Contacts of the helix formed by residues 236 - 253 (chain D) in PDB entry 4J1R
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 SER 236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D HIS* 3.2 55.3 + - - +
176D GLY 5.9 2.7 - - - -
177D ILE 4.6 2.0 - - - -
178D CYS* 3.6 22.4 - - - -
207D LEU* 4.0 4.5 - - - +
235D THR* 1.3 71.0 - - - +
237D SER* 1.3 55.9 + - - +
238D ILE 3.0 5.8 - - - -
239D ASP* 3.0 17.9 + - - +
240D VAL* 3.9 1.1 + - - -
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Residues in contact with SER 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D GLU* 4.3 1.6 + - - -
235D THR* 2.7 24.9 + - - -
236D SER* 1.3 77.3 + - - +
238D ILE* 1.3 63.8 + - - +
239D ASP 3.2 0.4 - - - -
240D VAL* 3.3 18.3 - - - +
241D TRP 3.3 11.3 + - - -
325D PRO* 3.5 37.5 - - - +
328D ARG* 2.8 21.5 + - - -
329D LEU 5.9 0.2 - - - -
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Residues in contact with ILE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D CYS* 3.6 27.6 - - - -
180D ARG* 4.1 14.4 - - + -
217D ILE* 4.9 1.1 - - + -
218D CYS* 5.8 2.9 - - + -
224D ALA* 3.8 15.6 - - + +
226D GLU* 3.3 22.0 - - + +
227D LEU* 4.1 17.7 - - + -
234D TYR* 3.7 37.2 - - + -
235D THR 3.2 12.3 - - - +
236D SER 3.0 0.8 - - - -
237D SER* 1.3 76.6 - - - +
239D ASP* 1.3 72.9 + - - +
241D TRP* 3.1 5.4 + - - +
242D SER* 3.1 25.4 + - - +
328D ARG* 3.7 6.7 - - - +
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Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 4.2 7.8 - - + +
172D ILE* 4.6 0.3 - - - +
173D HIS* 3.1 25.5 - - + +
178D CYS* 3.3 13.0 - - - -
179D HIS* 2.7 28.8 + - - +
180D ARG* 3.0 24.5 + - - -
182D ILE* 3.8 23.8 + - + +
236D SER 3.0 9.2 + - - +
238D ILE* 1.3 84.2 - - - +
240D VAL* 1.3 50.9 + - - +
242D SER* 3.2 6.9 + - - -
243D ALA* 2.8 33.8 + - - +
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D PHE* 5.2 4.5 - - + -
169D LEU* 5.0 3.1 - - + -
173D HIS* 4.8 2.2 - - + +
236D SER 4.2 3.4 - - - +
237D SER* 3.3 24.7 - - - +
239D ASP* 1.3 74.6 - - - +
241D TRP* 1.3 65.2 + - - +
243D ALA* 3.3 7.5 + - - +
244D GLY* 3.0 19.8 + - - -
320D LEU* 3.8 28.4 - - + +
328D ARG* 4.1 14.6 - - + -
329D LEU 3.3 27.4 - - - +
330D THR 5.7 0.4 - - - -
331D PRO* 4.4 24.7 - - + -
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Residues in contact with TRP 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D TYR 5.0 0.4 + - - -
222D TYR 3.5 12.3 - - - -
223D ARG 3.3 11.5 + - - -
224D ALA* 3.5 17.7 - - + -
225D PRO* 3.4 29.6 - - + -
237D SER 3.3 2.6 + - - -
238D ILE 3.1 10.4 + - - +
240D VAL* 1.3 77.5 - - - +
242D SER* 1.3 66.5 + - - +
244D GLY 3.0 11.3 + - - -
245D CYS* 3.0 23.7 + - - -
257D PHE* 3.5 24.1 - + - -
269D ILE* 3.5 21.4 - - + +
273D LEU* 3.7 21.8 - - + -
320D LEU 4.4 6.7 - - - -
321D LEU* 3.4 39.1 - - + +
322D GLU 3.5 26.9 - - - -
328D ARG* 3.8 19.9 - - - +
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ILE* 3.4 31.3 - - - +
218D CYS* 3.5 14.2 - - - -
222D TYR* 2.6 31.3 + - - -
224D ALA 5.1 0.3 + - - -
238D ILE 3.1 11.1 + - - -
239D ASP* 3.2 10.6 + - - -
241D TRP* 1.3 78.8 - - - +
243D ALA* 1.3 62.6 + - - +
245D CYS* 3.1 6.2 + - - +
246D VAL* 3.0 25.1 + - - +
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D MET* 3.3 12.3 - - - +
165D LEU* 4.0 20.0 - - + -
166D PHE* 3.8 25.4 - - + -
169D LEU* 4.3 7.6 - - + -
182D ILE* 4.1 8.0 - - + +
239D ASP 2.8 16.5 + - - +
240D VAL* 3.5 7.2 - - - +
242D SER* 1.3 78.2 - - - +
244D GLY* 1.3 56.6 + - - +
246D VAL* 3.0 3.8 + - - +
247D LEU 2.9 24.3 + - - -
320D LEU* 4.5 0.7 - - - -
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Residues in contact with GLY 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D VAL 3.0 12.2 + - - -
241D TRP 3.0 4.9 + - - -
243D ALA* 1.3 75.6 - - - +
245D CYS* 1.3 56.9 + - - +
247D LEU* 3.4 3.8 + - - +
248D ALA* 3.0 29.6 + - - +
317D CYS* 4.4 2.8 - - - -
320D LEU* 3.5 25.0 - - - +
321D LEU* 3.9 18.6 - - - +
