Contacts of the helix formed by residues 232 - 250 (chain A) in PDB entry 1JQP
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLN* 3.6 1.0 - - - +
230A CYS* 2.7 28.0 + - - -
231A GLY* 1.3 71.7 - - - -
233A CYS* 1.3 65.7 + - - +
234A TYR* 3.2 10.8 - - - -
235A SER* 2.8 21.9 + - - -
236A PHE* 3.2 18.1 - - - -
264A VAL* 3.6 21.3 - - - -
299A TYR* 2.7 26.1 + - - -
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Residues in contact with CYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 3.5 20.7 - - - +
231A GLY* 4.3 12.6 - - - -
232A SER* 1.3 76.4 - - - +
234A TYR* 1.3 72.2 + - - +
235A SER 2.9 1.6 + - - -
236A PHE* 2.9 14.0 + - - +
237A ALA* 2.9 13.7 + - - +
275A GLY* 6.0 1.6 - - - -
379A ASN 4.8 3.6 - - - -
380A HIS* 3.4 43.5 - - + +
381A ALA* 3.6 19.6 - - - +
403A SER* 4.2 4.7 - - - -
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Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLY 3.2 25.8 - - - -
232A SER* 3.7 5.8 - - - -
233A CYS* 1.3 83.1 - - - +
235A SER* 1.3 72.3 + - - +
237A ALA* 4.0 1.5 - - - +
238A SER* 2.8 33.8 + - - -
263A VAL* 3.9 10.1 - - + -
264A VAL* 4.1 10.9 - - - +
270A ALA* 3.5 27.5 - - + +
272A GLY* 2.7 25.4 + - - -
275A GLY* 3.2 17.0 - - - -
276A GLY* 3.1 39.5 - - - +
277A PHE* 3.9 2.0 - - - +
278A PRO* 4.1 9.6 - - + +
281A ILE* 3.8 19.5 - - + -
381A ALA* 3.5 16.3 - - + +
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 2.8 26.7 + - - -
234A TYR* 1.3 95.4 - - - +
236A PHE* 1.3 57.3 + - - -
238A SER* 3.5 3.6 + - - -
239A LEU* 3.1 35.8 + - - +
260A PRO* 3.2 37.2 + - - +
263A VAL* 3.6 13.4 - - - +
264A VAL* 4.7 0.4 - - - -
281A ILE* 5.0 0.7 - - - -
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Residues in contact with PHE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ARG* 3.7 44.2 - - + -
226A ASN 4.2 1.6 - - - -
227A GLN* 3.4 24.0 - - + -
232A SER* 3.2 40.8 + - - -
233A CYS* 2.9 6.4 + - - +
235A SER* 1.3 73.7 - - - +
237A ALA* 1.3 57.6 + - - +
239A LEU* 4.9 2.9 - - - -
240A GLY* 2.7 34.2 + - - +
260A PRO* 3.7 31.6 - - + -
299A TYR* 3.6 26.5 - + - -
383A LEU* 5.7 0.2 - - - +
403A SER* 3.9 22.2 - - - -
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A CYS 2.9 14.4 + - - +
234A TYR 4.0 1.8 - - - +
236A PHE* 1.3 79.0 - - - +
238A SER* 1.3 62.1 + - - +
241A MET* 3.1 22.9 + - - +
278A PRO* 4.6 0.9 - - + -
346A ALA* 4.5 11.9 - - + +
381A ALA* 3.7 24.4 + - + +
382A VAL* 3.7 29.2 - - - +
383A LEU* 3.8 11.8 - - - +
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A TYR 2.8 22.4 + - - -
235A SER 3.7 2.7 - - - -
236A PHE 3.3 0.2 - - - -
237A ALA* 1.3 76.2 - - - +
239A LEU* 1.3 63.3 + - - +
241A MET* 3.2 13.1 + - - +
242A LEU* 3.3 17.9 + - - +
278A PRO* 3.1 28.5 - - - +
281A ILE* 3.5 16.1 - - - +
282A ALA* 3.3 30.9 + - - +
346A ALA* 5.3 0.9 - - - -
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A SER* 3.1 16.6 + - - +
236A PHE* 4.3 2.7 - - + +
238A SER* 1.3 76.9 - - - +
240A GLY* 1.3 60.8 + - - +
242A LEU* 3.7 9.8 - - + +
243A GLU* 2.8 42.1 + - - +
258A LEU* 3.9 27.4 - - + -
259A SER 3.4 15.9 - - - +
260A PRO* 3.3 44.4 - - + -
263A VAL* 4.4 7.0 - - + -
281A ILE* 5.1 1.6 - - + -
282A ALA* 6.1 0.2 - - - -
291A VAL* 3.9 27.1 - - + -
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A VAL* 5.8 0.2 - - - +
222A SER* 4.7 5.3 + - - -
236A PHE 2.7 24.5 + - - -
237A ALA 3.9 1.3 - - - -
239A LEU* 1.3 73.7 - - - +
241A MET* 1.3 59.5 + - - +
243A GLU* 3.7 13.9 + - - +
244A ALA* 3.2 19.1 + - - +
383A LEU* 3.5 22.8 - - - +
401A LYS* 4.9 5.4 - - - -
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Residues in contact with MET 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ALA 3.1 7.5 + - - +
238A SER 3.5 5.4 - - - +
239A LEU 3.1 0.6 - - - -
240A GLY* 1.3 74.3 - - - +
242A LEU* 1.3 62.8 + - + +
244A ALA* 3.3 2.9 + - - +
245A ARG* 2.8 47.9 + - - +
282A ALA* 3.7 26.7 - - + -
344A PRO 3.3 21.5 - - - +
