Contacts of the helix formed by residues 226 - 238 (chain B) in PDB entry 2EZT
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 ALA 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ALA* 2.8 19.4 + - + +
225B LYS* 1.3 78.9 - - - +
227B GLY* 1.3 65.2 + - - +
228B LYS 3.3 3.1 - - - -
229B GLU* 3.3 11.4 + - + +
230B LEU* 2.9 24.8 + - + +
327B GLN* 3.7 28.3 - - + +
330B LEU* 3.7 20.6 - - + -
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Residues in contact with GLY 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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223B ALA 3.9 3.2 + - - -
224B ARG 4.4 2.4 + - - -
225B LYS 3.5 3.0 - - - -
226B ALA* 1.3 75.6 - - - +
228B LYS* 1.3 61.8 + - - +
230B LEU 3.5 0.2 + - - -
231B GLU* 3.2 27.1 + - - +
250B ILE* 3.5 34.1 - - - +
251B VAL* 3.7 8.7 - - - +
409B PRO* 5.9 2.2 - - - -
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Residues in contact with LYS 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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225B LYS 5.2 0.8 + - - +
226B ALA 3.3 0.2 - - - -
227B GLY* 1.3 77.1 - - - +
229B GLU* 1.3 67.3 + - - +
231B GLU* 4.0 3.9 - - - +
232B GLN* 3.0 30.7 + - + +
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Residues in contact with GLU 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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225B LYS 3.8 2.9 - - - +
226B ALA* 3.3 24.2 + - + +
228B LYS* 1.3 83.0 - - + +
230B LEU* 1.3 59.8 + - - +
232B GLN* 3.7 0.5 - - - +
233B LEU* 2.8 40.8 + - + +
327B GLN* 3.6 26.9 + - - +
330B LEU* 4.0 18.2 - - + -
331B ALA* 4.0 30.0 - - + +
334B LEU* 4.4 15.4 - - + +
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Residues in contact with LEU 230 (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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217B ILE* 3.7 30.1 - - + -
219B TYR* 3.6 44.4 - - + -
223B ALA* 4.0 14.4 - - + -
226B ALA 2.9 24.2 + - - +
227B GLY 3.8 3.6 - - - +
229B GLU* 1.3 75.6 - - - +
231B GLU* 1.3 58.3 + - - +
233B LEU* 3.5 6.0 + - - +
234B SER* 3.0 29.6 + - - -
241B LEU* 3.8 12.3 - - + +
250B ILE* 4.1 7.9 - - + -
251B VAL* 3.9 7.2 - - + -
283B VAL* 5.2 0.7 - - + -
330B LEU* 3.7 24.7 - - + +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLY 3.2 14.9 + - - +
228B LYS* 4.0 3.4 - - - +
230B LEU* 1.3 80.3 - - - +
232B GLN* 1.3 55.6 + - - +
234B SER* 3.5 2.1 + - - -
235B LYS* 3.0 56.7 + - + +
241B LEU* 4.1 9.3 - - - +
251B VAL* 3.8 20.3 - - + +
252B ALA* 4.7 7.1 + - - +
255B TYR* 3.9 31.2 - - + +
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Residues in contact with GLN 232 (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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228B LYS* 3.0 19.7 + - + +
229B GLU 4.0 2.2 - - - +
231B GLU* 1.3 74.9 - - - +
233B LEU* 1.3 64.9 + - - +
235B LYS* 4.0 23.8 + - - +
236B THR* 2.9 53.0 + - - +
334B LEU* 4.1 24.0 - - + -
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Residues in contact with LEU 233 (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* 6.0 0.2 - - + -
217B ILE* 4.3 16.8 - - + -
229B GLU 2.8 34.6 + - - +
230B LEU* 3.6 5.4 - - - +
232B GLN* 1.3 71.5 - - - +
234B SER* 1.3 58.7 + - - +
236B THR* 4.6 0.9 - - - -
237B LEU* 2.9 60.7 + - + +
281B LEU* 6.3 0.7 - - + -
330B LEU* 3.5 41.1 - - + +
333B ILE* 3.7 23.3 - - + -
334B LEU* 3.8 26.3 - - + +
337B VAL* 4.3 1.8 - - + -
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Residues in contact with SER 234 (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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217B ILE* 4.7 1.2 - - - +
230B LEU 3.0 15.0 + - - -
231B GLU 3.6 2.7 - - - -
233B LEU* 1.3 78.4 - - - +
235B LYS* 1.3 56.0 - - - +
238B LYS* 2.9 28.1 + - - -
239B ILE* 2.5 36.4 + - - +
241B LEU* 3.6 19.1 - - - +
255B TYR* 2.7 28.4 + - - -
257B ALA* 4.1 0.9 - - - +
346B TRP* 3.7 6.1 - - - -
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Residues in contact with LYS 235 (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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231B GLU* 3.0 45.7 + - + +
232B GLN* 3.8 24.1 + - - +
233B LEU 3.4 0.2 - - - -
234B SER* 1.3 77.2 - - - +
236B THR* 1.3 60.3 + - - +
238B LYS* 2.9 28.8 + - - +
255B TYR* 3.3 28.5 + - + +
256B PRO* 6.0 0.2 - - - -
339B GLU* 4.5 0.7 - - - +
346B TRP* 4.4 6.9 - - + -
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Residues in contact with THR 236 (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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232B GLN* 2.9 39.1 + - - +
233B LEU* 3.9 3.6 - - - -
235B LYS* 1.3 75.8 - - - +
237B LEU* 1.3 65.0 - - + +
238B LYS* 3.2 9.5 + - - -
334B LEU* 4.5 5.5 - - + +
337B VAL* 4.5 7.0 - - + -
338B SER* 3.5 33.2 - - - +
339B GLU* 3.6 14.9 + - - +
340B ARG 2.9 26.0 + - - -
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.7 5.6 - - + -
210B LEU* 3.8 29.6 - - + -
233B LEU* 2.9 43.7 + - + +
236B THR* 1.3 76.7 - - + +
238B LYS* 1.3 66.9 + - - +
239B ILE* 3.6 24.5 - - + -
333B ILE* 5.0 0.9 - - + -
337B VAL* 3.8 29.4 - - + -
338B SER 3.8 16.4 - - - +
340B ARG* 2.8 45.9 + - + +
343B THR* 5.5 0.2 - - - +
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Residues in contact with LYS 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PRO* 4.8 1.0 - - - +
234B SER 2.9 11.9 + - - -
235B LYS 2.9 23.5 + - - +
236B THR 3.2 5.3 + - - -
237B LEU* 1.3 80.4 - - - +
239B ILE* 1.3 57.1 + - - +
240B PRO* 3.8 3.6 - - - +
339B GLU* 2.6 29.9 + - - -
340B ARG* 2.6 29.4 + - - +
341B GLU* 3.6 15.9 - - - +
342B SER* 3.9 14.1 - - - +
343B THR* 4.5 8.8 + - + +
345B TRP* 4.7 4.2 - - - -
346B TRP* 3.3 59.5 - - + +
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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