Contacts of the helix formed by residues 232 - 249 (chain D) in PDB entry 4QG0
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 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D ASP* 4.8 5.2 - - - +
230D LYS 5.1 1.3 - - - +
231D TRP* 1.3 93.2 - - - +
233D HIS* 1.3 64.2 + - - +
234D GLU* 3.1 22.2 + - - +
235D GLN* 2.8 38.3 + - - +
236D GLY 3.2 16.8 + - - -
273D VAL* 5.8 0.2 - - - +
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Residues in contact with HIS 233 (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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206D ARG* 4.1 24.1 + - - -
209D GLY* 3.5 21.7 - - - +
210D HIS* 3.7 33.4 + + - +
215D HIS* 3.9 9.6 - + - -
218D ASP* 3.0 30.6 + - + +
231D TRP* 4.2 4.6 - - - +
232D THR* 1.3 74.3 - - - +
234D GLU* 1.3 82.1 + - + +
236D GLY 3.4 0.8 + - - +
237D SER* 2.8 30.8 + - - -
703D DUT 3.5 32.5 + - - -
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Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ARG* 5.4 5.2 - - - +
232D THR* 3.1 25.6 - - - +
233D HIS* 1.3 102.3 + - + +
235D GLN* 1.3 60.7 + - - +
237D SER* 2.9 23.7 + - - -
238D VAL* 2.9 12.8 + - - +
272D ILE* 3.9 23.0 - - + +
273D VAL* 3.8 18.8 - - + -
304D LYS* 5.0 9.4 + - - +
703D DUT 5.2 3.6 + - - -
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Residues in contact with GLN 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D LYS 3.4 23.8 + - - +
231D TRP* 3.9 8.4 - - + -
232D THR* 2.8 33.7 + - - +
234D GLU* 1.3 76.1 - - - +
236D GLY* 1.3 64.2 + - - +
238D VAL* 3.0 7.8 + - - +
239D MET* 2.9 45.1 + - + +
273D VAL* 3.9 15.9 - - + +
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Residues in contact with GLY 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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209D GLY* 3.5 9.1 - - - -
231D TRP* 3.3 31.0 - - - -
232D THR 3.2 7.5 + - - -
233D HIS 3.6 4.5 - - - -
234D GLU 3.2 0.2 - - - -
235D GLN* 1.3 78.5 - - - +
237D SER* 1.3 57.4 + - - +
239D MET* 3.5 4.3 + - - +
240D MET* 2.9 32.4 + - - +
416D MET* 4.5 3.3 - - - +
419D TYR* 5.4 1.2 - - - -
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Residues in contact with SER 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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205D CYS 3.8 9.3 - - - +
206D ARG 2.9 25.9 + - - -
207D ASN 3.8 0.2 - - - -
208D LEU* 3.5 5.6 + - - +
209D GLY* 2.9 24.9 + - - +
233D HIS* 2.8 16.7 + - - -
234D GLU 2.9 11.6 + - - -
236D GLY* 1.3 76.6 - - - +
238D VAL* 1.3 56.0 + - - +
240D MET* 3.9 0.7 - - - +
241D PHE* 2.9 31.6 + - - +
272D ILE* 3.8 15.7 - - - -
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D GLU 2.9 9.9 + - - +
235D GLN* 3.0 9.6 + - - +
237D SER* 1.3 77.0 - - - +
239D MET* 1.3 61.2 + - + +
241D PHE* 3.2 6.7 + - - +
242D GLU* 2.9 28.3 + - + +
269D LYS* 3.9 48.7 - - + +
272D ILE* 4.2 8.5 - - + -
273D VAL* 3.8 32.8 - - + -
276D LEU* 5.8 2.9 - - + -
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Residues in contact with MET 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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231D TRP* 4.5 16.8 - - + -
235D GLN* 2.9 36.2 + - + +
236D GLY* 4.0 2.0 - - - +
238D VAL* 1.3 80.6 - - + +
240D MET* 1.3 62.8 + - - +
242D GLU* 3.3 8.5 + - - +
243D HIS* 2.9 23.6 + - - +
413D ILE 4.6 4.7 - - - +
416D MET* 3.8 31.2 - - + +
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Residues in contact with MET 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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140D GLN* 3.7 34.5 - - + +
143D ARG* 4.7 4.3 - - - -
208D LEU* 3.8 38.6 - - + +
209D GLY* 5.0 0.4 - - - -
236D GLY 2.9 18.8 + - - +
237D SER 4.0 2.7 - - - +
239D MET* 1.3 76.6 - - - +
241D PHE* 1.3 56.6 + - - +
243D HIS* 3.2 8.6 + - - +
244D LEU* 2.9 26.7 + - - +
416D MET* 3.5 29.1 - - - +
419D TYR* 3.5 33.2 - - + +
420D THR* 3.8 14.1 - - - +
