Contacts of the helix formed by residues 245 - 263 (chain B) in PDB entry 1R88
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 GLN 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 3.4 26.4 - - + -
182B ALA* 3.4 47.3 + - + +
185B ALA* 5.0 6.1 - - - +
186B GLY* 4.8 4.4 - - - +
189B GLN* 5.8 2.4 + - - -
242B MET* 3.0 12.4 + - - +
243B ILE* 3.4 16.6 + - + +
244B GLY* 1.3 85.5 + - - +
246B ALA* 1.3 64.3 + - - +
247B ALA* 3.2 4.7 - - - +
248B GLU* 3.2 18.7 + - + +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PRO* 3.3 31.4 - - + +
236B ALA* 4.3 7.0 - - + -
242B MET* 3.8 30.7 + - + +
244B GLY 3.8 2.0 - - - -
245B GLN* 1.3 75.4 - - - +
247B ALA* 1.3 61.8 + - - +
249B ALA* 3.3 3.8 + - - +
250B MET* 3.1 22.2 + - - +
278B ASN* 4.1 14.5 + - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PRO* 4.1 10.7 - - + +
245B GLN* 3.2 1.7 - - - +
246B ALA* 1.3 79.0 - - - +
248B GLU* 1.3 58.4 + - + +
250B MET* 3.4 24.5 - - + +
251B GLY* 3.1 22.9 + - - -
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 4.0 11.0 - - + -
176B ASN* 4.3 0.9 + - - -
178B THR* 3.2 29.0 + - - +
179B THR* 2.6 38.0 + - + -
182B ALA* 3.7 22.0 - - + +
245B GLN* 3.2 19.5 + - + +
247B ALA* 1.3 78.3 - - + +
249B ALA* 1.3 59.1 + - - +
251B GLY* 3.5 1.5 + - - -
252B ASN* 2.9 37.7 + - - +
255B MET* 5.6 1.2 - - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 3.5 27.8 - - - +
170B GLY 3.4 11.9 - - - +
171B PHE* 3.9 14.5 - - + -
230B SER* 3.9 2.6 + - - +
242B MET* 3.5 21.8 - - + -
245B GLN 3.5 2.8 + - - -
246B ALA 3.3 4.3 + - - +
248B GLU* 1.3 74.9 - - - +
250B MET* 1.3 64.5 + - - +
252B ASN* 4.2 2.0 - - - -
253B SER* 3.0 30.3 + - - -
278B ASN* 5.6 0.4 - - - +
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Residues in contact with MET 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B SER* 4.0 12.4 + - - -
231B PRO 3.6 13.2 - - - +
232B THR* 3.3 39.7 - - + +
233B ASN 3.5 6.1 - - - +
234B PRO* 3.5 38.4 - - + -
246B ALA 3.1 9.1 + - - +
247B ALA* 3.4 20.4 - - + +
249B ALA* 1.3 77.9 - - - +
251B GLY* 1.3 61.2 + - - +
253B SER* 3.5 2.6 + - - -
254B ARG* 3.3 21.8 + - - +
272B PHE* 5.2 1.6 - - - -
278B ASN* 5.8 1.5 + - - +
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Residues in contact with GLY 251 (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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247B ALA 3.1 10.9 + - - -
248B GLU* 3.9 3.1 - - - -
250B MET* 1.3 77.0 - - - +
252B ASN* 1.3 59.5 + - - +
254B ARG* 3.5 6.0 + - - +
255B MET* 3.0 44.7 + - - +
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Residues in contact with ASN 252 (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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170B GLY 4.0 1.6 - - - +
171B PHE* 3.4 16.4 - - - +
172B LEU* 3.6 16.8 - - - +
173B TYR* 3.1 35.9 - - - +
179B THR* 3.0 40.9 + - - +
248B GLU* 2.9 23.4 + - - +
249B ALA 3.7 4.9 - - - +
250B MET 3.4 0.2 - - - -
251B GLY* 1.3 75.6 - - - +
253B SER* 1.3 57.5 + - - +
255B MET* 3.5 13.8 + - - +
256B PHE* 2.9 29.6 + - - +
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B SER* 4.9 0.3 + - - -
170B GLY 3.3 17.7 + - - -
172B LEU* 4.1 15.0 - - - +
228B VAL* 4.0 16.9 - - - +
229B TRP 4.7 0.5 + - - -
230B SER* 3.6 28.0 + - - -
249B ALA 3.0 17.6 + - - -
250B MET 3.9 1.3 - - - -
252B ASN* 1.3 73.8 - - - +
254B ARG* 1.3 65.2 + - - +
256B PHE* 3.4 2.4 + - - +
257B TYR* 3.1 17.2 + - - +
272B PHE* 3.6 13.0 - - - -
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Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 4.5 10.1 - - - +
250B MET 3.3 14.2 + - - +
251B GLY* 3.8 6.7 - - - +
252B ASN 3.4 0.2 - - - -
253B SER* 1.3 79.4 - - - +
255B MET* 1.3 64.9 + - + +
257B TYR* 3.2 30.5 + - - +
258B ASN* 3.2 38.2 + - - +
272B PHE* 3.8 46.7 - - + +
