Contacts of the helix formed by residues 338 - 350 (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 ASP 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B LYS* 2.8 34.7 + - - -
194B PRO 4.9 5.5 - - - +
196B GLY* 5.7 5.6 - - - -
197B VAL 4.4 0.2 + - - -
198B VAL* 4.2 9.6 - - + +
230B SER* 2.7 22.2 + - - -
320B PRO* 4.4 11.6 - - + +
337B THR* 1.3 78.5 + - - +
339B VAL* 1.3 64.7 + - - +
341B ALA* 3.2 32.6 + - + +
342B PHE 2.9 18.0 + - - -
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Residues in contact with VAL 339 (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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226B ALA 4.3 4.9 - - - +
227B ALA* 3.8 23.8 - - + +
230B SER* 3.5 12.0 + - - +
232B ALA* 3.9 9.9 - - + -
294B VAL* 3.6 28.9 - - + -
295B GLY* 3.9 25.6 - - - +
318B ILE* 4.5 10.1 - - + +
320B PRO* 4.3 17.0 - - + +
337B THR 3.5 1.3 + - - -
338B ASP* 1.3 74.6 + - - +
340B LEU* 1.3 57.5 + - - +
342B PHE* 3.1 8.8 + - - +
343B VAL* 2.9 30.0 + - + +
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Residues in contact with LEU 340 (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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193B LYS* 3.8 7.4 - - + +
230B SER* 3.0 24.0 + - - +
231B GLY* 4.0 14.4 - - - +
232B ALA* 4.0 15.7 - - + +
235B ALA* 3.6 31.2 - - + -
338B ASP* 3.3 9.2 + - - +
339B VAL* 1.3 75.4 - - - +
341B ALA* 1.3 58.6 + - - +
343B VAL* 3.1 2.2 + - - -
344B GLU* 2.9 60.3 + - + +
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Residues in contact with ALA 341 (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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202B TRP* 3.6 15.2 - - + -
337B THR* 4.2 10.5 - - - +
338B ASP* 3.2 25.8 + - + +
340B LEU* 1.3 78.1 - - - +
342B PHE* 1.3 62.5 + - - +
344B GLU* 3.5 9.0 + - - +
345B HIS* 3.0 23.7 + - - +
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Residues in contact with PHE 342 (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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202B TRP* 3.9 8.5 - - - -
206B ALA* 3.9 26.5 - - + -
209B ALA* 4.7 3.1 - - + -
221B LEU* 6.4 0.7 - - + -
239B LEU* 5.7 3.1 - - + -
292B LEU* 4.6 7.9 - - + -
294B VAL* 5.1 9.6 - - + -
318B ILE* 3.7 45.3 - - + -
335B VAL* 4.0 13.9 - - + -
337B THR* 3.7 17.8 - - + +
338B ASP 2.9 7.5 + - - +
339B VAL 3.1 6.7 + - - +
341B ALA* 1.3 76.3 - - - +
343B VAL* 1.3 67.8 + - + +
345B HIS* 3.2 2.9 + - - +
346B PHE* 2.8 78.3 + + + +
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Residues in contact with VAL 343 (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 ALA* 4.7 1.3 - - + -
235B ALA* 3.7 41.5 - - + +
236B ILE* 3.9 24.9 - - + +
239B LEU* 4.5 15.3 - - + -
294B VAL* 4.9 2.2 - - + -
339B VAL* 2.9 25.5 + - + +
340B LEU* 3.1 8.0 + - - +
342B PHE* 1.3 90.7 - - + +
344B GLU* 1.3 57.5 + - - +
346B PHE* 3.2 4.8 + - - +
347B GLU* 2.8 34.8 + - + +
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Residues in contact with GLU 344 (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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235B ALA* 5.3 3.6 - - + -
340B LEU* 2.9 49.2 + - + +
341B ALA* 4.0 6.8 - - - +
343B VAL* 1.3 73.5 - - + +
345B HIS* 1.3 64.4 + - - +
347B GLU* 3.5 8.7 + - - +
348B THR* 3.4 23.0 + - - -
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Residues in contact with HIS 345 (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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202B TRP* 3.7 16.6 - + + -
203B GLN* 3.4 33.5 + - + +
206B ALA* 3.5 24.9 - - + -
207B ASP* 2.8 29.7 + - - -
341B ALA 3.0 17.9 + - - +
342B PHE 3.6 3.4 - - - +
344B GLU* 1.3 77.1 - - - +
346B PHE* 1.3 59.1 + - - +
348B THR* 3.3 9.8 + - + -
349B ALA* 3.0 26.3 + - + +
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Residues in contact with PHE 346 (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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206B ALA* 3.9 10.1 - - + -
209B ALA* 3.8 10.1 - - + -
210B ALA* 3.5 33.0 - - + -
213B LEU* 3.6 36.1 - - + -
221B LEU* 6.1 1.8 - - + -
239B LEU* 3.8 31.2 - - + -
245B ILE* 5.7 1.8 - - + -
292B LEU* 4.3 15.3 - - + -
342B PHE* 2.8 46.1 + + + +
343B VAL* 3.5 7.9 - - - +
345B HIS* 1.3 77.5 - - - +
347B GLU* 1.3 54.2 + - - +
349B ALA* 3.4 3.5 + - - +
350B THR* 2.8 47.7 + - + +
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Residues in contact with GLU 347 (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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235B ALA* 4.1 4.5 - - + +
238B ALA* 4.0 7.3 - - - +
239B LEU* 3.5 40.1 + - + +
242B ARG* 2.7 37.2 + - - -
343B VAL* 2.8 27.7 + - + +
344B GLU* 3.6 8.7 - - - +
345B HIS 3.3 0.2 - - - -
346B PHE* 1.3 73.6 - - - +
348B THR* 1.3 60.0 + - - +
350B THR* 3.6 3.4 + - - -
351B ALA* 2.9 32.4 + - - +
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Residues in contact with THR 348 (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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344B GLU 3.4 10.7 + - - -
345B HIS* 3.3 13.2 + - + -
347B GLU* 1.3 79.0 - - - +
349B ALA* 1.3 62.1 + - - +
350B THR 3.4 0.5 + - - -
351B ALA* 3.5 16.3 + - - +
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Residues in contact with ALA 349 (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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206B ALA 5.4 0.2 - - - +
207B ASP* 4.0 18.8 - - - +
210B ALA* 4.0 22.3 - - + +
345B HIS* 3.0 19.2 + - + +
346B PHE* 3.7 8.1 - - + +
347B GLU 3.4 0.2 - - - -
348B THR* 1.3 76.7 - - - +
350B THR* 1.3 60.2 + - - +
351B ALA 3.5 0.6 + - - -
352B SER* 4.9 2.6 + - - -
353B PHE* 3.8 13.5 - - - -
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Residues in contact with THR 350 (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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210B ALA* 4.0 9.4 - - + -
213B LEU* 4.0 1.8 - - + -
239B LEU* 4.0 3.1 - - - +
242B ARG* 3.0 28.7 + - - -
243B LEU* 4.0 7.8 - - - +
346B PHE* 2.8 52.6 + - + +
347B GLU* 3.9 0.2 - - - -
349B ALA* 1.3 77.0 - - - +
351B ALA* 1.3 64.3 + - - +
352B SER 3.1 3.6 - - - -
353B PHE* 3.0 51.3 + - + +
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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