Contacts of the helix formed by residues 239 - 256 (chain D) in PDB entry 4DAJ
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 PHE 239 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D VAL* 5.5 0.2 - - + -
235D ALA 2.5 17.6 + - - +
238D ALA* 1.3 74.8 - - - +
240D TYR* 1.3 85.1 + + - +
242D PRO* 2.8 7.5 - - - +
243D VAL* 2.8 53.1 + - + +
499D PHE* 3.6 14.1 - + - -
500D ILE* 4.8 1.1 - - - -
503D TRP* 3.4 41.3 - + + -
504D THR* 3.3 39.9 - - + -
507D ASN* 3.4 34.8 - - + +
2000D 0HK 3.5 8.7 - - - +
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Residues in contact with TYR 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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232D PHE* 4.9 8.1 - + - -
235D ALA* 2.9 31.1 + - + -
236D ILE* 3.3 44.2 - - + +
239D PHE* 1.3 86.6 - + - +
241D MET* 1.3 64.1 + - - +
243D VAL* 3.2 2.5 + - - +
244D THR* 2.9 32.8 + - + +
504D THR* 6.2 2.0 - - + -
507D ASN* 2.6 43.3 + - + -
508D ILE* 3.6 8.5 + - + +
511D LEU* 3.8 19.7 - - + +
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Residues in contact with MET 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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230C ILE* 5.3 0.9 - - - +
233C GLY* 3.4 49.8 - - - +
234C THR* 4.0 4.0 - - - +
236C ILE* 3.4 29.7 - - + +
237C ALA* 4.7 5.8 - - + +
159D LEU* 5.5 4.9 - - + -
236D ILE 2.8 15.2 + - - +
237D ALA* 3.9 10.3 - - - +
240D TYR* 1.3 71.8 - - - +
242D PRO* 1.3 92.5 - - + +
244D THR* 2.5 25.2 + - - -
245D ILE* 2.9 21.3 + - + +
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Residues in contact with PRO 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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155D VAL* 5.2 8.5 - - + -
159D LEU* 3.9 28.7 - - + +
237D ALA 3.2 12.6 - - - +
238D ALA* 3.1 24.0 - - - +
239D PHE* 2.8 20.6 - - - +
241D MET* 1.3 101.4 - - + +
243D VAL* 1.3 56.2 + - + +
245D ILE* 3.8 1.8 - - + +
246D MET* 2.9 42.1 + - + +
499D PHE* 6.3 0.4 - - + -
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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
----------------------------------------------------------
239D PHE* 2.8 64.9 + - + +
240D TYR* 3.6 4.3 - - - +
242D PRO* 1.3 71.9 - - + +
244D THR* 1.3 63.8 - - + +
246D MET* 3.3 12.0 + - + +
247D THR* 2.9 32.5 + - - +
496D LEU* 5.5 0.3 - - - +
499D PHE* 3.8 14.8 - - + -
500D ILE* 4.5 27.4 - - + -
504D THR* 5.1 1.3 - - + -
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Residues in contact with THR 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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232C PHE* 4.6 5.5 - - - -
236C ILE* 3.9 15.3 - - + +
240D TYR* 2.9 19.7 + - + +
241D MET* 2.5 26.3 + - - -
243D VAL* 1.3 77.9 - - + +
245D ILE* 1.3 67.0 + - - +
247D THR* 2.9 19.8 + - - -
248D ILE* 2.9 18.3 + - - +
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Residues in contact with ILE 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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229C THR* 3.8 17.5 - - + +
230C ILE* 5.0 3.6 - - - -
232C PHE* 4.4 10.8 - - + -
233C GLY* 3.3 37.9 - - - +
159D LEU* 3.9 18.8 - - + -
163D PHE* 4.0 20.0 - - + -
241D MET* 2.9 29.9 + - + +
242D PRO* 3.8 3.8 - - + +
244D THR* 1.3 82.9 + - - +
246D MET* 1.3 59.4 + - - +
248D ILE* 3.0 11.1 + - + +
249D LEU* 2.9 35.3 + - + +
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Residues in contact with MET 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL* 4.6 2.7 - - + +
158D LEU* 3.6 31.9 - - + -
159D LEU* 3.5 24.7 - - + -
162D SER* 4.1 14.4 + - - +
242D PRO* 2.9 30.6 + - + +
243D VAL* 3.4 20.6 - - + +
245D ILE* 1.3 76.7 - - - +
247D THR* 1.3 56.4 + - - +
249D LEU* 4.2 5.5 - - - +
250D TYR* 2.9 31.4 + - - +
496D LEU* 3.5 24.6 - - + +
499D PHE* 4.0 27.4 - - + -
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Residues in contact with THR 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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243D VAL* 2.9 22.4 + - - +
244D THR* 2.9 9.8 + - - -
246D MET* 1.3 74.2 - - - +
248D ILE* 1.3 67.8 + - - +
250D TYR* 3.3 5.9 + - + +
251D TRP* 2.9 55.5 + - + +
496D LEU* 4.6 7.0 - - + +
