Contacts of the helix formed by residues 180 - 197 (chain B) in PDB entry 2R5S
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 4.5 5.0 - - - +
177B GLU 5.9 0.9 - - - +
178B TYR* 2.9 14.9 + - - +
179B GLN* 1.3 74.8 - - - +
181B ASN* 1.3 78.5 + - - +
182B SER* 2.9 25.5 + - - -
183B TYR* 3.0 18.1 + - - +
184B LYS* 3.0 20.3 + - - +
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Residues in contact with ASN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 2.8 45.2 - - + +
180B ASP* 1.3 85.2 - - - +
182B SER* 1.3 59.5 + - - +
184B LYS* 3.7 14.0 + - - +
185B SER* 3.1 28.9 + - - -
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 3.7 31.1 - - - -
152B LEU* 4.5 9.6 - - - +
180B ASP* 2.9 21.0 + - - -
181B ASN* 1.3 80.7 - - - +
183B TYR* 1.3 66.3 + - - +
185B SER* 3.3 4.8 + - - -
186B LEU* 3.0 31.7 + - - +
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Residues in contact with TYR 183 (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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152B LEU* 3.8 19.8 - - + +
171B LEU* 3.7 29.9 + - + -
172B ALA* 5.4 1.4 - - - -
174B ILE* 3.8 28.3 - - + -
178B TYR 4.0 0.4 - - - +
179B GLN* 3.7 42.1 + - + -
180B ASP* 3.0 24.8 + - - +
182B SER* 1.3 76.4 + - - +
184B LYS* 1.3 75.6 + - + +
186B LEU* 3.0 4.3 + - - +
187B ILE* 3.0 60.0 + - + +
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Residues in contact with LYS 184 (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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248A GLY* 6.0 8.1 - - - -
252A GLY* 6.0 5.6 - - - -
255A LYS* 4.4 14.8 + - - -
179B GLN* 3.2 22.4 + - - +
180B ASP* 3.0 19.6 + - - +
181B ASN* 3.9 9.4 - - - +
183B TYR* 1.3 88.3 - - + +
185B SER* 1.3 57.5 + - - +
187B ILE* 3.4 7.1 + - - +
188B ALA* 3.1 27.9 + - - +
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.3 8.7 - - - +
255A LYS* 4.8 2.7 + - - +
283A LEU* 3.7 17.8 - - - +
284A TYR* 2.9 43.4 + - - +
181B ASN 3.1 20.0 + - - -
182B SER 3.8 3.6 - - - -
183B TYR 3.2 0.2 - - - -
184B LYS* 1.3 73.8 - - - +
186B LEU* 1.3 62.8 + - - +
188B ALA* 3.4 3.0 + - - +
189B LYS* 2.8 34.9 + - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR 5.3 4.0 - - - +
152B LEU* 3.5 39.0 - - + +
155B ALA* 4.3 7.2 - - + -
156B ASP* 4.0 28.7 - - + +
159B LEU* 3.7 27.8 - - + +
171B LEU* 3.9 16.8 - - + +
182B SER* 3.0 20.9 + - - +
183B TYR 3.5 7.4 - - - +
185B SER* 1.3 79.0 - - - +
187B ILE* 1.3 57.5 + - - +
189B LYS* 3.4 12.4 + - + +
190B LEU* 2.9 29.8 + - - +
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Residues in contact with ILE 187 (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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171B LEU* 4.3 21.1 - - + +
183B TYR* 3.0 61.7 + - + +
184B LYS* 3.7 8.3 - - - +
185B SER 3.2 0.2 - - - -
186B LEU* 1.3 74.0 - - - +
188B ALA* 1.3 67.7 + - - +
190B LEU* 3.3 10.2 + - + +
191B GLU* 3.1 24.8 + - + +
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Residues in contact with ALA 188 (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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255A LYS* 3.5 33.0 - - + +
259A MSE 4.0 24.0 - - + +
279A LEU* 5.0 0.2 - - + -
283A LEU* 3.9 11.7 - - + -
184B LYS 3.1 11.9 + - - +
185B SER 3.8 3.6 - - - +
187B ILE* 1.3 79.7 - - - +
189B LYS* 1.3 62.2 + - - +
191B GLU* 3.6 2.1 + - - +
192B LEU* 3.2 26.5 + - - +
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Residues in contact with LYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TYR* 3.7 36.8 - - + +
283A LEU* 3.5 36.6 + - + -
284A TYR 3.6 19.3 + - - +
156B ASP* 4.8 9.1 + - - -
