Contacts of the helix formed by residues 229 - 241 (chain D) in PDB entry 5ZR1
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 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A LEU* 3.3 31.7 - - - +
518A MET 4.3 13.5 - - - +
519A VAL* 5.9 1.6 - - - -
139D GLU* 4.0 12.4 + - - -
143D ILE* 6.5 1.1 - - + -
181D PHE* 5.0 6.1 - - + -
227D ARG* 3.1 34.2 + - - +
228D GLN* 1.3 73.4 - - - +
230D LEU* 1.3 64.5 + - - +
232D TYR* 3.1 14.4 + - - +
233D ASN* 2.9 25.5 + - - +
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Residues in contact with LEU 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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132D LEU* 4.5 6.5 - - + -
138D SER 5.9 0.2 - - - +
139D GLU* 4.0 21.2 + - - +
142D ALA* 4.3 12.8 - - + -
143D ILE* 3.8 28.9 - - + -
146D ILE* 4.0 17.7 - - + -
181D PHE* 5.2 5.2 - - + -
216D PHE* 3.6 35.0 - - + -
222D PHE* 4.3 17.7 - - + -
228D GLN* 3.6 0.4 - - - +
229D THR* 1.3 79.1 - - - +
231D LEU* 1.3 62.0 + - + +
233D ASN* 3.7 5.0 + - + +
234D LEU* 3.4 27.6 + - + +
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Residues in contact with LEU 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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216D PHE* 3.6 29.8 - - + -
219D ILE* 3.7 24.9 - - + +
222D PHE* 3.6 18.1 + - + +
223D ALA* 3.6 40.6 - - + +
228D GLN* 4.3 7.7 + - + +
229D THR 3.3 0.4 - - - -
230D LEU* 1.3 75.3 - - - +
232D TYR* 1.3 65.1 + - - +
234D LEU* 4.2 3.8 - - + +
235D PHE* 3.2 41.8 + - + -
260D LEU* 4.1 11.9 - - + -
264D VAL* 4.0 14.4 - - + -
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Residues in contact with TYR 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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514A ASN* 3.6 17.1 + - - -
516A LEU* 3.5 29.4 - - + -
566A ASP* 5.4 0.3 + - - -
567A GLU* 2.5 39.9 + - - -
228D GLN 3.4 16.4 + - - +
229D THR* 3.1 10.8 + - - +
231D LEU* 1.3 79.2 - - - +
233D ASN* 1.3 72.1 + - - +
235D PHE* 3.9 3.1 - - - +
236D ASP* 3.1 45.0 + - - +
263D ARG* 4.4 7.0 - - + -
264D VAL* 4.3 19.7 - - + +
267D ARG* 2.7 46.3 + - - +
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Residues in contact with ASN 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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516A LEU 3.1 17.2 + - - +
517A LYS* 3.3 35.6 - - - +
181D PHE* 3.3 29.0 - - + -
185D LEU* 4.5 11.5 - - + +
189D ASP* 4.5 2.1 + - - +
229D THR* 2.9 22.6 + - - +
230D LEU* 3.7 5.5 + - + +
231D LEU 3.4 0.2 - - - -
232D TYR* 1.3 86.2 - - - +
234D LEU* 1.3 65.0 + - + +
236D ASP* 3.2 14.3 + - - +
237D MET* 3.2 23.5 + - + +
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Residues in contact with LEU 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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146D ILE* 4.5 10.5 - - + -
188D LEU* 5.2 0.4 - - + -
214D PHE* 3.8 32.5 - - + -
216D PHE* 3.5 35.2 - - + -
230D LEU* 3.4 33.4 + - + +
231D LEU* 4.6 3.1 - - + +
232D TYR 3.4 0.4 - - - -
233D ASN* 1.3 75.0 - - + +
235D PHE* 1.3 66.8 + - + +
237D MET* 3.2 39.9 + - + +
238D VAL 3.4 6.6 + - - -
247D ILE* 3.3 27.4 - - + +
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Residues in contact with PHE 235 (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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97D SER* 4.2 13.0 - - - -
99D ILE* 5.0 4.0 - - + -
219D ILE* 4.5 11.2 - - + -
231D LEU* 3.2 40.5 + - + +
232D TYR* 4.0 1.3 - - - +
234D LEU* 1.3 80.7 - - + +
