Contacts of the strand formed by residues 201 - 210 (chain E) in PDB entry 4QRR
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 201 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E GLY 3.4 6.6 + - - -
163E PHE* 2.9 57.3 + - + -
164E TYR* 4.0 23.7 - + - -
165E PRO* 4.1 1.6 - - + -
166E ASP* 3.5 40.6 - - + -
189E PRO* 4.1 20.4 - - + -
190E LEU 3.7 3.8 - - - -
191E LYS* 3.7 37.0 - - + +
192E GLU* 3.9 0.4 - - - +
197E ASN 5.4 2.9 + - - -
199E SER 4.4 5.8 - - - -
200E ARG* 1.3 74.2 - - - +
202E ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 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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172D TYR* 6.2 1.1 - - + -
174D THR* 6.1 0.2 - - - +
194D TRP* 4.0 26.5 - - + -
160E ALA 3.4 9.4 - - - +
161E THR* 4.1 11.0 - - + -
163E PHE* 3.8 2.7 - - - -
189E PRO* 3.4 5.0 - - - +
190E LEU* 2.8 43.2 + - + +
192E GLU* 4.5 12.1 - - + +
201E TYR* 1.3 74.9 - - - +
203E LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 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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174D THR* 6.0 1.3 - - - -
194D TRP* 5.4 1.3 - - - -
158E CYS 4.8 0.2 - - - -
159E LEU* 3.6 5.7 - - - +
160E ALA* 2.8 39.4 + - + +
163E PHE* 4.2 13.2 - - + -
168E VAL* 4.3 19.3 - - + -
170E LEU* 4.0 22.2 - - + +
185E THR* 3.9 19.1 - - + -
186E ASP* 3.6 35.7 - - + +
187E PRO 5.3 0.4 - - - +
188E GLN 4.1 0.7 - - - +
189E PRO* 3.9 24.5 - - + -
202E ALA* 1.3 73.9 - - - +
204E SER* 1.3 63.4 + - - +
225E VAL* 6.3 0.4 - - + -
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Residues in contact with SER 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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174D THR* 3.4 20.7 + - - +
192D VAL* 3.9 23.9 - - - +
194D TRP* 4.4 0.2 - - - -
157E VAL* 5.0 0.2 - - - -
158E CYS 3.4 12.6 - - - -
159E LEU* 4.0 8.5 - - - -
170E LEU* 5.0 0.7 - - - -
185E THR* 3.9 3.6 - - - +
186E ASP* 2.6 53.1 + - - +
203E LEU* 1.3 74.5 - - - +
205E SER* 1.3 62.7 + - - +
206E ARG* 3.6 8.9 + - - -
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Residues in contact with SER 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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157E VAL* 3.4 5.2 - - - +
158E CYS* 2.9 33.3 + - - +
170E LEU* 3.6 22.1 - - - +
172E TRP* 2.7 32.7 + - - -
183E VAL* 4.2 0.2 - - - +
184E SER 3.5 6.6 + - - -
185E THR* 2.9 25.5 + - - -
204E SER* 1.3 74.5 - - - +
206E ARG* 1.3 65.1 + - - +
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Residues in contact with ARG 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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153D LEU* 4.3 10.5 - - + -
174D THR* 3.0 27.9 + - - -
175D ASP 3.8 9.3 + - - -
177D THR* 3.0 20.8 + - - -
179D LEU* 4.3 11.2 - - + -
190D SER* 3.4 27.6 + - - +
192D VAL* 3.5 28.1 - - + +
155E THR* 4.1 13.7 - - + -
156E LEU 3.4 4.7 - - - -
157E VAL* 4.4 3.1 - - + -
172E TRP* 4.1 3.3 + - - -
182E GLY 3.5 2.0 - - - +
183E VAL* 3.5 4.2 - - - -
184E SER* 2.8 44.9 + - - +
186E ASP* 3.0 30.3 + - - +
204E SER* 3.6 18.6 + - - -
205E SER* 1.3 78.6 + - - +
207E LEU* 1.3 58.8 + - - +
208E ARG 4.2 0.2 - - - -
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Residues in contact with LEU 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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154E ALA 3.6 1.4 - - - +
155E THR* 3.3 2.8 - - - -
156E LEU* 2.8 54.9 + - + +
172E TRP* 3.7 38.8 - - + -
174E VAL* 4.5 8.3 - - + -
179E VAL* 3.8 18.6 - - + -
181E SER 4.8 3.6 - - - +
182E GLY 3.4 4.5 - - - +
183E VAL* 3.7 25.6 - - + -
206E ARG* 1.3 72.8 - - - +
208E ARG* 1.3 62.0 - - - +
209E VAL* 4.5 11.9 - - + -
221E PHE* 4.0 26.7 - - + -
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Residues in contact with ARG 208 (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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142D TYR* 5.6 0.2 - - - -
155D THR* 3.4 17.3 + - - +
156D ASP* 2.8 36.2 + - - -
179D LEU* 3.7 30.2 - - + +
181D MET* 3.7 30.3 - - + +
186D PHE* 4.4 1.1 - - - -
188D SER* 3.3 19.2 + - - -
147E GLU* 3.5 11.4 + - - +
151E THR* 3.4 28.7 + - - +
153E LYS* 3.5 20.4 - - + +
154E ALA 3.4 7.9 - - - +
155E THR* 3.3 20.6 + - - +
181E SER 4.8 2.3 - - - +
182E GLY* 2.9 20.3 + - - -
207E LEU* 1.3 74.5 - - - +
209E VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 209 (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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181D MET* 4.9 6.3 - - - -
153E LYS* 3.5 7.1 - - - +
154E ALA 2.8 42.4 + - - +
156E LEU* 4.1 18.8 - - + -
174E VAL* 5.4 2.7 - - + -
207E LEU* 4.5 15.9 - - + -
208E ARG* 1.3 78.8 - - - +
210E SER* 1.3 65.0 + - - +
213E PHE* 3.9 28.3 - - + -
214E TRP* 4.1 17.9 - - + +
221E PHE* 4.3 9.9 - - + -
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Residues in contact with SER 210 (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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181D MET* 5.3 2.5 - - - -
184D MET* 5.5 13.2 - - - -
152E GLN 4.2 6.7 - - - -
153E LYS* 4.5 4.0 - - - +
154E ALA 4.5 0.4 + - - -
209E VAL* 1.3 78.9 - - - +
211E ALA* 1.3 65.2 - - - +
212E THR* 4.0 9.7 + - - -
213E PHE* 3.1 31.9 + - - +
214E TRP* 3.3 10.9 + - - +
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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