159B LEU* 4.1 23.6 - - + -
160B GLU* 4.5 14.0 + - - +
185B SER 2.8 25.7 + - - +
186B LEU* 3.8 10.1 - - + +
188B ALA* 1.3 75.6 - - - +
190B LEU* 1.3 62.0 + - - +
192B LEU* 3.3 3.9 + - - +
193B HIS* 3.1 29.2 + - - -
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 4.3 8.9 - - + +
164B PHE* 3.5 45.8 - - + +
167B ALA* 4.5 4.9 - - + -
168B GLN* 3.5 38.8 - - + +
171B LEU* 3.8 17.5 - - + -
186B LEU 2.9 18.0 + - - +
187B ILE* 3.7 10.5 - - + +
188B ALA 3.3 0.4 - - - -
189B LYS* 1.3 76.3 - - - +
191B GLU* 1.3 57.2 + - - +
193B HIS* 3.4 2.3 + - - +
194B GLN* 2.9 48.2 + - + +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MSE 3.7 23.3 - - + -
263A SER* 5.7 0.3 - - - -
187B ILE* 3.1 17.4 + - + +
188B ALA 3.7 4.9 - - - +
190B LEU* 1.3 77.2 - - - +
192B LEU* 1.3 56.1 + - + +
194B GLN* 3.8 18.8 + - - +
195B GLN* 3.0 65.3 + - - +
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MSE 4.4 17.3 - - + -
262A LEU* 4.7 5.8 - - + -
267A GLN* 5.3 0.5 - - - +
276A ARG* 4.2 48.4 - - + +
279A LEU* 4.3 19.7 - - + -
280A TYR* 4.3 10.8 - - + -
283A LEU* 4.3 13.5 - - + -
188B ALA 3.2 18.8 + - - +
189B LYS* 3.3 5.5 + - - +
191B GLU* 1.3 75.4 - - - +
193B HIS* 1.3 58.8 + - - +
195B GLN* 3.4 13.6 + - - +
196B ALA* 3.0 26.7 + - - +
285B MES 3.5 18.7 - - - +
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Residues in contact with HIS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TYR* 3.0 31.5 + + - -
159B LEU* 3.6 15.5 + - + +
162B LYS* 5.9 1.8 - - + -
164B PHE* 3.5 49.5 - + + -
189B LYS 3.1 22.9 + - - -
190B LEU 3.8 4.7 - - - +
192B LEU* 1.3 72.5 - - - +
194B GLN* 1.3 65.9 + - - +
196B ALA* 3.0 17.9 + - - +
197B ALA* 3.0 14.1 + - - +
229B VAL* 5.0 2.4 - - - +
285B MES 3.5 28.6 - - - -
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Residues in contact with GLN 194 (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 PHE* 4.8 9.7 - - + +
165B GLU* 4.7 6.8 - - - +
168B GLN* 3.2 31.4 + - - +
190B LEU* 2.9 41.4 + - + +
191B GLU* 3.8 30.7 + - - +
193B HIS* 1.3 75.0 - - - +
195B GLN* 1.3 64.0 + - + +
197B ALA* 3.1 20.6 + - - +
198B GLU* 3.9 11.1 + - - +
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Residues in contact with GLN 195 (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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259A MSE 5.1 1.2 - - - +
262A LEU* 5.8 0.9 - - - +
263A SER* 3.4 30.3 + - - +
266A GLY* 5.8 0.6 - - - -
267A GLN* 3.6 30.4 + - + +
276A ARG* 3.8 21.6 - - - +
191B GLU* 3.0 47.6 + - - +
192B LEU* 3.7 12.2 - - - +
194B GLN* 1.3 76.0 - - - +
196B ALA* 1.3 62.8 + - - +
197B ALA 3.0 1.6 + - - -
198B GLU* 3.3 20.3 + - - +
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Residues in contact with ALA 196 (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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267A GLN* 3.2 20.0 + - - +
192B LEU 3.0 14.9 + - - +
193B HIS* 3.0 11.8 + - - +
195B GLN* 1.3 77.1 - - - +
197B ALA* 1.3 56.2 + - - +
198B GLU 3.3 1.8 + - - -
199B SER* 3.9 16.2 + - - -
202B LEU* 4.9 0.2 - - - +
229B VAL* 3.7 20.7 - - + +
285B MES 4.0 20.4 - - - -
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 5.9 1.6 - - + -
193B HIS 3.0 9.6 + - - +
194B GLN* 3.5 13.7 - - - +
195B GLN 3.0 1.8 - - - -
196B ALA* 1.3 76.6 - - - +
198B GLU* 1.3 59.2 + - - +
199B SER 3.6 1.3 - - - -
202B LEU* 3.9 3.9 - - - +
229B VAL* 3.9 28.0 - - - +
231B ARG* 2.6 49.0 + - + -
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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
------------------------------------------------------------
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