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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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135D ILE* 5.2 3.6 - - + -
201D ILE* 3.8 20.6 - - + -
205D CYS* 3.7 25.8 - - + -
208D LEU* 3.9 11.2 - - + +
237D SER 2.9 19.7 + - - +
238D VAL* 3.5 4.5 - - - +
240D MET* 1.3 74.9 - - - +
242D GLU* 1.3 65.9 + - - +
244D LEU* 3.1 8.4 + - + +
245D ILE* 2.9 60.3 + - + +
254D MET* 5.9 0.9 - - - -
265D ILE* 4.2 20.4 - - + -
268D ILE* 3.9 40.2 - - + -
269D LYS* 4.4 18.6 - - + -
272D ILE* 5.2 5.2 - - + -
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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
----------------------------------------------------------
238D VAL* 2.9 14.9 + - + +
239D MET* 3.5 11.9 - - - +
241D PHE* 1.3 78.1 - - - +
243D HIS* 1.3 58.4 + - - +
245D ILE* 3.4 7.8 + - - +
246D ASN* 2.4 66.0 + - - +
251D LYS* 5.5 3.4 + - - -
265D ILE* 4.8 4.5 - - - +
269D LYS* 2.6 35.9 + - - +
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Residues in contact with HIS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLN* 3.5 35.0 - - - +
239D MET 2.9 16.6 + - - +
240D MET* 3.6 4.9 - - - +
242D GLU* 1.3 76.4 - - - +
244D LEU* 1.3 58.9 + - - +
246D ASN* 4.5 4.0 - - + +
247D SER* 2.7 60.9 + - - -
416D MET* 3.6 28.6 + - + +
417D GLU* 3.9 36.4 + - + +
420D THR* 4.0 1.7 + - - -
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Residues in contact with LEU 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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135D ILE* 3.7 34.1 - - + +
138D THR* 3.2 32.5 - - + +
140D GLN* 3.9 21.3 - - + +
141D PHE* 4.1 10.8 - - + +
205D CYS* 5.2 0.9 - - - -
208D LEU* 4.5 15.5 - - + -
240D MET 2.9 13.8 + - - +
241D PHE* 3.1 11.6 + - + +
243D HIS* 1.3 72.1 - - - +
245D ILE* 1.3 78.6 + - + +
248D ASN* 3.0 36.5 + - - +
250D ILE* 3.9 17.0 - - + +
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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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135D ILE* 5.2 2.2 - - + -
241D PHE* 2.9 56.7 + - + +
242D GLU* 3.5 10.5 - - - +
244D LEU* 1.3 85.1 - - + +
246D ASN* 1.3 70.6 + - - +
248D ASN 3.4 5.0 + - - -
249D GLY* 3.4 1.4 + - - -
250D ILE* 3.4 48.6 + - + -
251D LYS* 3.7 34.7 - - + +
254D MET* 4.6 7.6 - - - -
265D ILE* 4.2 10.5 - - + -
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Residues in contact with ASN 246 (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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242D GLU* 2.4 51.0 + - - +
243D HIS* 4.3 4.4 - - + +
245D ILE* 1.3 88.1 - - - +
247D SER* 1.3 60.4 - - - +
248D ASN 3.5 0.5 + - - -
249D GLY* 4.1 4.9 + - - -
251D LYS* 3.9 15.4 + - - -
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Residues in contact with SER 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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450A TYR* 5.7 0.5 + - - -
140D GLN* 4.7 4.5 - - - -
243D HIS* 2.7 51.7 + - - -
246D ASN* 1.3 77.1 - - - +
248D ASN* 1.3 73.4 + - - +
249D GLY 3.7 0.7 - - - -
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Residues in contact with ASN 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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450A TYR* 3.5 29.5 + - - -
134D ARG* 4.4 9.9 + - - -
138D THR* 3.4 27.6 - - + +
139D PRO* 3.9 1.2 - - - +
140D GLN* 2.7 30.5 + - - -
244D LEU* 3.0 26.3 + - - +
247D SER* 1.3 86.8 - - - +
249D GLY* 1.3 63.5 + - - +
250D ILE* 3.4 14.8 + - + +
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Residues in contact with GLY 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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134D ARG* 4.7 2.3 + - - -
245D ILE 3.4 4.0 + - - -
246D ASN 4.1 5.0 + - - -
247D SER 3.7 2.2 + - - -
248D ASN* 1.3 79.4 - - - +
250D ILE* 1.3 62.1 + - - +
251D LYS 3.7 1.8 - - - -
252D PRO* 3.6 17.7 - - - +
253D VAL* 3.4 17.2 - - - +
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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