Contacts of the helix formed by residues 232 - 249 (chain A) in PDB entry 5I4E
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 GLY 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLY* 2.8 34.6 + - - -
230A VAL 3.6 0.6 + - - -
231A PRO* 1.3 76.8 - - - +
233A GLU* 1.3 67.1 + - - +
234A LEU 3.5 1.8 - - - -
235A GLU* 3.4 6.1 + - - +
236A ARG* 3.0 27.1 + - - +
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Residues in contact with GLU 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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224A GLY* 4.9 3.2 - - - -
232A GLY* 1.3 70.0 - - - +
234A LEU* 1.3 65.2 + - - +
236A ARG* 3.2 22.1 + - - +
237A GLN* 3.0 48.9 + - + +
354A VAL 5.5 0.7 - - - +
465A ARG* 3.7 24.4 + - - +
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Residues in contact with LEU 234 (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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224A GLY* 5.7 5.8 - - - -
232A GLY 3.5 0.2 - - - -
233A GLU* 1.3 77.3 - - - +
235A GLU* 1.3 57.0 + - - +
237A GLN* 3.5 1.9 + - - +
238A LEU* 3.0 46.7 + - + +
276A ILE* 4.0 20.2 - - + +
277A VAL* 3.8 29.2 - - - +
278A GLY* 4.0 4.5 - - - +
463A LEU* 4.0 30.5 - - + +
465A ARG* 3.9 34.3 - - - +
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Residues in contact with GLU 235 (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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216A ALA* 3.2 41.7 - - + +
217A HIS* 3.8 15.7 + - - +
220A SER* 4.2 15.5 + - - -
224A GLY* 4.6 3.7 + - - +
225A ARG* 5.3 5.0 - - - +
231A PRO* 3.4 32.1 - - + +
232A GLY 3.4 12.4 + - - +
233A GLU 3.3 0.6 - - - -
234A LEU* 1.3 77.1 - - - +
236A ARG* 1.4 64.7 + - - +
238A LEU* 3.3 7.4 + - - +
239A LEU* 3.1 38.4 + - + +
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Residues in contact with ARG 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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230A VAL* 5.2 4.8 - - - +
231A PRO* 3.1 40.0 + - + +
232A GLY* 3.0 19.8 + - - +
233A GLU* 3.7 23.3 + - - +
235A GLU* 1.4 74.8 - - - +
237A GLN* 1.3 61.1 + - - +
239A LEU* 3.6 6.3 + - - +
240A GLN* 3.1 28.8 + - + +
354A VAL* 3.8 25.4 + - + +
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Residues in contact with GLN 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 GLU* 3.0 37.2 + - + +
234A LEU 3.9 2.2 - - - +
236A ARG* 1.3 71.7 - - - +
238A LEU* 1.3 58.6 + - - +
240A GLN* 2.8 22.2 + - - -
241A ALA* 3.0 12.5 + - - +
354A VAL* 3.0 31.3 + - + +
355A LEU* 3.6 30.0 - - + +
356A GLY* 3.7 9.9 - - - +
462A ALA* 3.6 14.1 - - - +
463A LEU* 3.7 15.5 - - + +
465A ARG* 3.0 28.1 + - - -
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Residues in contact with LEU 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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212A ILE* 4.0 24.4 - - + +
216A ALA* 4.6 10.1 - - + -
234A LEU* 3.0 28.5 + - + +
235A GLU* 3.4 6.1 - - - +
237A GLN* 1.3 74.0 - - - +
239A LEU* 1.3 61.7 + - + +
240A GLN 3.8 0.2 + - - -
241A ALA* 3.9 11.4 + - - +
242A ASN* 4.8 4.7 + - - +
266A ILE* 6.0 2.2 - - + -
268A ILE* 5.1 11.4 - - + -
276A ILE* 3.9 39.0 - - + -
279A ALA* 3.5 30.7 - - + -
463A LEU* 3.6 16.9 - - + +
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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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209A LYS 5.4 0.4 - - - +
212A ILE* 3.6 27.4 - - + -
213A GLN* 3.9 23.8 - - + +
216A ALA* 3.8 22.4 - - + -
235A GLU* 3.1 25.8 + - + +
236A ARG* 4.0 5.2 - - - +
237A GLN 3.1 0.8 - - - -
238A LEU* 1.3 76.9 - - - +
240A GLN* 1.4 66.6 + - - +
241A ALA 3.3 3.1 - - - -
242A ASN* 4.4 3.0 + - - +
243A PRO* 3.4 18.9 - - - +
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Residues in contact with GLN 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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236A ARG* 3.1 19.4 + - + +
237A GLN 2.8 10.4 + - - +
239A LEU* 1.4 82.2 + - - +
241A ALA* 1.4 59.3 + - - +
242A ASN 3.6 0.7 - - - -
243A PRO* 3.7 13.2 - - - +
244A ILE* 3.1 28.9 + - - +
351A SER* 2.7 32.5 + - - +
354A VAL* 3.8 23.6 - - + -
355A LEU* 3.8 14.4 - - + -
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Residues in contact with ALA 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 GLN 3.0 8.6 + - - +
