Contacts of the helix formed by residues 232 - 244 (chain B) in PDB entry 2IHU
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 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B ALA 3.0 16.5 + - - +
228B ILE 4.2 0.2 + - - -
230B SER* 4.4 1.1 - - - -
231B GLY* 1.3 77.5 - - - +
233B VAL* 1.3 59.5 + - - +
234B PRO* 3.5 1.8 - - - -
235B ALA* 3.3 3.9 + - - +
236B ILE* 2.8 40.6 + - + +
339B VAL* 3.9 24.2 - - + -
340B LEU* 4.0 26.9 - - + +
343B VAL* 4.7 2.0 - - + -
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Residues in contact with VAL 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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223B VAL* 6.2 0.2 - - + -
227B ALA* 4.2 1.1 + - + -
228B ILE* 3.7 38.8 - - + +
231B GLY* 3.5 0.6 - - - -
232B ALA* 1.3 76.7 - - - +
234B PRO* 1.4 74.2 - - + +
236B ILE* 3.7 7.5 - - + +
237B ARG* 2.9 24.9 + - + +
256B VAL* 3.5 37.4 - - + +
426B PRO* 4.0 24.9 - - + -
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Residues in contact with PRO 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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231B GLY 4.1 10.5 - - - +
232B ALA 3.8 1.6 - - - -
233B VAL* 1.4 96.5 - - + +
235B ALA* 1.3 57.8 + - - +
237B ARG* 3.3 9.0 + - + +
238B ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLY 5.5 0.2 - - - +
232B ALA 3.3 5.3 + - - +
234B PRO* 1.3 79.3 - - - +
236B ILE* 1.3 58.7 + - - +
238B ALA* 3.5 6.1 + - - +
239B LEU* 3.1 28.1 + - - +
340B LEU* 3.6 30.7 - - + -
343B VAL* 3.7 20.3 - - + +
344B GLU* 5.3 3.8 - - + -
347B GLU* 4.1 3.0 - - + +
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Residues in contact with ILE 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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221B LEU* 4.1 20.6 - - + +
223B VAL* 4.3 21.5 - - + -
227B ALA* 3.7 31.0 - - + -
232B ALA* 2.8 30.7 + - + +
233B VAL* 3.7 7.2 - - + +
235B ALA* 1.3 69.4 - - - +
237B ARG* 1.3 61.7 + - - +
239B LEU* 3.4 7.5 + - + +
240B ALA* 3.0 28.1 + - - +
247B VAL* 4.9 8.1 - - + -
256B VAL* 6.1 3.8 - - + -
257B LEU* 6.4 0.2 - - + -
294B VAL* 3.9 17.3 - - + -
339B VAL* 4.4 0.7 - - + -
343B VAL* 3.9 19.7 - - + -
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Residues in contact with ARG 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 2.9 18.8 + - - +
234B PRO* 3.5 8.7 - - + +
236B ILE* 1.3 77.2 - - - +
238B ALA* 1.3 56.4 + - - +
240B ALA* 3.4 3.5 + - - +
241B GLU* 3.0 59.2 + - - +
256B VAL 4.7 6.1 - - - +
257B LEU* 3.6 28.9 - - + -
258B PRO* 3.5 34.0 - - - +
261B HIS* 4.2 7.4 + - - -
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PRO 2.9 16.9 + - - +
235B ALA* 3.9 7.0 - - - +
237B ARG* 1.3 75.8 - - - +
239B LEU* 1.3 60.9 + - - +
241B GLU* 4.1 9.8 - - - +
242B ARG* 3.1 25.5 + - - +
347B GLU* 4.0 8.4 - - - +
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Residues in contact with LEU 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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221B LEU* 4.7 21.3 - - + -
235B ALA 3.1 17.9 + - - +
236B ILE* 3.6 5.6 - - + +
238B ALA* 1.3 74.5 - - - +
240B ALA* 1.3 66.4 + - - +
242B ARG* 3.4 17.7 + - - +
243B LEU* 3.1 42.7 + - + +
245B ILE* 5.1 4.9 - - + -
342B PHE* 5.7 3.4 - - + -
343B VAL* 4.5 16.8 - - + -
346B PHE* 3.8 28.3 - - + -
347B GLU* 3.5 29.3 + - + +
350B THR* 4.0 6.7 - - - +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 4.0 6.5 - - + -
236B ILE 3.0 17.1 + - - +
237B ARG* 3.8 4.9 - - - +
239B LEU* 1.3 76.5 - - - +
241B GLU* 1.3 58.2 + - + +
244B ASN* 2.8 26.3 + - - -
245B ILE* 3.0 36.9 + - - +
247B VAL* 3.7 20.0 - - + -
257B LEU* 5.4 1.8 - - + -
263B LEU* 3.3 9.6 - - + +
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Residues in contact with GLU 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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237B ARG* 3.0 51.9 + - + +
238B ALA* 4.1 6.8 - - - +
240B ALA* 1.3 78.9 - - + +
242B ARG* 1.3 62.9 + - - +
244B ASN* 3.6 8.1 + - - +
257B LEU* 5.7 0.2 - - + -
261B HIS* 2.7 39.9 + - + +
263B LEU* 3.8 6.5 - - + +
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Residues in contact with ARG 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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238B ALA 3.1 18.1 + - - +
239B LEU* 3.9 9.0 - - - +
241B GLU* 1.3 79.3 - - - +
243B LEU* 1.3 77.3 + - + +
244B ASN 3.7 0.2 + - - -
347B GLU* 2.7 35.5 + - - -
350B THR* 3.0 47.3 + - - -
351B ALA* 3.6 13.2 + - - -
353B PHE 3.5 11.1 + - - +
354B GLY 4.8 0.2 - - - -
355B ALA* 3.7 16.1 + - - +
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Residues in contact with LEU 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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213B LEU* 3.8 29.4 - - + -
239B LEU* 3.1 33.1 + - + +
242B ARG* 1.3 103.5 - - + +
244B ASN* 1.3 65.2 + - - +
245B ILE* 3.4 19.8 - - + +
350B THR* 4.0 11.4 - - - +
353B PHE* 3.7 16.2 - - + +
354B GLY 3.5 21.5 - - - +
355B ALA* 3.8 3.4 - - - +
356B LYS* 2.9 30.8 + - + +
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Residues in contact with ASN 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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219B PRO* 5.8 0.3 - - - +
240B ALA 2.8 11.0 + - - -
241B GLU 3.6 6.1 + - - +
242B ARG 3.4 3.2 - - - -
243B LEU* 1.3 81.0 - - - +
245B ILE* 1.3 57.8 + - - +
246B PRO* 3.6 9.6 - - - +
262B GLU* 5.3 1.6 - - - +
263B LEU* 3.6 11.7 - - - +
355B ALA* 3.9 10.3 - - + +
356B LYS* 2.8 30.8 + - - +
357B GLN* 4.1 2.6 + - - +
358B ARG* 2.9 53.1 + - - +
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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