Contacts of the helix formed by residues 221 - 232 (chain D) in PDB entry 1TYE
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 GLY 221 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156D PHE* 3.9 10.9 - - - +
157D VAL 3.0 9.9 + - - -
158D ASP* 3.6 17.3 - - - -
159D LYS 5.2 0.2 - - - -
189D GLY 5.0 2.3 - - - +
190D TYR* 5.9 0.2 - - - +
220D GLU* 1.3 76.0 - - - +
222D GLY* 1.3 62.9 + - - +
223D PHE 3.3 2.7 - - - -
224D ASP* 3.1 22.2 + - - +
225D ALA* 3.6 3.3 + - - +
255D HIS* 5.0 0.4 - - - -
289D TYR* 4.0 17.3 - - - -
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Residues in contact with GLY 222 (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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156D PHE* 3.4 29.8 - - - -
220D GLU 3.5 5.3 + - - -
221D GLY* 1.3 70.5 - - - +
223D PHE* 1.3 60.3 + - - +
224D ASP 3.0 2.2 - - - -
225D ALA* 2.8 19.9 + - - +
226D ILE* 2.8 15.9 + - - +
248D PHE* 3.5 22.0 - - - -
254D THR* 4.4 2.4 + - - -
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Residues in contact with PHE 223 (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 GLY* 3.3 1.0 - - - -
222D GLY* 1.3 76.8 - - - +
224D ASP* 1.3 61.5 + - - +
226D ILE* 3.8 23.7 - - + +
227D MET 3.2 17.5 + - - -
248D PHE* 4.7 4.3 - + - -
254D THR* 3.7 29.1 + - + -
255D HIS 3.6 19.3 - - - +
256D ILE* 4.1 15.0 - - + -
289D TYR* 5.4 1.8 - - + -
290D PRO* 3.5 27.9 - - + +
292D LEU* 3.6 17.0 - - + -
295D MET* 3.3 37.1 - - + +
308D PHE* 4.5 19.3 - + - -
318D TYR* 4.6 4.7 - + - -
321D TYR* 4.7 13.7 - + + -
325D ILE* 5.3 0.9 - - + -
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Residues in contact with ASP 224 (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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159D LYS* 2.9 29.4 + - - +
189D GLY 6.0 2.0 - - - +
190D TYR* 5.1 2.2 - - + -
221D GLY* 3.1 18.0 + - - +
222D GLY 3.0 0.6 - - - -
223D PHE* 1.3 80.5 - - - +
225D ALA* 1.3 58.2 + - - +
227D MET* 3.8 3.4 + - - +
228D GLN* 3.3 27.5 + - - +
269D ASN* 4.2 3.3 + - - +
281D TYR* 3.3 28.8 + - + -
284D SER* 4.1 6.3 + - - +
288D ASP 4.0 4.0 - - - +
289D TYR* 3.5 17.7 - - + -
290D PRO* 3.3 22.7 - - - +
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Residues in contact with ALA 225 (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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117D LEU* 3.8 15.9 - - + -
156D PHE* 3.9 20.6 - - + -
190D TYR* 3.4 36.6 - - + +
221D GLY 3.6 0.4 + - - -
222D GLY 2.8 10.4 + - - +
224D ASP* 1.3 76.8 - - - +
226D ILE* 1.3 59.5 + - - +
227D MET 3.2 1.8 - - - -
228D GLN* 3.3 0.7 + - - +
229D ALA* 2.8 33.3 + - - +
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Residues in contact with ILE 226 (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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117D LEU* 4.0 10.1 - - + -
222D GLY 2.8 13.4 + - - +
223D PHE* 3.4 25.3 + - + +
225D ALA* 1.3 75.4 - - - +
227D MET* 1.3 60.5 + - - +
229D ALA* 3.9 0.9 - - - +
230D THR* 2.7 40.1 + - - +
246D LEU* 4.1 10.0 - - + +
248D PHE* 3.6 35.0 - - + -
295D MET* 4.5 15.0 - - + -
299D LEU* 4.8 8.3 - - + -
306D LEU* 3.9 35.9 - - + -
308D PHE* 4.2 4.5 - - + -