500D ILE* 5.9 2.1 - - - +
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Residues in contact with ILE 248 (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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229C THR* 3.9 24.0 - - + -
232C PHE* 4.4 21.3 - - + -
514C THR* 4.3 9.0 - - + -
515C PHE* 3.9 33.4 - - + -
244D THR* 2.9 17.2 + - - +
245D ILE* 3.0 11.6 + - + +
247D THR* 1.3 77.8 - - - +
249D LEU* 1.3 66.4 + - - +
251D TRP* 3.2 4.3 + - - +
252D ARG* 2.9 43.6 + - + +
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Residues in contact with LEU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C THR* 3.9 25.1 - - + +
159D LEU* 5.8 0.4 - - + -
162D SER* 4.0 15.5 - - - +
163D PHE* 3.4 60.6 - - + +
166D TYR* 3.5 36.6 - - + -
245D ILE* 2.9 27.2 + - + +
246D MET* 4.2 2.7 - - - +
248D ILE* 1.3 70.3 - - - +
250D TYR* 1.3 64.4 + - - +
252D ARG* 2.9 16.9 + - - +
253D ILE* 2.9 18.4 + - + +
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Residues in contact with TYR 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D SER* 5.3 1.2 - - - -
246D MET 2.9 22.9 + - - +
247D THR* 3.6 4.9 - - + +
249D LEU* 1.3 75.9 - - - +
251D TRP* 1.3 106.6 + + - +
253D ILE* 3.7 6.9 + - - +
254D TYR* 2.9 49.6 + + + +
489D ALA* 4.9 7.2 - - + -
492D LEU* 3.4 32.8 - - + -
493D SER* 2.8 41.1 + - - -
496D LEU* 4.5 13.5 - - + -
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Residues in contact with TRP 251 (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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247D THR* 2.9 48.9 + - + +
248D ILE* 3.9 3.8 - - - +
250D TYR* 1.3 101.7 - + - +
252D ARG* 1.3 66.0 + - - +
254D TYR* 3.5 38.2 - + + +
255D LYS* 2.9 45.4 + - + +
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Residues in contact with ARG 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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228C PRO* 4.6 11.3 - - - +
229C THR* 4.6 5.6 - - - +
514C THR* 2.8 32.5 + - - +
515C PHE* 3.7 20.6 + - - +
166D TYR* 3.4 43.5 + - + -
248D ILE* 2.9 43.3 + - + +
249D LEU* 2.9 8.7 + - - +
251D TRP* 1.3 79.3 - - + +
253D ILE* 1.3 63.4 + - - +
255D LYS* 3.3 11.5 + - - +
256D GLU* 3.4 15.6 + - - +
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Residues in contact with ILE 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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162D SER* 3.5 18.6 - - - +
165D ARG* 3.4 29.6 - - + -
166D TYR* 3.5 24.2 - - + +
169D ILE* 4.0 21.8 - - + -
249D LEU 2.9 22.4 + - - +
250D TYR* 3.8 7.4 - - + +
252D ARG* 1.3 70.2 - - - +
254D TYR* 1.3 65.7 + - - +
255D LYS 2.9 3.8 - - - -
256D GLU 2.8 29.4 + - - +
257D THR* 3.8 1.8 + - - +
488D ALA* 4.4 3.1 - - + -
489D ALA* 3.9 32.3 - - + +
492D LEU* 5.6 3.6 - - + -
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Residues in contact with TYR 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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250D TYR* 2.9 45.7 + + + +
251D TRP* 3.5 35.4 - + + +
253D ILE* 1.3 74.2 - - - +
255D LYS* 1.3 80.4 + - - +
256D GLU 4.9 0.2 - - - -
257D THR* 4.8 6.2 + - - -
489D ALA* 4.7 12.8 - - + -
493D SER* 5.0 2.7 - - - -
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Residues in contact with LYS 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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251D TRP* 2.9 35.8 + - + +
252D ARG* 3.5 7.2 - - - +
253D ILE 2.8 1.8 + - - -
254D TYR* 1.3 115.7 + - - +
256D GLU* 1.3 66.0 + - + +
257D THR 4.0 1.3 + - - -
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Residues in contact with GLU 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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169D ILE* 3.8 31.6 - - + +
170D THR* 6.1 0.3 - - - +
252D ARG 3.4 8.3 + - - +
253D ILE* 2.8 20.2 + - - +
255D LYS* 1.3 84.5 - - + +
257D THR* 1.3 59.2 + - - +
258D GLU* 4.2 3.6 - - + +
259D LYS* 3.4 42.0 + - + +
1072D ASP* 4.2 10.9 - - - +
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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
------------------------------------------------------------
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