Contacts of the helix formed by residues 243 - 259 (chain D) in PDB entry 5ID3
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 GLU 243 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B GLU* 5.7 0.2 - - - +
243C GLU* 4.0 12.5 - - - +
242D VAL* 1.4 83.8 - - + +
244D PRO* 1.4 63.9 - - - +
245D VAL* 3.7 3.7 + - - -
246D THR 4.0 3.0 + - - -
247D TYR* 3.2 43.2 + - + +
243E GLU* 2.6 43.7 - - + +
247E TYR* 3.5 38.5 - - + +
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Residues in contact with PRO 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D VAL* 4.8 13.7 - - + -
227D GLY 6.0 4.0 - - - +
228D LEU* 4.7 16.2 - - + -
231D ARG* 6.4 0.7 - - - +
241D ILE* 3.6 12.8 - - + +
242D VAL* 3.1 12.8 - - - +
243D GLU 1.4 87.6 - - - +
245D VAL* 1.4 65.9 + - + +
246D THR 3.6 0.2 + - - -
247D TYR* 3.3 44.3 - - + +
248D PHE* 3.6 10.6 + - - -
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Residues in contact with VAL 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ALA* 5.4 4.2 - - + +
224D VAL* 4.2 13.5 - - + +
225D GLN* 3.1 42.4 - - - +
228D LEU* 4.3 26.2 - - + +
243D GLU 5.5 1.1 - - - -
244D PRO* 1.4 81.8 - - + +
246D THR* 1.4 73.4 + - - +
248D PHE* 3.7 4.2 + - - +
249D ALA* 3.3 16.9 + - + +
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Residues in contact with THR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLU 4.0 1.6 + - - -
244D PRO 3.5 0.6 - - - -
245D VAL* 1.4 83.1 - - - +
247D TYR* 1.4 58.1 + - - +
249D ALA* 2.8 28.6 + - + +
250D THR* 2.8 18.4 + - + +
247E TYR* 3.5 50.4 + - + -
248E PHE* 3.2 45.2 - - + -
251E TYR* 5.9 1.6 - - + -
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Residues in contact with TYR 247 (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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242C VAL* 4.8 9.1 - - + +
243C GLU* 3.0 64.4 + - + +
246C THR* 3.8 21.0 + - + +
250C THR* 5.2 3.9 - - + +
242D VAL 4.9 2.5 - - - -
243D GLU* 3.2 42.7 + - + +
244D PRO* 3.3 39.6 + - + +
245D VAL 3.6 0.2 - - - -
246D THR* 1.4 74.5 - - - +
248D PHE* 1.4 86.0 + + - +
250D THR* 2.4 31.5 + - + +
251D TYR* 3.3 5.7 + - - +
247E TYR* 4.7 3.5 - - + -
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Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 5.8 1.3 - - + -
246C THR* 3.0 41.1 - - + -
220D ALA* 4.3 19.6 - - + +
221D ALA* 4.5 15.9 + - - +
224D VAL* 3.7 42.0 - - + -
244D PRO* 3.6 14.0 + - + -
245D VAL 4.0 7.4 - - - +
246D THR 3.3 0.4 - - - -
247D TYR* 1.4 90.7 - + - +
249D ALA* 1.4 61.6 + - - +
251D TYR* 3.1 33.4 + + + +
252D SER* 3.4 6.4 + - - -
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Residues in contact with ALA 249 (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 ALA* 5.0 10.0 - - + +
245D VAL* 3.3 11.6 + - + +
246D THR* 2.8 30.2 + - + +
248D PHE* 1.4 69.4 - - - +
250D THR* 1.4 58.5 + - - +
252D SER* 3.0 24.3 + - - -
253D THR 3.2 4.7 + - - -
248E PHE* 5.6 4.3 - - + -
251E TYR* 3.4 19.5 - - + -
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Residues in contact with THR 250 (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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250C THR* 4.8 9.3 - - - +
246D THR* 2.8 24.5 + - + +
247D TYR* 2.4 31.7 + - + +
249D ALA* 1.4 71.1 - - - +
251D TYR* 1.4 54.5 + - - +
253D THR* 2.8 44.5 + - + +
254D VAL* 3.4 5.4 + - - +
247E TYR* 4.2 18.8 - - + +
250E THR* 3.8 20.9 - - - +
251E TYR* 4.5 6.9 - - + -
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Residues in contact with TYR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C THR* 6.0 2.7 - - + -
249C ALA* 4.0 29.8 - - + -
250C THR* 4.5 13.6 - - + +
252C SER* 4.8 3.7 + - - -
253C THR* 3.2 31.2 - - + +
216D TRP* 3.7 36.3 - + - -
217D ALA* 5.9 2.7 - - + -
220D ALA* 4.4 22.4 - - + -
247D TYR 3.3 3.6 + - - +
248D PHE* 3.1 31.1 + + + +
250D THR* 1.4 78.3 + - - +
252D SER* 1.4 60.7 + - - +
254D VAL* 3.0 27.1 - - - +
