Contacts of the helix formed by residues 205 - 218 (chain P) in PDB entry 1ZD2
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204P GLN* 1.3 88.1 + - + +
206P THR* 1.3 66.6 + - - +
207P ASP* 3.7 8.7 + - - +
208P THR* 2.7 52.1 + - - +
209P ALA* 3.3 9.9 + - - +
211P LYS* 4.9 0.7 + - - -
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Residues in contact with THR 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU* 3.9 10.9 - - - +
102P ASN* 3.2 41.8 + - - +
104P PRO* 4.1 10.1 - - + -
105P MET* 3.7 21.3 - - + -
203P VAL* 4.9 2.6 - - - +
204P GLN 3.7 3.1 + - - -
205P ASP* 1.3 69.8 - - - +
207P ASP* 1.3 67.4 + - - +
208P THR 3.1 0.9 + - - -
209P ALA* 3.1 5.9 + - - +
210P LEU* 3.0 38.7 + - + +
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Residues in contact with ASP 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P PRO* 5.4 5.2 - - - +
205P ASP* 3.4 7.0 + - - +
206P THR* 1.3 80.3 - - - +
208P THR* 1.3 60.6 + - - +
210P LEU* 3.5 11.2 + - - +
211P LYS* 3.0 39.5 + - - +
222P LEU* 3.7 32.6 - - - +
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Residues in contact with THR 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205P ASP* 2.7 43.1 + - - +
207P ASP* 1.3 69.8 - - - +
209P ALA* 1.3 70.3 + - - +
211P LYS* 2.7 39.3 + - + +
212P GLU* 2.9 30.1 + - + +
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Residues in contact with ALA 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P MET* 4.5 7.0 - - + -
183P LEU* 5.5 1.6 - - + -
201P ILE* 4.0 15.7 - - + +
202P LEU 5.0 2.6 + - - -
203P VAL* 3.6 41.5 - - + -
204P GLN 5.6 0.2 - - - +
205P ASP 3.3 8.0 + - - +
206P THR 3.1 9.1 + - - +
208P THR* 1.3 79.5 - - - +
210P LEU* 1.3 58.7 + - + +
212P GLU* 3.0 7.5 + - - +
213P LEU* 2.8 28.0 + - - +
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Residues in contact with LEU 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P PRO* 4.3 20.4 - - + +
105P MET* 3.4 31.6 - - - -
108P ALA* 3.8 22.2 - - + -
206P THR* 3.0 30.0 + - + +
207P ASP* 3.5 8.5 - - - +
209P ALA* 1.3 77.2 - - + +
211P LYS* 1.3 52.4 + - - +
213P LEU* 2.9 12.5 + - + +
214P GLU* 2.5 39.9 + - - +
221P LEU* 4.5 8.5 - - + +
222P LEU* 3.7 29.8 - - + -
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Residues in contact with LYS 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205P ASP* 4.9 0.4 + - - -
207P ASP* 3.0 38.7 + - - +
208P THR* 2.7 37.5 + - + +
210P LEU* 1.3 70.9 - - - +
212P GLU* 1.3 55.7 + - + +
214P GLU* 3.2 12.9 + - - +
215P LYS* 2.8 29.6 + - - +
222P LEU* 3.9 19.5 - - + +
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Residues in contact with GLU 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200P THR 5.0 1.0 - - - +
201P ILE* 3.8 35.0 - - + +
202P LEU 4.8 8.5 + - - +
208P THR* 2.9 30.4 + - + +
209P ALA* 3.4 7.7 - - - +
211P LYS* 1.3 76.7 - - + +
213P LEU* 1.3 53.1 + - - +
215P LYS* 3.0 8.5 + - - +
216P VAL* 2.7 37.1 + - - +
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Residues in contact with LEU 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 4.1 20.6 - - + -
108P ALA* 4.7 2.2 - - + -
112P LEU* 3.8 19.1 - - + -
181P VAL* 3.8 25.8 - - + -
183P LEU* 4.6 9.4 - - + -
201P ILE* 3.5 10.5 - - + +
209P ALA 2.8 17.4 + - - +
210P LEU* 3.3 19.7 - - + +
212P GLU* 1.3 72.9 - - - +
214P GLU* 1.3 56.6 + - - +
216P VAL* 3.8 0.9 - - - -
217P THR* 2.8 59.2 + - + +
221P LEU* 3.2 25.8 - - + -
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Residues in contact with GLU 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P LEU 2.5 20.6 + - - +
211P LYS* 3.3 10.7 - - - +
213P LEU* 1.3 71.9 - - - +
215P LYS* 1.3 56.6 + - - +
217P THR* 3.9 1.8 - - - -
218P GLY* 2.9 25.6 + - - -
219P ILE 2.9 32.5 + - - +
220P GLN* 3.4 10.9 - - - +
221P LEU* 2.9 13.6 + - + +
222P LEU* 2.8 44.0 + - - +
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Residues in contact with LYS 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211P LYS 2.8 13.5 + - - +
212P GLU* 3.0 13.9 - - - +
214P GLU* 1.3 74.3 - - - +
216P VAL* 1.3 68.0 + - - +
218P GLY* 3.1 13.3 + - - -
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Residues in contact with VAL 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P THR* 5.7 2.8 - - - +
3P LEU* 3.4 23.1 - - + +
181P VAL* 4.0 13.7 - - + -
199P VAL* 3.3 32.8 - - + -
201P ILE* 4.4 4.0 - - + -
212P GLU 2.7 17.2 + - - +
213P LEU* 3.2 16.2 - - - +
215P LYS* 1.3 74.0 - - - +
217P THR* 1.3 73.6 + - + +
218P GLY 3.8 0.2 + - - -
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Residues in contact with THR 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P LEU* 4.1 9.6 - - + -
112P LEU* 3.9 24.3 - - + +
117P PHE* 4.1 21.1 - - + -
181P VAL* 4.5 1.1 - - + -
213P LEU* 2.8 51.8 + - + +
214P GLU* 3.5 2.8 + - - -
216P VAL* 1.3 78.9 - - + +
218P GLY* 1.3 64.8 + - - +
219P ILE* 3.3 25.3 + - - +
221P LEU* 4.5 1.6 - - - +
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Residues in contact with GLY 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214P GLU 2.9 12.3 + - - -
215P LYS 3.1 8.8 + - - -
216P VAL 3.5 0.4 + - - -
217P THR* 1.3 78.9 - - - +
219P ILE* 1.3 61.0 + - - +
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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