Contacts of the helix formed by residues 205 - 222 (chain A) in PDB entry 4R1Z
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 ASP 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A SER 5.1 1.2 - - - +
201A TYR* 3.7 20.6 - - - -
202A LYS* 3.0 33.1 + - + +
203A ARG 3.2 1.6 + - - -
204A GLY* 1.3 76.9 - - - +
206A ALA* 1.3 58.2 + - - +
207A GLU* 2.4 39.0 + - - +
208A PHE* 3.1 11.9 + - + +
209A GLU* 3.0 29.7 + - - +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY 3.3 3.7 + - - -
205A ASP* 1.3 77.0 + - - +
207A GLU* 1.3 55.2 + - - +
209A GLU* 3.8 7.9 - - - +
210A SER* 3.1 24.8 + - - -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A TYR* 2.5 34.4 + - + -
205A ASP* 2.4 23.4 + - - +
206A ALA* 1.3 66.4 - - - +
208A PHE* 1.3 58.1 + - - +
210A SER* 2.6 25.2 + - - +
211A MET* 2.9 16.1 + - - +
255A LEU* 3.5 31.5 - - + +
258A LYS* 4.3 19.6 + - - +
259A LYS* 3.3 23.2 + - - -
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Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 4.6 4.7 - - + -
185A THR* 4.3 1.6 - - + -
186A ARG* 3.4 54.1 - - + -
189A THR* 3.7 22.7 - - + -
201A TYR* 3.5 44.6 - + + -
202A LYS 5.2 2.0 - - - -
204A GLY 5.6 0.9 - - - -
205A ASP* 3.1 13.0 + - + +
207A GLU* 1.3 75.8 - - - +
209A GLU* 1.3 79.5 + - - +
211A MET* 2.9 19.1 + - + +
212A LEU* 2.9 49.6 + - + +
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLY* 3.9 22.7 + - - +
205A ASP 3.0 21.0 + - - +
206A ALA* 3.8 8.5 - - - +
208A PHE* 1.3 92.8 - - - +
210A SER* 1.3 63.9 + - - +
211A MET 2.9 0.9 + - - -
212A LEU* 3.1 22.8 + - - +
213A GLN* 3.2 14.1 + - - +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA 3.1 11.6 + - - -
207A GLU* 2.6 28.3 + - - +
209A GLU* 1.3 80.1 - - - +
211A MET* 1.3 58.0 + - - +
213A GLN* 3.2 9.0 - - - +
214A TYR* 3.0 30.9 + - - +
251A ILE* 4.5 18.6 - - - +
255A LEU* 4.5 4.5 - - - +
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Residues in contact with MET 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR* 3.4 29.8 - - + +
201A TYR* 5.0 2.2 - - + +
207A GLU 2.9 11.7 + - - +
208A PHE* 2.9 12.9 + - + +
210A SER* 1.3 76.6 + - - +
212A LEU* 1.3 79.7 + - - +
214A TYR* 3.3 34.8 - - + +
215A SER* 3.2 35.9 + - - +
255A LEU* 4.3 6.1 - - + -
311A PHE* 3.3 35.9 - - + +
315A VAL* 3.9 19.1 - - + -
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 5.6 11.2 - - + +
185A THR* 4.1 17.7 - - + -
208A PHE* 2.9 57.2 + - + +
209A GLU* 3.5 20.2 - - - +
211A MET* 1.3 83.4 - - - +
213A GLN* 1.3 66.3 + - - +
215A SER* 3.5 3.3 + - - -
216A GLN* 3.1 22.4 + - - +
315A VAL* 5.8 0.9 - - + -
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLU 3.2 8.6 + - - +
210A SER* 3.2 13.9 - - - +
212A LEU* 1.3 79.4 - - - +
214A TYR* 1.3 64.9 + - + +
216A GLN* 3.0 25.4 - - - +
217A GLY 3.4 3.8 + - - -
248A CYS* 5.0 0.9 - - - -
251A ILE* 6.4 1.8 - - + -
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER* 3.0 24.1 + - - +
211A MET* 3.3 34.0 - - + +
212A LEU 3.4 0.2 - - - -
213A GLN* 1.3 79.1 - - + +
