Contacts of the helix formed by residues 236 - 248 (chain B) in PDB entry 2IZZ
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 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ARG* 3.9 4.3 - - - -
268A LEU* 4.4 11.7 - - - -
233B SER* 3.0 24.3 + - - -
234B PRO 3.1 2.6 - - - -
235B GLY* 1.3 77.8 - - - +
237B ALA* 1.3 63.9 + - - -
238B THR 3.4 2.2 - - - -
239B ILE* 3.3 9.7 - - - +
240B HIS* 2.8 25.1 + - - -
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Residues in contact with ALA 237 (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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97A ALA* 5.4 1.1 - - + -
171A THR* 4.6 5.6 - - + -
176A SER* 4.4 1.8 - - - +
261A SER* 3.3 29.2 - - - +
264A ARG* 3.7 13.5 - - + +
265A THR* 3.2 30.5 - - - +
268A LEU* 4.2 6.7 - - + +
1273A EDO 5.0 7.3 + - - +
236B GLY* 1.3 72.4 - - - -
238B THR* 1.3 65.4 + - - +
240B HIS* 3.3 5.0 + - - +
241B ALA 3.0 17.3 + - - -
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Residues in contact with THR 238 (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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176A SER* 2.8 31.1 + - - -
179A ALA* 3.5 33.0 - - + -
180A TYR* 5.4 0.7 - - + -
1273A EDO 2.9 24.6 + - - -
231B VAL* 3.8 15.9 - - + -
232B SER* 3.7 15.5 - - - +
233B SER 5.2 0.9 - - - -
236B GLY 3.4 0.6 - - - -
237B ALA* 1.3 77.6 - - - +
239B ILE* 1.3 58.9 + - - +
241B ALA* 3.0 5.1 + - - +
242B LEU* 2.8 30.1 + - + +
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Residues in contact with ILE 239 (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 SER* 4.4 8.4 - - - +
233B SER 3.9 6.2 + - - +
235B GLY 4.1 0.7 - - - +
236B GLY 3.3 28.9 - - - +
238B THR* 1.3 79.0 - - - +
240B HIS* 1.3 68.0 + - - +
242B LEU* 3.4 21.9 + - + -
243B HIS* 3.1 23.5 + - + +
255C ILE* 5.9 2.2 - - + -
190D ASP* 3.8 34.5 - - + +
193D VAL* 4.1 9.6 - - + +
194D LYS* 3.7 41.3 - - + +
199D ARG* 4.4 9.4 - - - +
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Residues in contact with HIS 240 (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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260A ALA* 4.2 9.1 - - + +
264A ARG* 3.2 51.3 + - + -
267A GLU* 5.3 1.5 + - - -
235B GLY 3.6 10.5 - - - -
236B GLY 2.8 18.5 + - - +
237B ALA 3.3 9.3 + - - +
238B THR 3.2 0.2 - - - -
239B ILE* 1.3 82.4 - - - +
241B ALA* 1.3 61.2 + - - +
243B HIS* 3.4 11.1 + - - +
244B VAL* 3.5 17.7 + - - +
194D LYS* 3.6 44.7 + - + +
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Residues in contact with ALA 241 (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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180A TYR* 3.4 27.1 - - + +
257A ALA* 3.2 29.8 - - - +
260A ALA* 4.1 8.2 - - - +
261A SER* 3.8 12.3 - - - -
237B ALA 3.0 6.1 + - - -
238B THR 3.0 5.8 + - - +
240B HIS* 1.3 72.5 - - - +
242B LEU* 1.3 65.7 + - - +
244B VAL* 3.2 8.8 - - - +
245B LEU* 3.2 22.2 + - - +
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Residues in contact with LEU 242 (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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179A ALA* 3.8 19.3 - - + +
180A TYR* 4.2 11.7 - - + -
183A THR* 3.5 25.4 - - + +
228B LYS* 3.7 26.0 - - + +
232B SER* 3.4 25.1 - - - +
