Contacts of the helix formed by residues 232 - 244 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D ALA 3.0 15.6 + - - +
228D ILE 4.5 0.2 + - - -
230D SER* 4.5 0.9 - - - -
231D GLY* 1.3 75.2 - - - +
233D VAL* 1.3 59.0 + - - +
234D PRO* 3.6 1.6 - - - -
235D ALA 3.3 2.8 + - - -
236D ILE* 2.8 40.7 + - + +
339D VAL* 3.9 24.5 - - + -
340D LEU* 3.9 28.3 - - + +
343D VAL* 4.5 3.1 - - + -
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ALA 4.9 0.7 - - - -
228D ILE* 3.7 40.4 - - + +
231D GLY* 3.5 0.8 - - - -
232D ALA* 1.3 76.6 - - - +
234D PRO* 1.3 75.8 - - + +
236D ILE* 3.8 7.8 - - + +
237D ARG* 2.9 24.2 + - + +
256D VAL* 3.4 43.7 - - + +
426D PRO* 4.2 18.6 - - + -
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Residues in contact with PRO 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D GLY 4.2 10.5 - - - +
232D ALA 3.9 0.7 - - - -
233D VAL* 1.3 96.3 - - + +
235D ALA* 1.3 56.1 + - - +
237D ARG* 3.5 8.7 - - + +
238D ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D GLY 5.5 0.2 + - - -
232D ALA 3.3 6.9 + - - +
233D VAL 3.2 0.6 - - - -
234D PRO* 1.3 76.5 - - - +
236D ILE* 1.3 65.9 + - - +
238D ALA* 3.4 5.8 + - - +
239D LEU* 3.0 24.4 + - - +
340D LEU* 3.9 23.8 - - + -
343D VAL* 3.7 22.2 - - + +
344D GLU* 5.4 4.5 - - + +
347D GLU* 4.1 3.9 - - + +
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 4.1 20.3 - - + +
223D VAL* 4.2 23.8 - - + -
227D ALA* 3.7 30.3 - - + -
232D ALA* 2.8 30.1 + - + +
233D VAL* 3.8 7.0 - - + +
235D ALA* 1.3 72.5 - - - +
237D ARG* 1.3 58.9 + - - +
239D LEU* 3.4 8.5 + - + +
240D ALA* 3.0 27.0 + - - +
247D VAL* 4.8 8.3 - - + -
256D VAL* 5.9 5.6 - - + -
257D LEU* 6.4 0.4 - - + -
294D VAL* 3.9 16.6 - - + -
343D VAL* 4.0 20.2 - - + -
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Residues in contact with ARG 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D VAL* 2.9 19.0 + - + +
234D PRO* 3.5 9.0 - - + +
236D ILE* 1.3 77.4 - - - +
238D ALA* 1.3 56.4 + - - +
240D ALA* 3.3 3.5 + - - +
241D GLU* 2.9 58.5 + - - +
247D VAL* 6.1 0.2 - - - -
256D VAL 4.7 6.2 + - - +
257D LEU* 3.7 28.0 - - + -
258D PRO* 3.5 32.3 - - - +
261D HIS* 4.0 9.7 + - - -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D PRO 3.0 16.9 + - - +
235D ALA* 3.8 6.7 - - - +
237D ARG* 1.3 77.5 - - - +
239D LEU* 1.3 60.6 + - - +
241D GLU* 4.1 10.3 - - - +
242D ARG* 3.2 25.3 + - - +
347D GLU* 4.0 8.5 - - - +
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 4.6 22.2 - - + -
235D ALA 3.0 17.4 + - - +
236D ILE* 3.6 6.1 - - + +
238D ALA* 1.3 75.1 - - - +
240D ALA* 1.3 65.0 + - - +
242D ARG* 3.5 27.7 + - - +
243D LEU* 3.2 33.7 + - + +
245D ILE* 4.8 4.7 - - + +
342D PHE* 5.6 2.9 - - + -
343D VAL* 4.5 16.8 - - + -
346D PHE* 3.8 31.0 - - + -
347D GLU* 3.5 20.1 + - + +
350D THR* 4.0 9.9 - - - +
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 4.0 7.6 - - + -
236D ILE 3.0 17.3 + - - +
237D ARG* 3.9 4.9 - - - +
239D LEU* 1.3 76.5 - - - +
241D GLU* 1.3 57.6 + - - +
244D ASN* 2.8 27.0 + - - -
245D ILE* 3.0 37.2 + - - +
247D VAL* 3.8 19.5 - - + -
257D LEU* 5.7 1.8 - - + -
263D LEU* 3.3 8.4 - - + +
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ARG* 2.9 48.5 + - + +
238D ALA* 4.1 9.8 - - - +
240D ALA* 1.3 78.7 - - + +
242D ARG* 1.3 61.7 + - - +
244D ASN* 3.7 7.4 + - - +
261D HIS* 2.8 39.8 + - + +
263D LEU* 3.8 6.6 - - + +
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Residues in contact with ARG 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ALA 3.2 15.7 + - - +
239D LEU* 3.7 11.5 + - - +
241D GLU* 1.3 79.9 - - - +
243D LEU* 1.3 81.5 + - + +
244D ASN 3.8 0.2 + - - -
347D GLU* 2.7 34.9 + - - -
350D THR* 3.0 44.0 + - - -
351D ALA* 3.6 17.9 + - - -
353D PHE 4.4 2.4 + - - -
355D ALA* 3.8 15.6 + - - +
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LEU* 3.8 29.6 - - + -
239D LEU* 3.2 20.8 + - + +
242D ARG* 1.3 107.7 - - + +
244D ASN* 1.3 65.8 + - - +
245D ILE* 3.4 14.2 + - + +
350D THR* 3.9 21.1 - - - +
353D PHE* 3.8 32.3 - - + +
354D GLY 4.1 10.1 - - - +
355D ALA* 4.0 1.6 - - - +
356D LYS* 2.9 34.0 + - + +
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Residues in contact with ASN 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D ALA 2.8 11.5 + - - -
241D GLU 3.7 6.2 + - - +
242D ARG 3.4 3.2 - - - -
243D LEU* 1.3 80.8 - - - +
245D ILE* 1.3 56.8 + - - +
246D PRO* 3.6 9.0 - - - +
262D GLU* 5.6 0.7 - - - +
263D LEU* 3.6 11.1 - - - +
355D ALA* 4.3 8.1 - - + -
356D LYS* 2.8 32.9 + - - +
357D GLN* 4.3 1.8 - - - +
358D ARG* 3.1 46.8 + - - +
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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