215A SER* 1.3 69.6 + - - +
217A GLY 3.3 1.9 + - - -
218A ILE* 3.1 31.6 + - + +
248A CYS* 3.4 29.5 - - + +
251A ILE* 3.5 29.2 - - + -
252A ARG* 3.5 44.7 - - + +
255A LEU* 4.0 14.1 - - + +
311A PHE* 3.9 14.2 - - - -
601A AER 3.5 20.9 - - - -
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A MET* 3.2 23.4 + - - +
212A LEU* 3.9 3.6 - - - -
214A TYR* 1.3 81.2 - - - +
216A GLN* 1.3 66.3 + - - +
218A ILE* 3.0 3.2 + - - -
219A VAL* 2.8 30.9 + - - +
316A GLU* 4.2 14.0 + - - -
601A AER 2.5 39.1 + - - -
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LEU 3.1 13.2 + - - +
213A GLN* 3.0 19.5 - - - +
215A SER* 1.3 75.2 - - - +
217A GLY* 1.3 64.4 + - - +
219A VAL* 3.9 6.0 - - - +
220A ASP* 2.9 59.5 + - - +
496A GLN* 5.9 1.4 - - - +
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Residues in contact with GLY 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN 3.4 4.2 + - - -
214A TYR 3.3 5.1 + - - -
216A GLN* 1.3 80.0 - - - +
218A ILE* 1.3 63.0 + - - +
220A ASP* 3.8 5.0 - - - +
221A THR* 3.0 30.7 + - - +
244A ILE* 4.7 12.8 - - - -
245A LEU* 5.3 0.4 - - - -
248A CYS* 3.8 19.1 - - - -
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.5 27.6 - - + -
214A TYR* 3.1 22.6 + - + +
215A SER* 3.0 8.1 + - - +
217A GLY* 1.3 73.8 - - - +
219A VAL* 1.3 68.8 + - - +
221A THR* 3.1 3.6 + - - -
222A VAL* 2.9 35.5 + - + +
245A LEU* 4.1 14.1 - - + -
248A CYS* 3.4 19.5 - - + -
249A ILE* 3.7 26.0 - - + +
252A ARG* 4.9 4.3 - - + -
601A AER 3.9 29.2 - - + +
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER 2.8 22.1 + - - +
216A GLN* 3.9 6.3 - - - +
218A ILE* 1.3 74.3 - - - +
220A ASP* 1.3 73.4 + - - +
222A VAL* 3.5 1.9 + - - +
223A ALA* 3.4 15.1 + - - +
316A GLU* 4.1 25.1 - - + +
492A GLY* 4.1 19.4 - - - -
493A VAL* 3.7 30.1 + - + +
496A GLN* 3.9 24.0 - - - +
601A AER 4.2 13.2 - - + -
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Residues in contact with ASP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLN* 2.9 48.9 + - - +
217A GLY* 3.8 5.8 - - - +
219A VAL* 1.3 82.0 - - - +
221A THR* 1.3 60.5 + - + +
223A ALA* 2.9 27.5 - - - +
492A GLY* 5.9 0.8 - - - -
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 4.5 10.7 - - - +
217A GLY 3.0 16.9 + - - +
218A ILE 3.6 0.2 + - - -
220A ASP* 1.3 76.3 - - + +
222A VAL* 1.3 59.3 + - - +
223A ALA* 3.1 11.3 + - - +
224A LYS* 4.3 7.1 - - - +
240A LYS 4.3 13.9 - - - +
241A ASP 3.4 24.7 - - - +
242A LEU* 5.5 1.1 - - - -
244A ILE* 3.6 20.0 - - + -
245A LEU* 3.1 35.1 - - - +
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 3.8 23.6 - - - +
115A THR* 5.1 7.9 - - + +
118A LEU* 4.8 10.5 - - + -
127A PHE* 6.0 4.5 - - + -
218A ILE* 2.9 38.4 + - + +
219A VAL 3.5 1.3 + - - -
221A THR* 1.3 75.0 - - - +
223A ALA* 1.3 54.4 + - - +
224A LYS 2.8 21.6 + - - +
226A SER* 4.0 13.2 - - - +
245A LEU* 4.8 6.3 - - + -
492A GLY 5.4 1.0 - - - +
493A VAL* 3.6 29.5 - - + +
601A AER 5.3 2.5 - - + -
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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