236D ASP* 1.3 59.7 + - - +
237D MET 3.2 0.6 + - - -
238D VAL* 3.6 7.8 + - - +
239D GLU* 3.6 25.8 + - - +
247D ILE* 4.1 26.9 - - + -
260D LEU* 4.6 8.5 - - + -
264D VAL* 3.6 32.8 - - + -
267D ARG* 3.6 21.1 - - + +
268D PHE* 3.6 37.2 - + + -
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Residues in contact with ASP 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASN* 4.7 0.5 + - - -
517A LYS* 3.7 26.2 + - - -
189D ASP* 4.0 8.8 - - - +
232D TYR* 3.1 32.7 + - - +
233D ASN* 3.3 13.0 - - - +
234D LEU 3.1 0.4 - - - -
235D PHE* 1.3 75.9 - - - +
237D MET* 1.3 58.3 + - - +
239D GLU 4.1 2.5 - - - +
240D HIS* 3.0 50.3 + - - +
241D SER 4.1 0.2 + - - -
267D ARG* 3.7 23.1 + - - +
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Residues in contact with MET 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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95D SER* 4.8 1.2 - - - -
181D PHE* 6.3 0.4 - - + -
184D ILE* 4.4 5.4 - - + +
185D LEU* 4.1 24.9 - - + -
188D LEU* 3.7 40.4 - - + -
189D ASP* 3.2 17.9 - - - +
233D ASN* 3.2 17.0 - - + +
234D LEU* 3.2 34.9 + - + +
236D ASP* 1.3 76.1 - - - +
238D VAL* 1.3 63.2 + - - +
239D GLU 3.3 1.1 - - - -
241D SER* 3.2 36.1 + - - +
243D VAL 4.2 6.2 - - - +
245D VAL* 4.1 20.2 - - + +
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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
----------------------------------------------------------
431A ASN* 5.6 3.6 + - - -
711A LYS* 6.2 1.3 - - - +
95D SER* 3.2 42.0 - - - +
96D HIS* 4.1 4.3 - - - -
97D SER* 3.7 36.6 - - - +
234D LEU 3.4 12.5 + - - +
235D PHE* 3.6 11.7 - - - +
237D MET* 1.3 79.2 - - - +
239D GLU* 1.3 73.4 + - - +
241D SER 5.4 0.7 - - - +
245D VAL* 3.6 11.9 - - + +
247D ILE* 3.7 8.3 - - + -
267D ARG 5.0 2.9 - - - +
269D SER* 5.2 4.9 - - - -
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Residues in contact with GLU 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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431A ASN* 5.3 3.1 + - - +
432A SER* 2.9 31.5 + - - -
433A SER* 3.5 26.2 + - - -
704A ARG* 5.6 5.2 - - - +
708A LYS* 3.1 21.4 + - - -
235D PHE 3.6 11.3 + - - +
236D ASP 4.0 0.4 + - - -
237D MET 3.3 0.2 - - - -
238D VAL* 1.3 88.9 - - + +
240D HIS* 1.3 81.5 + - + +
241D SER 5.3 0.7 - - - -
266D SER 5.3 0.2 - - - -
267D ARG* 2.9 37.9 - - + +
269D SER* 4.9 3.6 + - - -
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Residues in contact with HIS 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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432A SER* 4.4 15.4 - - - -
433A SER* 4.2 20.2 - - - -
490A ARG* 5.5 10.3 + - - -
704A ARG* 4.2 18.2 + - - -
2001A AGS 3.7 23.8 - - - -
189D ASP* 4.6 3.4 - - - +
236D ASP* 3.0 36.7 + - - +
239D GLU* 1.3 93.4 + - + +
241D SER* 1.3 66.9 + - - +
242D ARG* 3.8 5.2 + - - +
267D ARG* 5.3 0.4 + - - -
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Residues in contact with SER 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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433A SER* 5.6 1.4 + - - -
95D SER* 5.0 4.3 + - - -
188D LEU 2.2 31.6 + - - -
189D ASP* 3.6 14.7 + - - +
236D ASP 4.1 1.2 + - - -
237D MET* 3.2 35.5 + - - +
238D VAL 5.4 1.0 - - - +
239D GLU 5.3 0.7 - - - -
240D HIS* 1.3 80.8 - - - +
242D ARG* 1.3 63.2 + - - +
243D VAL* 3.0 20.1 + - - +
245D VAL* 4.9 0.4 - - - +
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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