345A MET* 3.5 14.6 - - - -
346A ALA* 3.9 6.3 - - + +
383A LEU* 3.6 19.7 - - + +
430A MET* 3.6 17.7 - - - +
431A ALA* 3.6 6.5 - - - -
432A ALA* 3.3 33.9 - - + +
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A SER 3.3 12.1 + - - +
239A LEU* 3.7 13.5 - - + +
241A MET* 1.3 81.6 - - + +
243A GLU* 1.3 63.3 + - - +
246A ILE* 3.0 34.3 + - + +
258A LEU* 3.8 12.8 - - + -
282A ALA* 4.0 14.1 - - + +
286A ALA* 4.2 15.9 - - + -
291A VAL* 4.0 27.8 - - + -
315A TYR* 5.9 2.5 - - + +
316A TYR 6.1 1.6 - - - +
317A SER* 3.6 19.1 - - - +
432A ALA* 4.2 13.0 - - + -
434A PRO* 3.9 24.4 - - + +
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A SER* 2.6 37.6 + - - +
225A ARG* 5.2 5.5 + - - -
239A LEU* 2.8 29.5 + - - +
240A GLY* 3.7 9.0 - - - +
242A LEU* 1.3 77.9 - - - +
244A ALA* 1.3 62.3 + - - +
246A ILE* 3.7 7.5 - - - +
247A ARG* 3.2 29.8 + - - +
256A PRO* 3.4 25.3 - - - +
257A ILE* 3.7 9.1 - - - +
258A LEU* 2.8 43.3 + - + +
401A LYS* 4.8 0.2 + - - -
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE 3.3 21.9 - - - +
221A VAL* 4.5 9.0 - - + +
222A SER 5.1 1.1 - - - +
240A GLY 3.2 15.8 + - - +
241A MET 3.8 2.5 - - - +
243A GLU* 1.3 75.5 - - - +
245A ARG* 1.3 67.2 + - - +
247A ARG* 3.1 4.4 + - - +
248A ILE* 3.0 28.6 + - + +
344A PRO* 3.9 28.7 - - + -
383A LEU* 5.0 2.5 - - + -
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Residues in contact with ARG 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A MET* 2.8 26.5 + - - +
244A ALA* 1.3 76.7 - - - +
246A ILE* 1.3 56.8 + - - +
248A ILE* 3.5 8.3 + - - +
249A LEU* 3.1 34.2 + - + +
321A TYR* 4.5 0.2 + - - -
338A GLU* 2.8 34.5 + - - +
342A HIS* 3.1 32.5 + - - +
343A GLY* 3.0 23.8 + - - -
344A PRO 3.0 18.8 + - - +
345A MET* 4.1 2.2 - - - +
431A ALA* 3.5 20.4 - - - +
432A ALA 2.8 30.6 + - - +
433A ILE* 3.8 8.5 - - - +
434A PRO* 3.6 20.6 - - + -
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Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.0 30.9 + - + +
243A GLU* 3.7 4.5 - - - +
244A ALA 3.2 0.2 - - - -
245A ARG* 1.3 74.0 - - - +
247A ARG* 1.3 64.8 + - - +
249A LEU* 3.4 6.0 + - - +
250A THR* 3.0 29.1 + - - +
254A GLN* 3.9 34.8 - - + +
256A PRO* 3.9 19.5 - - + -
258A LEU* 5.2 4.9 - - + -
315A TYR* 3.9 30.7 - - + -
434A PRO* 3.6 23.8 - - + -
435A ILE 4.8 0.4 - - - +
436A PRO* 4.5 15.9 - - + -
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASN* 3.1 28.7 + - - +
220A PHE* 3.5 27.3 + - + +
221A VAL 3.7 14.5 + - - -
222A SER* 3.9 15.5 - - - +
223A PRO* 5.0 3.8 - - - +
243A GLU* 3.2 16.4 - - - +
244A ALA 3.1 7.5 + - - +
246A ILE* 1.3 77.4 - - - +
248A ILE* 1.3 61.7 + - - +
250A THR* 3.3 1.0 + - - -
251A ASN* 3.0 4.0 + - - -
252A ASN* 2.7 58.8 + - - +
254A GLN 3.2 21.3 - - - +
255A THR* 3.6 28.7 - - - +
256A PRO* 5.1 0.7 - - + -
257A ILE* 6.1 1.4 - - - +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TRP* 3.5 50.3 - - + -
220A PHE* 3.6 32.1 - - + -
244A ALA 3.0 17.7 + - - +
245A ARG* 3.7 7.4 - - - +
247A ARG* 1.3 73.7 - - - +
249A LEU* 1.3 70.4 + - + +
250A THR 3.2 0.7 + - - -
251A ASN* 3.3 10.0 + - - -
341A LYS 6.1 1.3 - - - +
342A HIS 4.5 5.6 - - - +
343A GLY* 3.9 15.0 - - - -
344A PRO* 3.9 6.7 - - + -
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ARG* 3.1 23.3 + - + +
246A ILE* 3.8 5.6 - - - +
247A ARG 3.4 0.2 - - - -
248A ILE* 1.3 81.9 - - + +
250A THR* 1.3 60.3 + - - +
251A ASN 3.8 0.7 + - - -
433A ILE* 5.1 6.5 - - + -
434A PRO* 3.6 35.2 - - + +
436A PRO* 4.1 20.4 - - + -
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Residues in contact with THR 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ILE 3.0 18.0 + - - +
247A ARG 3.5 3.6 + - - -
249A LEU* 1.3 81.2 - - - +
251A ASN* 1.3 66.3 + - - +
252A ASN 2.8 1.5 + - - -
253A SER* 2.6 34.9 + - - -
254A GLN* 3.1 51.0 + - + +
436A PRO* 4.0 15.7 - - + -
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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