Contacts of the strand formed by residues 198 - 207 (chain E) in PDB entry 2ZUQ
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 TYR 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E GLU* 3.6 26.8 + - - +
163E ASN* 2.8 13.3 + - - -
164E PHE* 2.8 52.8 + - + +
165E TYR* 3.7 23.1 - + - -
167E LYS* 3.3 52.2 - - + +
188E TRP* 6.1 1.6 - - + -
189E THR* 3.9 15.3 - - - +
190E ASP* 3.9 4.0 - - - -
191E GLN* 2.7 58.4 + - + -
197E THR* 1.3 77.2 - - - +
199E SER* 1.3 57.1 + - - +
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Residues in contact with SER 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LEU 3.2 7.2 - - - -
162E ASN* 3.2 17.8 - - - -
163E ASN* 2.8 32.1 + - - -
164E PHE* 3.5 2.7 - - - -
188E TRP* 4.0 0.5 - - - +
189E THR* 2.7 35.1 + - - +
195E ASP* 5.6 0.2 + - - -
197E THR 5.2 0.3 + - - -
198E TYR* 1.3 71.6 + - - +
200E MET* 1.3 61.0 + - - +
170F HIS* 3.2 24.5 + - - -
172F PHE* 3.0 15.0 - - - -
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Residues in contact with MET 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E PHE 3.6 0.3 - - - -
161E LEU* 2.6 66.8 + - + +
164E PHE* 4.2 8.5 - - + -
169E ILE* 3.8 15.0 - - - -
171E VAL* 3.3 30.5 - - + -
186E ASN* 4.1 2.9 - - - +
187E SER 3.1 17.3 - - - +
188E TRP* 3.1 48.5 - - + +
199E SER* 1.3 75.8 - - - +
201E SER* 1.3 78.0 + - - +
202E SER* 3.7 6.5 - - - -
172F PHE* 3.4 5.2 - - - -
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Residues in contact with SER 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E VAL* 6.0 0.7 - - - -
159E CYS 3.6 3.8 - - - -
160E PHE* 3.4 32.3 - - - -
185E LEU 4.7 0.4 - - - -
186E ASN* 3.5 2.8 - - - -
187E SER* 3.0 37.2 + - - -
200E MET* 1.3 79.6 - - - +
202E SER* 1.3 62.0 + - - +
203E THR* 5.2 4.1 + - - -
172F PHE* 3.4 29.1 - - - +
184F SER* 3.7 7.1 + - - -
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Residues in contact with SER 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E VAL* 3.4 1.6 - - - -
159E CYS* 2.9 37.7 + - - -
171E VAL* 4.4 8.0 - - - +
173E TRP* 3.1 28.4 + - - -
184E VAL* 3.5 4.9 - - - +
185E LEU 3.3 5.6 - - - -
186E ASN* 2.8 26.8 + - - -
200E MET* 3.7 10.3 - - - -
201E SER* 1.3 75.2 - - - +
203E THR* 1.3 62.8 + - - +
204E LEU 4.2 0.7 - - - -
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Residues in contact with THR 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E SER* 4.0 20.4 - - - +
157E VAL 3.3 12.8 - - - +
158E VAL* 3.2 27.8 - - + +
183E GLY 3.6 1.6 - - - +
184E VAL* 3.6 2.1 - - - -
185E LEU* 2.8 44.3 + - + +
201E SER* 5.2 3.8 + - - -
202E SER* 1.3 76.4 + - - +
204E LEU* 1.3 61.6 + - - +
205E THR* 3.5 9.5 + - - +
147F LEU* 5.0 5.4 - - + +
149F LYS* 5.2 6.7 - - + +
182F THR* 6.1 3.6 - - + -
184F SER* 5.4 1.9 + - - -
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Residues in contact with LEU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E VAL* 3.0 36.6 + - + +
173E TRP* 3.8 49.1 - - + -
175E ILE* 3.7 24.9 - - + -
180E ARG* 3.8 20.2 - - - +
183E GLY* 3.9 7.0 - - - +
184E VAL* 3.8 17.4 - - + +
203E THR* 1.3 70.9 - - - +
205E THR* 1.3 63.6 + - - +
206E LEU* 3.6 36.1 - - + -
217E TYR* 5.4 2.2 - - + -
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Residues in contact with THR 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ALA 3.4 6.1 + - - -
156E SER* 2.5 29.9 + - - +
183E GLY* 3.3 26.0 + - - +
185E LEU* 5.3 7.2 - - + -
203E THR* 4.3 7.4 - - - +
204E LEU* 1.3 77.0 - - - +
206E LEU* 1.3 68.1 + - - +
149F LYS* 3.8 22.5 - - - +
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Residues in contact with LEU 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E GLY* 4.2 0.7 - - - -
155E ALA* 2.8 44.6 + - - +
157E VAL* 6.1 1.6 - - + -
175E ILE* 4.8 5.4 - - + -
180E ARG* 3.9 28.0 - - - +
204E LEU* 3.6 22.9 + - + -
205E THR* 1.3 78.2 + - - +
207E THR* 1.3 68.4 + - + +
208E LYS 3.3 0.2 + - - -
210E GLU* 3.9 33.7 - - + +
211E TYR* 4.0 9.9 - - + +
213E ARG* 5.7 1.3 - - - +
217E TYR* 3.8 28.9 - - + +
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Residues in contact with THR 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E GLY 4.3 11.0 - - - -
154E GLY* 4.8 1.3 - - - -
206E LEU* 1.3 72.6 - - + +
208E LYS* 1.3 53.3 + - - +
209E ASP* 3.5 13.3 - - - +
210E GLU* 2.6 58.6 + - - +
211E TYR 2.9 8.5 + - - -
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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