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Residues in contact with MET 255 (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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173B TYR* 3.7 28.3 - - + -
176B ASN* 4.2 15.7 - - - +
213B TRP* 3.1 22.4 + - + +
248B GLU* 5.6 0.9 - - - +
251B GLY* 3.0 33.2 + - - +
252B ASN* 3.9 13.9 - - - +
254B ARG* 1.3 79.8 - - + +
256B PHE* 1.3 58.0 + - - +
258B ASN* 3.5 11.1 + - - +
259B GLN* 3.0 22.7 + - - +
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Residues in contact with PHE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B MET* 3.8 19.7 - - + -
172B LEU* 3.8 29.2 - - + -
212B PRO 3.7 20.4 - - - -
213B TRP* 3.7 28.4 - - + -
216B ALA* 4.5 7.6 - - + -
219B LEU* 3.8 23.6 - - + -
226B VAL* 5.0 4.0 - - + -
228B VAL* 4.0 21.8 - - + -
252B ASN 2.9 18.5 + - - +
253B SER 3.7 4.3 - - - +
254B ARG 3.2 0.2 - - - -
255B MET* 1.3 74.0 - - - +
257B TYR* 1.3 61.9 + - - +
259B GLN* 3.8 0.2 - - - +
260B TYR* 2.8 51.2 + + + +
270B PHE* 4.1 11.4 - + - -
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Residues in contact with TYR 257 (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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253B SER 3.1 13.6 + - - +
254B ARG* 3.2 32.5 + - - +
256B PHE* 1.3 76.9 - - - +
258B ASN* 1.3 76.4 + - - +
260B TYR* 3.8 1.0 - - - +
261B ARG* 3.2 54.9 + - + +
270B PHE* 3.4 56.1 - + + -
272B PHE* 3.9 10.8 - + + -
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Residues in contact with ASN 258 (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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254B ARG* 3.2 31.7 + - - +
255B MET* 3.8 10.2 - - - +
256B PHE 3.3 0.2 - - - -
257B TYR* 1.3 90.9 - - - +
259B GLN* 1.3 63.9 + - - +
261B ARG* 3.7 4.0 + - - +
262B SER* 3.1 29.6 + - - +
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Residues in contact with GLN 259 (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 TRP* 3.1 84.4 + - + +
214B VAL 4.5 5.9 + - - -
216B ALA* 3.8 10.5 - - + +
255B MET 3.0 7.7 + - - +
256B PHE* 3.8 2.5 - - - +
258B ASN* 1.3 75.4 - - - +
260B TYR* 1.3 65.5 + - - +
262B SER* 3.2 8.0 + - - -
263B VAL* 3.1 37.5 + - + +
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Residues in contact with TYR 260 (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 ALA* 4.3 15.0 - - + +
219B LEU* 4.4 3.5 + - + -
220B ALA* 4.2 18.0 - - + -
223B ASN* 5.9 0.5 - - - -
224B THR 3.9 6.4 + - - -
226B VAL* 3.6 28.8 - - + +
256B PHE* 2.8 45.5 + + + +
257B TYR 3.8 2.9 - - - +
259B GLN* 1.3 73.9 - - - +
261B ARG* 1.3 79.3 + - + +
263B VAL* 3.2 15.7 - - - +
265B GLY* 2.9 48.3 + - - -
266B HIS 3.6 1.9 + - - -
267B ASN* 3.1 29.8 + - - +
268B GLY 4.1 0.7 - - - -
270B PHE* 3.6 20.9 - + + -
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Residues in contact with ARG 261 (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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257B TYR* 3.2 43.5 + - + +
258B ASN* 4.1 3.6 - - - +
260B TYR* 1.3 86.7 - - + +
262B SER* 1.3 62.0 + - - +
264B GLY* 3.3 13.2 + - - -
265B GLY 3.5 21.1 + - - +
266B HIS* 3.7 18.4 - - - +
268B GLY* 3.5 37.8 + - - +
270B PHE* 4.2 7.9 - - - -
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASN* 3.1 19.9 + - - +
259B GLN* 3.2 11.8 + - - -
261B ARG* 1.3 79.0 - - - +
263B VAL* 1.3 59.1 + - - +
264B GLY 3.3 1.4 + - - -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA* 3.8 28.0 - - + +
217B SER* 3.8 23.2 + - - +
220B ALA* 4.0 10.8 - - + +
221B GLN* 5.4 4.5 + - - +
259B GLN* 3.1 31.1 + - + +
260B TYR* 3.2 17.7 - - - +
262B SER* 1.3 77.8 - - - +
264B GLY* 1.3 57.7 + - - +
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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