Contacts of the helix formed by residues 338 - 350 (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 ASP 338 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D LYS* 2.9 34.2 + - - -
194D PRO 5.0 4.2 - - - +
196D GLY* 6.2 2.0 - - - -
197D VAL 4.5 0.4 + - - -
198D VAL* 4.3 8.6 - - + +
230D SER* 2.8 20.3 + - - -
320D PRO* 4.6 9.4 - - - +
337D THR* 1.3 80.3 + - - +
339D VAL* 1.3 64.7 + - - +
340D LEU* 3.3 1.6 + - - +
341D ALA* 3.2 30.4 + - + +
342D PHE 2.9 19.4 + - - -
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ALA 4.3 5.4 - - - +
227D ALA* 3.7 22.4 - - + -
230D SER* 3.5 11.3 + - - +
232D ALA* 3.9 10.5 - - + -
294D VAL* 3.6 28.5 - - + -
295D GLY* 3.9 26.0 - - - +
318D ILE* 4.5 9.4 - - + +
320D PRO* 4.1 19.8 - - + +
337D THR 3.5 0.9 + - - +
338D ASP* 1.3 74.0 + - - +
340D LEU* 1.3 63.0 + - - +
342D PHE* 3.2 7.9 + - - +
343D VAL* 3.0 27.3 + - + +
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Residues in contact with LEU 340 (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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193D LYS* 4.1 6.5 - - - +
230D SER* 3.0 29.8 + - - +
231D GLY 4.1 9.0 - - - +
232D ALA* 3.9 17.0 - - + -
235D ALA* 3.9 27.6 - - + -
338D ASP* 3.3 9.6 + - - +
339D VAL* 1.3 72.9 - - - +
341D ALA* 1.3 65.6 + - - +
343D VAL* 3.1 2.3 + - + +
344D GLU* 2.9 50.1 + - + +
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Residues in contact with ALA 341 (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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202D TRP* 3.5 25.9 - - + -
337D THR* 4.2 5.8 - - - +
338D ASP* 3.2 28.5 + - + +
340D LEU* 1.3 75.1 - - - +
342D PHE* 1.3 63.1 + - - +
344D GLU* 3.5 9.0 + - - +
345D HIS* 3.0 18.0 + - - +
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Residues in contact with PHE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D TRP* 3.8 10.0 - - - -
206D ALA* 4.0 24.7 - - + -
209D ALA* 4.8 3.1 - - + -
221D LEU* 6.3 0.7 - - + -
239D LEU* 5.6 2.9 - - + -
292D LEU* 4.7 6.1 - - + -
294D VAL* 4.9 10.3 - - + -
318D ILE* 3.7 53.2 - - + -
335D VAL* 4.0 10.8 - - + -
337D THR* 3.8 7.2 - - + -
338D ASP 2.9 12.8 + - - +
339D VAL 3.4 7.0 - - - +
340D LEU 3.2 0.2 - - - -
341D ALA* 1.3 77.2 - - - +
343D VAL* 1.3 67.3 + - + +
345D HIS* 3.3 1.7 + - - +
346D PHE* 2.8 84.5 + + + +
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Residues in contact with VAL 343 (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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232D ALA* 4.5 3.1 - - + -
235D ALA* 3.7 41.5 - - + +
236D ILE* 4.0 23.8 - - + +
239D LEU* 4.5 14.1 - - + +
294D VAL* 4.9 2.2 - - + -
339D VAL* 3.0 22.6 + - + +
340D LEU* 3.1 6.5 + - - +
342D PHE* 1.3 89.9 - - + +
344D GLU* 1.3 57.6 + - - +
346D PHE* 3.2 4.4 + - - +
347D GLU* 2.8 35.3 + - + +
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Residues in contact with GLU 344 (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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235D ALA* 5.4 4.2 - - + +
340D LEU* 2.9 47.1 + - + +
341D ALA* 4.0 8.1 - - - +
343D VAL* 1.3 78.5 - - + +
345D HIS* 1.3 61.7 + - - +
347D GLU* 3.5 13.0 + - - +
348D THR* 3.5 15.6 + - - -
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Residues in contact with HIS 345 (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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202D TRP* 3.8 14.8 - + + -
203D GLN* 3.4 34.1 + - + +
206D ALA* 3.6 24.0 - - + -
207D ASP* 2.8 28.8 + - - -
341D ALA 3.0 17.9 + - - +
342D PHE 3.7 3.1 - - - +
344D GLU* 1.3 75.5 - - - +
346D PHE* 1.3 61.0 + - - +
348D THR* 3.1 10.5 + - - -
349D ALA* 3.0 27.2 + - + +
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Residues in contact with PHE 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ALA 3.9 11.0 - - - -
209D ALA* 3.8 9.4 - - + -
210D ALA* 3.4 33.7 - - + -
213D LEU* 3.6 33.7 - - + -
221D LEU* 6.0 2.0 - - + -
239D LEU* 3.8 30.3 - - + -
245D ILE* 5.9 0.7 - - + -
292D LEU* 4.1 20.9 - - + -
342D PHE* 2.8 50.6 + + + +
343D VAL* 3.6 6.7 - - - +
345D HIS* 1.3 71.9 - - - +
347D GLU* 1.3 55.4 + - - +
349D ALA* 4.3 4.0 - - + -
350D THR* 2.8 46.2 + - + +
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Residues in contact with GLU 347 (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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235D ALA* 4.1 5.2 - - + +
238D ALA* 4.0 8.5 - - - +
239D LEU* 3.5 35.1 + - + +
242D ARG* 2.7 37.5 + - - -
343D VAL* 2.8 27.6 + - + +
344D GLU* 3.6 10.8 - - + +
345D HIS 3.2 0.4 - - - -
346D PHE* 1.3 76.2 - - - +
348D THR* 1.3 56.9 + - - +
350D THR* 3.7 3.2 + - - -
351D ALA* 3.0 29.8 + - - +
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Residues in contact with THR 348 (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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344D GLU 3.5 10.2 + - - -
345D HIS* 3.1 12.2 + - - -
347D GLU* 1.3 76.7 - - - +
349D ALA* 1.3 63.3 + - - +
350D THR 3.2 0.7 + - - -
351D ALA* 3.4 16.9 + - - +
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Residues in contact with ALA 349 (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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207D ASP* 4.0 20.4 - - - +
210D ALA* 3.9 22.3 - - + +
345D HIS* 3.0 18.1 + - + +
346D PHE* 3.4 8.5 + - + +
347D GLU 3.4 0.2 - - - -
348D THR* 1.3 77.0 - - - +
350D THR* 1.3 58.3 + - - +
351D ALA 3.6 0.6 + - - -
352D SER* 5.6 0.3 + - - -
353D PHE* 3.6 16.5 - - - -
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Residues in contact with THR 350 (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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210D ALA* 3.8 15.7 - - + -
213D LEU* 3.9 4.3 - - + -
239D LEU* 4.0 3.6 - - - +
242D ARG* 3.0 32.1 + - - -
243D LEU* 3.9 8.8 - - - +
346D PHE* 2.8 40.4 + - + +
347D GLU 3.7 0.2 - - - -
349D ALA* 1.3 79.2 - - - +
351D ALA* 1.3 64.4 + - - +
352D SER 3.1 4.1 + - - -
353D PHE* 3.2 42.5 + - + +
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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