Contacts of the helix formed by residues 233 - 245 (chain D) in PDB entry 3QEM
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 THR 233 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D GLU* 3.4 21.4 + - - +
176D PHE* 3.1 47.1 - - + -
232D CYS* 1.3 82.3 - - - +
234D LYS* 1.3 59.8 + - - +
235D GLU* 3.5 6.7 + - - +
236D GLU* 2.8 36.4 + - - +
237D ALA* 2.8 26.1 + - - +
261D LEU* 4.3 7.2 - - + -
262D VAL* 4.7 1.3 - - - -
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Residues in contact with LYS 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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104D ASP* 2.8 54.2 + - + +
233D THR* 1.3 74.2 - - - +
235D GLU* 1.3 64.5 + - - +
237D ALA* 3.0 16.8 + - - +
238D THR* 3.0 23.5 + - + +
261D LEU 3.7 15.7 + - - +
262D VAL* 3.2 17.0 - - - +
263D ALA 2.9 28.7 + - - -
264D GLY* 4.7 1.1 - - - -
265D ASP 3.3 6.3 + - - +
268D THR* 3.6 23.4 + - + +
270D PRO* 4.3 12.3 - - + -
273D PHE* 4.4 7.9 - - + -
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Residues in contact with GLU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D THR* 3.4 6.2 + - - +
234D LYS* 1.3 79.7 - - - +
236D GLU* 1.3 60.5 + - + +
238D THR* 3.0 24.1 + - - -
239D TYR* 3.7 5.9 + - - +
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Residues in contact with GLU 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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115C ARG* 5.1 9.2 + - - +
174D THR* 2.6 34.4 + - + -
176D PHE* 4.1 6.6 + - - +
207D MET* 3.5 35.4 - - + +
232D CYS* 4.1 7.2 - - + -
233D THR* 2.8 45.9 + - - +
234D LYS 3.1 0.6 - - - -
235D GLU* 1.3 75.4 - - + +
237D ALA* 1.3 66.4 + - - +
239D TYR* 2.9 9.5 + - - +
240D ILE* 2.9 23.2 + - - +
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Residues in contact with ALA 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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230D LEU* 4.1 10.8 - - + -
232D CYS* 3.5 16.8 - - - -
233D THR 2.8 13.3 + - - +
234D LYS* 3.3 9.2 - - - +
236D GLU* 1.3 74.6 - - - +
238D THR* 1.3 68.3 + - - +
239D TYR 3.0 0.3 + - - -
240D ILE* 3.2 2.7 + - - +
241D PHE* 2.8 31.1 + - + -
262D VAL* 3.8 24.7 - - + -
273D PHE* 4.3 7.2 - - + -
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Residues in contact with THR 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 LYS* 3.0 19.4 + - + +
235D GLU* 3.0 15.6 + - - -
237D ALA* 1.3 75.6 - - - +
239D TYR* 1.3 65.1 + - - +
241D PHE* 3.7 3.6 - - - +
242D GLU* 3.1 23.1 + - - +
270D PRO* 3.8 33.2 - - + -
272D GLU* 3.7 26.1 - - - +
273D PHE* 4.1 7.6 - - + -
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Residues in contact with TYR 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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207D MET* 4.2 24.2 - - + -
211D ASP* 2.7 46.8 + - + +
216D ILE* 4.4 8.7 - - + -
235D GLU 4.2 6.3 - - - +
236D GLU* 2.9 12.4 + - - +
238D THR* 1.3 78.1 + - - +
240D ILE* 1.3 71.7 - - + +
241D PHE 2.8 3.4 + - - -
242D GLU* 2.9 22.0 + - + +
243D VAL* 3.0 34.0 + - + +
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Residues in contact with ILE 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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172D VAL* 5.7 0.7 - - + -
174D THR* 6.1 2.5 - - + -
205D LEU* 4.5 21.8 - - + -
207D MET* 5.9 3.1 - - - -
220D LEU* 3.6 14.7 - - + +
230D LEU* 4.9 15.7 - - + -
232D CYS* 5.6 1.3 - - - -
236D GLU 2.9 17.7 + - - +
237D ALA* 4.0 6.3 - - - +
239D TYR* 1.3 79.4 - - + +
241D PHE* 1.3 58.3 + - + +
243D VAL* 3.4 4.0 + - - +
244D ALA* 3.0 27.4 + - - +
256D TRP* 5.9 3.8 - - + -
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Residues in contact with PHE 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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230D LEU* 3.8 22.7 - - + -
237D ALA* 2.8 22.8 + - + +
238D THR 3.7 3.6 - - - +
239D TYR 2.8 1.0 + - - -
240D ILE* 1.3 71.5 - - - +
242D GLU* 1.3 55.0 + - - +
243D VAL 3.0 1.1 - - - -
244D ALA* 2.6 7.1 + - + +
245D ASN* 2.6 37.8 + - - +
250D THR* 4.4 10.2 - - + +
256D TRP* 3.4 39.9 - + + -
258D VAL* 5.0 1.6 - - + -
262D VAL* 5.0 2.0 - - + -
272D GLU 3.5 16.6 - - - +
273D PHE* 3.7 26.5 - + - -
274D PRO* 3.5 34.5 - - + -
277D LEU* 3.9 24.2 - - + -
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Residues in contact with GLU 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 THR 3.1 13.6 + - - +
239D TYR* 2.9 19.0 + - + +
241D PHE* 1.3 72.9 - - - +
243D VAL* 1.3 63.5 + - + +
245D ASN* 3.6 6.8 + - - +
246D SER* 3.4 20.6 + - - -
272D GLU* 4.5 17.3 - - + +
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Residues in contact with VAL 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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211D ASP* 4.8 2.5 - - - +
216D ILE* 4.3 1.6 - - + -
217D GLN* 3.4 37.8 - - + +
220D LEU* 3.2 19.9 - - + +
239D TYR* 3.0 49.7 + - + +
240D ILE* 3.7 7.9 - - - +
242D GLU* 1.3 78.2 - - + +
244D ALA* 1.3 58.1 - - - +
246D SER* 3.5 5.5 - - - -
247D VAL* 3.2 24.9 + - - +
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Residues in contact with ALA 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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220D LEU* 4.0 11.7 - - + -
240D ILE 3.0 15.3 + - - +
241D PHE* 2.6 14.2 + - - +
243D VAL* 1.3 71.1 - - - +
245D ASN* 1.3 57.6 + - - +
246D SER 2.9 5.6 - - - -
247D VAL 4.4 0.4 - - - +
248D GLY 3.1 6.6 + - - -
249D LEU* 2.9 39.1 + - + +
250D THR* 4.2 5.2 - - + -
256D TRP* 4.0 29.8 - - + -
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Residues in contact with ASN 245 (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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241D PHE 2.6 19.6 + - - +
242D GLU* 4.1 6.7 - - - +
244D ALA* 1.3 71.0 - - - +
246D SER* 1.3 59.0 + - - +
248D GLY* 4.1 4.9 + - - -
250D THR* 3.2 27.0 + - + +
272D GLU* 5.5 5.4 - - + +
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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