Contacts of the helix formed by residues 215 - 229 (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 ASN 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B LEU* 3.5 9.0 - - - +
212B ASN* 3.2 30.7 + - - +
213B PRO 3.3 0.9 - - - +
214B ASP* 1.3 74.8 - - - +
216B PHE* 1.3 63.4 + - - +
217B GLU* 3.1 13.9 + - - +
218B LEU* 3.1 46.1 + - + +
219B ALA* 3.4 15.2 + - - +
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Residues in contact with PHE 216 (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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213B PRO 4.7 3.4 - - - -
214B ASP* 3.1 32.6 + - + -
215B ASN* 1.3 73.8 + - - +
217B GLU* 1.3 65.7 + - - +
219B ALA* 3.2 5.8 + - - +
220B CYS* 3.1 25.8 + - - -
242B ILE* 3.7 41.1 - - + -
246B ASN* 4.9 9.0 - - + -
249B ALA* 4.1 14.4 - - + -
250B GLN* 3.7 46.1 + - + +
254B VAL* 4.1 4.4 - - + +
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Residues in contact with GLU 217 (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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215B ASN* 3.1 9.7 + - - +
216B PHE* 1.3 80.4 - - - +
218B LEU* 1.3 63.1 + - + +
220B CYS* 3.4 7.0 + - - +
221B GLU* 3.2 44.0 + - - +
250B GLN* 4.1 25.0 + - - +
253B GLU* 4.1 20.4 - - - +
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Residues in contact with LEU 218 (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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205B LEU* 5.7 4.2 - - + +
208B GLU* 3.7 42.8 - - + +
209B LEU* 3.7 21.4 - - + +
212B ASN* 4.3 13.0 - - + -
215B ASN* 3.1 38.7 + - + +
217B GLU* 1.3 76.1 - - + +
219B ALA* 1.3 61.1 + - - +
221B GLU* 3.6 21.6 - - - +
222B LEU* 3.0 29.5 + - - +
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Residues in contact with ALA 219 (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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209B LEU* 3.7 21.2 - - + +
213B PRO 5.9 0.7 - - - +
215B ASN 3.4 9.8 + - - +
216B PHE 3.2 10.2 + - - +
218B LEU* 1.3 76.5 - - - +
220B CYS* 1.3 64.4 + - - +
222B LEU* 3.2 1.7 + - - +
223B ALA* 2.9 24.6 + - - +
238B LEU* 3.9 6.4 - - + +
239B LEU* 3.7 8.3 - - + +
242B ILE* 3.5 31.0 - - + -
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Residues in contact with CYS 220 (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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216B PHE 3.1 11.9 + - - -
217B GLU 3.6 8.5 - - - +
219B ALA* 1.3 74.4 - - - +
221B GLU* 1.3 57.0 + - + +
223B ALA* 3.4 3.6 + - - +
224B VAL* 3.0 33.2 + - + +
239B LEU* 4.2 7.2 - - - +
253B GLU* 3.6 23.3 - - - +
254B VAL* 3.4 32.5 - - - -
257B THR* 3.3 34.5 + - + -
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Residues in contact with GLU 221 (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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205B LEU* 5.1 9.5 - - + +
217B GLU* 3.2 32.8 + - + +
218B LEU* 3.6 28.2 - - - +
220B CYS* 1.3 73.2 - - + +
222B LEU* 1.3 67.0 + - - +
224B VAL* 3.2 8.1 + - - +
225B GLN* 2.9 28.8 + - + +
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Residues in contact with LEU 222 (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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202B LEU* 3.5 30.3 - - + +
205B LEU* 3.9 27.6 - - + +
206B GLU* 4.1 15.9 - - + +
209B LEU* 3.9 23.1 - - + -
218B LEU 3.0 19.6 + - - +