255D ALA* 3.5 6.2 + - + +
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Residues in contact with SER 252 (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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217D ALA* 3.4 29.6 + - - +
220D ALA* 6.2 0.8 - - - +
221D ALA* 5.8 4.3 - - - -
248D PHE 3.4 4.7 + - - -
249D ALA* 3.0 18.5 + - - -
251D TYR* 1.4 81.8 - - - +
253D THR* 1.4 55.7 + - - +
255D ALA* 3.0 28.4 + - - +
256D ALA* 3.3 6.4 + - - +
251E TYR* 4.1 10.5 + - - -
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Residues in contact with THR 253 (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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249D ALA 3.2 4.4 + - - -
250D THR* 2.8 36.4 + - - +
252D SER* 1.4 68.7 - - - +
254D VAL* 1.4 62.2 + - + +
256D ALA* 3.1 22.9 + - - +
257D THR 3.5 2.8 + - - -
250E THR* 5.0 4.5 - - - +
251E TYR* 2.9 56.5 + - + +
254E VAL* 3.0 37.6 - - + +
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Residues in contact with VAL 254 (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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250C THR* 5.9 1.6 - - - -
253C THR* 3.3 53.4 - - + +
254C VAL* 4.4 5.4 - - + +
256C ALA* 5.9 0.9 - - + -
257C THR* 5.4 1.3 - - - +
250D THR 4.0 4.0 - - - +
251D TYR* 3.0 30.1 - - - +
253D THR* 1.4 81.6 - - + +
255D ALA* 1.4 56.8 + - - +
257D THR* 2.9 48.9 + - + +
258D PHE* 3.3 2.8 + - - +
254E VAL* 5.1 3.4 - - + -
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Residues in contact with ALA 255 (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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214D VAL* 4.2 12.8 - - + +
216D TRP* 3.8 31.9 + - + +
217D ALA* 3.8 19.3 - - + -
251D TYR* 3.5 8.3 + - + +
252D SER* 3.0 16.9 + - - +
254D VAL* 1.4 75.9 - - - +
256D ALA* 1.4 61.4 + - - +
258D PHE* 3.1 22.7 + - - +
259D GLY 3.9 2.4 + - - -
262D LEU* 6.1 0.2 - - - +
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Residues in contact with ALA 256 (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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214D VAL* 4.4 13.2 - - + +
252D SER 3.3 6.9 + - - +
253D THR* 3.1 16.8 + - - +
255D ALA* 1.4 74.2 - - - +
257D THR* 1.4 62.7 + - - +
259D GLY* 3.3 15.2 + - - -
251E TYR* 6.1 1.6 - - + -
254E VAL* 5.2 8.1 - - + -
258E PHE* 4.1 27.4 - - + -
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Residues in contact with THR 257 (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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257C THR* 3.4 25.8 - - - +
253D THR 3.5 2.5 + - - -
254D VAL* 2.9 33.0 + - + +
256D ALA* 1.4 79.9 - - - +
258D PHE* 1.4 61.5 + - + +
259D GLY 3.2 0.7 + - - -
260D TYR* 2.8 39.4 + - + +
254E VAL* 5.2 7.8 - - - +
257E THR* 3.5 28.6 - - - +
258E PHE* 5.9 1.1 - - - -
260E TYR* 5.5 1.1 - - - -
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Residues in contact with PHE 258 (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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256C ALA* 3.7 39.7 - - + -
257C THR 5.2 0.2 - - - -
259C GLY* 6.1 1.8 - - - -
260C TYR 6.1 1.3 - - - -
216D TRP* 6.0 3.1 - - - +
254D VAL 3.3 6.1 + - - +
255D ALA* 3.1 17.7 + - - +
257D THR* 1.4 75.0 - - - +
259D GLY* 1.3 53.0 + - - +
260D TYR* 2.8 40.8 + + - -
261D TYR* 3.1 37.5 + + - +
262D LEU* 4.0 30.1 - - + -
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Residues in contact with GLY 259 (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 HIS* 4.5 7.7 + - - -
214D VAL* 5.6 5.5 - - - +
255D ALA 3.9 3.0 + - - -
256D ALA 3.3 12.6 + - - -
257D THR 3.2 2.8 - - - -
258D PHE* 1.3 75.8 - - - +
260D TYR* 1.4 57.4 + - - +
261D TYR 3.1 3.5 + - - -
262D LEU* 3.5 25.6 + - - +
263D TYR* 3.0 29.5 + - - -
258E PHE* 5.8 2.7 - - - -
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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