238B THR* 2.8 25.2 + - + +
239B ILE* 3.8 16.2 - - + +
240B HIS 3.4 0.2 - - - -
241B ALA* 1.3 75.3 - - - +
243B HIS* 1.3 55.8 + - - +
245B LEU* 3.2 13.5 + - + +
246B GLU* 2.9 35.6 + - + +
255C ILE* 5.7 0.2 - - - -
190D ASP* 5.8 2.9 - - - +
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Residues in contact with HIS 243 (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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239B ILE* 3.1 13.3 + - - +
240B HIS 3.6 9.9 - - - +
241B ALA 3.2 0.4 - - - -
242B LEU* 1.3 76.4 - - - +
244B VAL* 1.3 57.6 + - + +
246B GLU* 3.2 6.1 + - - +
247B SER* 2.9 37.1 + - - -
252C SER* 3.7 6.9 + - - -
255C ILE* 3.5 43.6 - - + +
256C ASN* 2.6 33.0 + - - -
259C GLU* 3.7 12.3 - - - -
194D LYS* 2.8 32.4 + - + +
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Residues in contact with VAL 244 (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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253A LEU* 4.6 7.8 - - - +
256A ASN* 3.7 20.8 + - + +
257A ALA* 3.6 30.3 - - + +
260A ALA* 4.0 12.8 - - + -
240B HIS 3.5 11.6 + - - +
241B ALA 3.2 20.1 + - - +
243B HIS* 1.3 73.9 - - + +
245B LEU* 1.3 65.2 + - - +
247B SER* 3.4 7.7 + - - -
248B GLY* 3.3 17.2 + - - -
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Residues in contact with LEU 245 (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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180A TYR* 3.8 37.0 - - + -
183A THR* 5.0 4.7 - - + -
253A LEU* 3.4 32.8 - - + +
254A LEU* 4.2 4.0 - - + +
257A ALA* 3.9 8.3 - - + -
241B ALA 3.2 12.8 + - - +
242B LEU* 3.2 21.4 + - + +
244B VAL* 1.3 76.1 - - - +
246B GLU* 1.3 63.9 + - + +
248B GLY* 3.2 8.0 + - - -
250B PHE* 3.2 71.3 + - + +
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Residues in contact with GLU 246 (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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183A THR* 4.5 6.0 + - - +
242B LEU* 2.9 21.8 + - + +
243B HIS* 3.5 8.1 - - - +
245B LEU* 1.3 76.9 - - - +
247B SER* 1.3 58.6 + - - +
249B GLY* 3.0 20.4 + - - +
250B PHE* 4.9 1.5 + - - +
251B ARG* 2.9 41.8 + - - +
246C GLU* 4.5 1.9 - - - +
249C GLY* 4.0 7.6 - - - -
251C ARG* 3.4 27.5 + - - +
252C SER* 3.5 25.6 + - - -
255C ILE* 4.2 16.4 - - + -
190D ASP* 4.8 7.4 - - - +
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Residues in contact with SER 247 (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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243B HIS* 2.9 35.0 + - - -
244B VAL* 3.8 9.6 - - - -
245B LEU 3.3 0.6 - - - -
246B GLU* 1.3 76.8 - - - +
248B GLY* 1.3 59.0 + - - +
249B GLY 3.6 0.3 + - - -
249C GLY* 5.4 2.4 - - - -
252C SER* 3.5 15.4 + - - -
256C ASN* 4.3 5.2 + - - -
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Residues in contact with GLY 248 (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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248A GLY 4.7 3.5 - - - +
253A LEU* 3.5 30.6 - - - +
244B VAL 3.3 5.5 + - - -
245B LEU 3.2 6.5 + - - -
246B GLU 3.2 0.8 - - - -
247B SER* 1.3 77.7 - - - +
249B GLY* 1.3 61.7 + - - +
250B PHE 3.3 3.3 + - - -
253B LEU* 4.4 6.9 - - - +
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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