219B ALA* 3.2 3.1 + - - +
221B GLU* 1.3 74.2 - - - +
223B ALA* 1.3 55.0 + - - +
225B GLN* 3.0 5.5 + - - +
226B TYR* 2.5 69.8 + - + +
238B LEU* 4.0 7.6 - - + -
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Residues in contact with ALA 223 (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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219B ALA 2.9 17.3 + - - +
220B CYS 3.6 3.8 - - - +
222B LEU* 1.3 78.4 - - - +
224B VAL* 1.4 55.9 + - - +
226B TYR* 3.5 5.1 + - - +
227B ASN* 3.1 27.9 + - - +
235B ALA* 3.6 27.0 - - + +
238B LEU* 4.5 1.7 - - + +
239B LEU* 3.5 33.9 - - + -
257B THR* 4.4 1.8 - - - +
261B ILE* 4.5 4.7 - - + +
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Residues in contact with VAL 224 (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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220B CYS* 3.0 22.0 + - + +
221B GLU* 3.2 8.0 + - - +
223B ALA* 1.4 74.5 - - - +
225B GLN* 1.3 73.4 + - - +
227B ASN* 3.6 9.4 + - - +
228B GLN* 3.3 33.3 + - + +
257B THR* 4.2 17.7 - - - +
261B ILE* 5.0 8.7 - - + -
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Residues in contact with GLN 225 (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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201B GLU* 4.8 14.2 - - - +
202B LEU* 3.5 21.7 - - + +
205B LEU* 4.0 18.4 - - + -
221B GLU* 2.9 18.1 + - + +
222B LEU 3.5 5.8 - - - +
224B VAL* 1.3 83.1 - - - +
226B TYR* 1.3 66.8 + - - +
228B GLN* 3.0 40.9 + - - +
229B VAL* 3.7 12.1 + - - +
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Residues in contact with TYR 226 (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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202B LEU* 3.8 13.2 - - + -
206B GLU* 2.6 32.3 + - - +
222B LEU* 2.5 51.5 + - + +
223B ALA* 3.6 6.1 - - - +
225B GLN* 1.3 71.9 - - - +
227B ASN* 1.4 59.0 + - - +
229B VAL* 3.1 11.3 + - - +
231B ARG* 2.8 76.1 + - + +
234B GLU* 3.8 23.6 + - + +
235B ALA* 3.5 24.5 - - + -
238B LEU* 4.6 7.9 - - + -
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Residues in contact with ASN 227 (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 LYS* 3.0 29.8 + - - +
223B ALA 3.1 14.7 + - - +
224B VAL* 3.7 8.6 - - - +
225B GLN 3.3 0.2 - - - -
226B TYR* 1.4 79.0 - - - +
228B GLN* 1.3 70.4 + - - +
230B GLY* 3.3 6.7 + - - -
232B ASP* 2.6 36.6 + - - +
235B ALA* 4.5 0.9 - - + +
261B ILE* 4.0 30.6 - - + +
264B ALA* 4.4 18.1 - - - +
265B LEU* 4.6 3.6 - - - +
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Residues in contact with GLN 228 (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 LYS* 3.8 13.7 - - - +
224B VAL* 3.3 22.6 - - + +
225B GLN* 3.0 41.6 + - - +
226B TYR 3.1 1.0 - - - -
227B ASN* 1.3 86.0 - - - +
229B VAL* 1.3 65.3 + - + +
230B GLY 3.4 0.2 - - - -
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Residues in contact with VAL 229 (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 LYS* 4.9 0.4 - - - -
164B PHE* 3.5 19.5 - - - -
193B HIS 5.0 1.1 - - - +
196B ALA* 3.7 23.1 - - + +
197B ALA* 3.9 22.9 - - + +
199B SER* 5.7 0.7 - - - +
202B LEU* 3.6 29.8 - - + -
225B GLN* 3.8 6.7 - - - +
226B TYR 3.3 12.3 - - - +
228B GLN* 1.3 83.2 - - + +
230B GLY* 1.3 59.6 + - - +
231B ARG* 3.5 15.4 + - - +
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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