238A LEU 3.9 8.7 - - - +
239A LEU 3.3 1.0 - - - -
240A GLN* 1.4 76.8 - - - +
242A ASN* 1.4 66.5 + - - +
244A ILE* 3.5 11.0 + - - +
245A LEU* 3.2 28.2 + - - +
281A ILE* 4.5 11.0 - - + -
355A LEU* 4.7 0.7 - - + -
459A LEU* 4.1 8.7 - - + +
463A LEU* 3.5 31.6 - - + -
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Residues in contact with ASN 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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208A THR* 5.3 0.2 - - - +
209A LYS* 3.9 21.9 + - + +
212A ILE* 3.4 27.5 - - - +
238A LEU 4.8 3.6 + - - +
239A LEU* 4.4 3.5 + - - +
241A ALA* 1.4 75.2 - - - +
243A PRO* 1.4 66.3 - - + +
245A LEU* 3.0 12.8 + - - +
246A GLU* 2.8 44.9 + - + +
264A LYS* 3.4 36.8 + - - +
266A ILE* 4.0 10.1 - - - +
281A ILE* 5.7 1.2 - - - +
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Residues in contact with PRO 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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209A LYS* 5.5 5.2 - - + +
239A LEU 3.4 20.0 - - - +
240A GLN* 3.7 19.5 - - - +
242A ASN* 1.4 91.5 - - + +
244A ILE* 1.4 55.7 + - - +
246A GLU* 3.4 12.1 + - + +
247A ALA* 3.0 27.0 + - - +
348A THR* 5.1 3.0 + - - -
351A SER* 4.2 14.6 - - - +
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Residues in contact with ILE 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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240A GLN 3.1 23.3 - - - +
241A ALA 3.5 6.9 + - - +
242A ASN 3.1 0.8 - - - -
243A PRO* 1.4 73.4 - - - +
245A LEU* 1.3 65.0 + - - +
247A ALA* 3.4 11.3 + - - +
248A PHE* 3.4 21.0 + - + -
348A THR* 4.9 5.4 - - + +
351A SER* 3.5 38.6 - - - +
352A LEU* 3.9 22.2 - - + +
355A LEU* 3.6 22.4 - - + -
357A PHE* 4.9 0.2 - - + -
455A LEU* 3.6 33.5 - - + +
459A LEU* 3.9 12.3 - - + -
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Residues in contact with LEU 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 ALA 3.2 18.0 + - - +
242A ASN* 3.0 18.1 + - - +
244A ILE* 1.3 74.6 - - - +
246A GLU* 1.3 55.3 + - + +
248A PHE* 3.4 0.9 + - - +
249A GLY* 2.7 35.7 + - - -
262A PHE* 3.8 17.9 - - + -
264A LYS* 4.5 10.1 - - + -
281A ILE* 3.9 32.1 - - + -
283A THR* 4.8 1.3 - - + -
452A PHE* 4.0 14.6 - - + -
455A LEU* 4.5 8.3 - - + -
456A VAL* 3.7 26.2 - - + -
459A LEU* 3.6 19.7 - - + -
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Residues in contact with GLU 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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205A THR* 3.6 11.9 - - + +
209A LYS* 3.2 41.2 + - - +
242A ASN* 2.8 25.6 + - + +
243A PRO* 3.8 9.3 - - + +
245A LEU* 1.3 79.4 - - + +
247A ALA* 1.3 58.1 + - - +
250A ASN* 3.0 57.4 + - + +
258A ASN* 3.2 22.6 + - - +
262A PHE* 5.7 2.2 - - + -
264A LYS* 5.8 4.3 - - - -
302A HIS* 3.8 5.2 - - - -
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Residues in contact with ALA 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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243A PRO 3.0 16.9 + - - +
244A ILE 3.7 6.3 - - - +
245A LEU 3.3 0.6 - - - -
246A GLU* 1.3 78.0 - - - +
248A PHE* 1.3 64.8 + - + +
301A PHE* 4.3 0.2 - - - +
302A HIS* 3.7 12.6 + - - -
303A ILE* 2.9 32.0 + - + +
306A GLN* 4.3 10.3 - - - +
348A THR* 3.8 33.4 - - + +
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Residues in contact with PHE 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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244A ILE* 3.4 16.4 + - + +
245A LEU 3.4 2.5 + - - +
247A ALA* 1.3 84.1 - - + +
249A GLY* 1.3 55.9 + - - +
286A LEU* 4.7 0.3 - - - +
301A PHE* 3.0 12.5 - - - -
303A ILE* 3.6 28.3 - - + -
348A THR* 4.6 7.9 - - + -
352A LEU* 5.0 2.0 - - + -
365A MET* 3.4 34.3 - - + -
366A LEU* 5.0 3.8 - - + -
369A VAL* 3.8 25.1 - - + -
448A TYR* 2.7 44.7 + + + +
451A LEU* 4.0 18.4 - - + -
452A PHE* 4.5 14.1 - - + -
455A LEU* 3.7 25.1 - - + -
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Residues in contact with GLY 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 LEU 2.7 19.1 + - - -
248A PHE* 1.3 75.7 - - - +
250A ASN* 1.3 62.4 + - - +
261A ARG* 3.0 32.1 + - - +
262A PHE* 3.4 19.2 - - - -
286A LEU* 4.3 4.7 - - - -
301A PHE* 3.7 9.9 - - - -
452A PHE* 4.6 2.5 - - - -
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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