - -
233B TRP* 4.0 17.5 - - + -
236B VAL* 3.9 24.9 - - + -
237B ILE* 3.9 19.3 - - + -
240B LEU* 4.3 10.5 - - + +
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Residues in contact with MET 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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6B TRP* 5.4 0.4 - - - -
9B LEU* 5.1 4.5 - - + -
166B PHE* 2.8 46.6 + - + +
169B LEU* 1.3 114.6 - - + +
171B PHE* 1.3 81.9 + - + +
190B ILE* 3.6 27.8 - - + -
191B ARG* 2.8 45.0 + - + +
194B PHE* 3.8 35.2 - - + -
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Residues in contact with PHE 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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140A LYS* 3.6 16.4 - - + -
141A ILE* 4.1 25.8 - - + -
144A SER* 3.4 35.9 - - - +
255A ILE* 5.1 10.1 - - + -
166B PHE* 4.7 7.4 - + - -
167B ASN* 2.8 22.9 + - + +
170B MET* 1.3 91.2 - - + +
172B ASP* 1.3 62.7 + - - -
173B ASN* 3.3 18.9 + - - +
194B PHE* 3.6 28.3 - + - -
195B ILE* 4.7 11.2 - - + -
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Residues in contact with ASP 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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167B ASN 3.3 3.2 + - - -
168B MET* 3.0 48.9 + - - +
170B MET 3.7 0.2 - - - -
171B PHE* 1.3 75.9 - - - +
173B ASN* 1.3 59.7 + - - +
174B GLU* 2.8 32.5 + - - +
175B TYR* 2.9 26.2 + - - +
183B LEU* 4.3 5.5 - - + +
184B LYS* 4.3 3.1 + - - +
191B ARG* 2.8 31.4 + - - +
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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