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Residues in contact with MET 227 (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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223D PHE 3.2 13.6 + - - +
224D ASP* 3.8 6.5 - - - +
225D ALA 3.2 0.4 - - - -
226D ILE* 1.3 79.4 - - - +
228D GLN* 1.3 70.0 + - - +
230D THR* 3.1 7.4 + - - -
231D VAL* 3.0 36.0 + - + +
269D ASN* 3.8 16.8 - - - +
271D GLY* 4.1 10.5 - - - -
290D PRO* 3.8 10.3 - - + -
294D LEU* 3.4 33.9 - - + +
295D MET* 3.6 36.6 - - + -
298D LYS* 3.8 19.7 - - + -
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Residues in contact with GLN 228 (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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190D TYR* 3.8 24.9 - - + -
224D ASP 3.3 16.8 + - - +
225D ALA 3.3 1.7 + - - +
227D MET* 1.3 91.9 - - - +
229D ALA* 1.3 57.9 + - - +
231D VAL* 4.2 2.2 - - - -
232D CYS* 3.1 37.6 + - - +
236D ILE* 4.6 0.2 - - - +
269D ASN* 5.4 1.2 + - - -
272D GLN 3.2 21.0 + - - -
274D HIS* 2.8 27.0 + - - -
275D VAL* 3.4 12.1 - - + +
281D TYR* 3.4 44.3 + - + -
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Residues in contact with ALA 229 (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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115D TYR* 3.9 32.1 - - + -
117D LEU* 4.2 10.3 - - + -
190D TYR* 4.2 4.4 + - - +
225D ALA 2.8 21.0 + - - +
226D ILE 4.0 2.9 - - - +
228D GLN* 1.3 73.4 - - - +
230D THR* 1.3 59.3 + - - +
232D CYS 4.4 0.2 + - - -
236D ILE* 3.5 17.2 - - - +
238D TRP* 2.8 28.8 + - - -
246D LEU* 4.3 7.9 - - + -
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Residues in contact with THR 230 (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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226D ILE* 2.7 22.6 + - - +
227D MET* 3.1 6.9 + - - -
229D ALA* 1.3 80.0 - - - +
231D VAL* 1.3 59.5 + - + +
232D CYS 3.6 0.4 + - - -
233D ASP* 4.0 5.0 - - - +
238D TRP* 4.2 2.3 + - - -
246D LEU* 3.8 8.1 - - - +
298D LYS* 3.5 42.8 - - + +
299D LEU* 3.5 23.5 - - + +
302D LYS* 3.5 15.6 - - + +
304D ILE* 3.5 24.0 - - + +
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Residues in contact with VAL 231 (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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227D MET* 3.0 24.8 + - + +
228D GLN* 4.2 4.9 - - - +
230D THR* 1.3 81.7 - - + +
232D CYS* 1.3 58.5 + - - +
233D ASP* 3.3 12.9 + - - +
271D GLY 3.7 17.5 - - - +
272D GLN* 3.7 9.4 - - - +
273D CYS* 3.6 34.6 + - - +
298D LYS* 3.9 31.4 - - + -
302D LYS* 4.2 17.7 + - - +
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Residues in contact with CYS 232 (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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228D GLN* 3.1 29.1 + - - +
229D ALA 4.4 0.4 + - - -
230D THR 3.6 1.6 - - - -
231D VAL* 1.3 74.8 - - - +
233D ASP* 1.3 64.9 + - - +
234D GLU 3.4 2.0 - - - -
235D LYS* 3.1 17.1 + - + -
236D ILE* 2.8 30.4 + - + +
238D TRP* 5.1 1.1 - - - -
273D CYS* 2.0 52.5 - - - -
275D VAL* 3.7 20.6 - - + -
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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