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Residues in contact with CYS 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D TYR 3.7 16.2 - - - +
222D TYR* 3.5 21.7 - - + -
241D TRP* 3.0 43.0 + - - -
242D SER 3.1 10.0 + - - +
244D GLY* 1.3 75.9 - - - +
246D VAL* 1.3 56.1 + - - +
248D ALA* 3.7 1.6 + - - +
249D GLU* 3.1 30.1 + - - +
256D ILE* 4.4 14.0 + - + +
257D PHE* 3.9 17.7 - - - -
321D LEU* 4.0 5.8 - - - -
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Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D VAL* 5.0 2.9 - - + -
162D MET* 4.0 15.7 - - + -
165D LEU* 4.8 1.3 - - + -
182D ILE* 4.3 15.3 - - + -
183D LYS* 4.4 1.6 - - - -
184D PRO* 3.9 34.1 - - + -
187D LEU* 4.2 20.4 - - + -
222D TYR* 4.3 7.2 - - + -
242D SER 3.0 21.2 + - - +
243D ALA* 3.0 8.5 + - - +
245D CYS* 1.3 72.2 - - - +
247D LEU* 1.3 68.0 + - - +
249D GLU* 3.3 6.8 + - - +
250D LEU* 3.0 38.2 + - + +
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D VAL* 3.7 27.1 - - + -
162D MET* 3.8 23.7 - - + -
243D ALA 2.9 11.5 + - - +
244D GLY* 3.6 7.9 - - - +
246D VAL* 1.3 78.3 - - - +
248D ALA* 1.3 62.6 + - - +
250D LEU* 3.1 14.3 + - - +
251D LEU* 3.1 21.1 + - + +
313D ALA* 4.3 4.5 - - + +
316D LEU* 3.7 35.0 - - + -
317D CYS* 3.6 24.9 - - - -
320D LEU* 4.2 9.2 - - + -
339D PHE* 4.3 10.3 - - + -
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Residues in contact with ALA 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D GLY 3.0 18.1 + - - +
245D CYS 3.9 0.2 - - - +
247D LEU* 1.3 76.8 - - - +
249D GLU* 1.3 58.4 + - - +
251D LEU* 3.2 3.3 + - - +
252D LEU* 2.9 34.9 + - + +
256D ILE* 3.9 38.8 - - + -
305D PHE* 4.2 16.4 - - + -
317D CYS* 4.2 9.2 - - - -
321D LEU* 4.8 1.3 - - + -
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Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D TYR* 4.8 12.1 - - - -
143D ALA* 5.5 10.6 - - + +
184D PRO* 4.2 13.4 - - + +
222D TYR* 2.8 39.5 + - - -
245D CYS 3.1 13.6 + - - +
246D VAL* 3.6 5.6 - - - +
247D LEU 3.2 0.2 - - - -
248D ALA* 1.3 79.3 - - - +
250D LEU* 1.3 61.0 + - + +
253D GLY* 2.8 28.4 + - - -
254D GLN* 3.4 26.9 - - - +
255D PRO* 3.8 25.7 - - + +
256D ILE 5.0 0.8 - - - +
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Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D VAL* 3.9 27.1 - - + -
143D ALA* 3.9 22.7 - - + -
152D THR* 3.7 11.1 + - - +
153D LEU* 4.5 25.9 + - + +
158D VAL* 4.1 37.8 - - + +
161D TYR* 5.1 7.9 - - + -
162D MET* 4.3 15.3 - - + -
184D PRO* 6.2 2.0 - - + -
246D VAL* 3.0 30.3 + - + +
247D LEU* 3.1 7.6 + - - +
249D GLU* 1.3 79.9 - - + +
251D LEU* 1.3 62.0 + - - +
253D GLY* 4.4 1.4 + - - -
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D THR* 3.3 16.3 + - + +
155D VAL* 5.7 6.1 - - + -
158D VAL* 4.5 19.3 - - + -
247D LEU* 3.1 24.1 + - + +
248D ALA 3.2 5.8 + - - +
250D LEU* 1.3 80.6 - - - +
252D LEU* 1.3 60.0 + - - +
253D GLY 3.7 0.2 - - - -
305D PHE* 4.1 26.7 - - + -
306D ARG* 3.7 18.5 - - - -
309D THR* 4.3 18.9 + - + +
310D PRO* 5.0 6.7 - - + -
313D ALA* 3.7 34.5 - - + -
314D ILE 4.8 0.2 - - - +
317D CYS* 4.3 10.3 - - - -
339D PHE* 5.4 1.1 - - + -
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D THR* 4.4 2.6 + - - -
248D ALA 2.9 18.2 + - - +
251D LEU* 1.3 79.4 - - - +
253D GLY* 1.3 58.4 + - - +
254D GLN* 3.2 31.8 + - + +
256D ILE* 4.0 34.1 - - + -
304D VAL* 3.5 28.0 - - + +
305D PHE* 3.6 30.3 - - + -
306D ARG* 4.0 25.7 + - + +
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Residues in contact with GLY 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ALA* 5.6 4.0 - - - -
147D SER* 3.1 34.3 + - - -
151D GLN 5.5 3.1 - - - -
152D THR* 4.4 7.1 + - - -
249D GLU* 2.8 14.4 + - - -
250D LEU 4.3 1.9 - - - -
251D LEU 3.7 1.4 - - - -
252D LEU* 1.3 77.1 - - - +
254D GLN* 1.3 61.7 + - - +
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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
------------------------------------------------------------
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