Contacts of the strand formed by residues 201 - 210 (chain E) in PDB entry 2QC8
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 GLN 201 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136E GLU* 5.0 2.7 - - + -
137E TYR 3.2 18.6 - - - +
138E THR* 3.6 17.0 + - - +
195E ALA* 4.0 1.6 - - - +
196E GLU* 2.8 46.7 + - + +
197E VAL 3.8 1.0 + - - -
198E MET* 3.0 40.9 + - + +
199E PRO 3.1 0.6 - - - -
200E ALA* 1.3 79.6 + - - +
202E TRP* 1.3 67.3 + - - +
242E PRO* 5.3 0.8 - - - +
248E ASN* 3.6 13.1 + - - +
249E GLY 3.0 33.8 + - - +
250E ALA* 3.8 10.5 - - - +
601E P3S 4.7 1.1 + - - -
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Residues in contact with TRP 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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136E GLU* 3.3 5.9 - - - +
137E TYR* 2.9 55.0 + - + +
139E LEU* 4.0 16.6 - - + +
170E ALA* 4.2 18.4 - - + -
171E TYR 2.9 26.1 + - - +
173E ARG* 3.8 49.6 - - + -
176E VAL* 3.3 32.8 - - + -
194E ASN* 3.6 9.0 - - - -
195E ALA* 3.4 42.8 - - + -
196E GLU* 4.2 3.3 - - - +
200E ALA* 3.6 16.9 - - - +
201E GLN* 1.3 81.2 + - - +
203E GLU* 1.3 62.7 + - - +
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Residues in contact with GLU 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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134E GLU* 2.9 14.4 - - + +
135E GLN 3.3 13.0 - - - +
136E GLU* 4.1 6.3 - - + -
137E TYR* 3.8 5.1 + - - -
176E VAL* 5.2 1.7 - - - +
193E THR* 3.2 9.0 - - - +
194E ASN* 2.9 48.4 + - - +
196E GLU* 2.9 7.6 - - + +
202E TRP* 1.3 79.1 - - - +
204E PHE* 1.3 67.7 + - - +
205E GLN* 2.9 14.9 + - - +
401E MN 2.1 34.2 + - - -
403E MN 2.3 28.5 + - - -
501E ADP 3.0 0.5 + - - -
601E P3S 2.9 1.2 + - - -
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Residues in contact with PHE 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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133E MET 3.8 0.3 - - - +
134E GLU* 3.6 1.2 - - - -
135E GLN* 2.8 60.6 + - + -
137E TYR* 3.7 14.8 - + - -
179E HIS* 3.5 30.5 - + + +
190E ILE* 3.9 9.0 - - + -
192E GLY 3.3 11.0 - - - +
193E THR* 3.9 11.7 - - + +
203E GLU* 1.3 74.9 - - - +
205E GLN* 1.3 62.1 + - - +
206E ILE* 3.6 23.3 - - + -
218E LEU* 3.9 3.8 - - + -
221E ALA* 3.6 33.7 - - + -
222E ARG* 4.6 3.1 - - - -
225E LEU* 3.8 24.7 - - + -
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Residues in contact with GLN 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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43D LYS* 6.2 0.6 - - - +
44D THR 4.4 2.1 - - - +
60D TRP* 5.0 6.5 - - - -
133E MET 3.4 4.9 - - - +
134E GLU* 4.0 7.9 - - + -
190E ILE* 3.6 6.2 - - - +
191E ALA* 2.8 27.6 + - + +
192E GLY* 3.0 34.7 + - - +
193E THR* 3.6 5.6 + - - +
194E ASN* 3.0 18.8 + - - -
203E GLU* 2.9 29.3 + - - +
204E PHE* 1.3 75.1 - - - +
206E ILE* 1.3 63.8 + - - +
501E ADP 3.2 45.9 + - - +
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Residues in contact with ILE 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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132E GLY* 3.3 1.9 - - - -
133E MET 2.8 33.6 + - - +
183E CYS* 5.2 0.2 - - - -
188E VAL* 3.5 26.0 - - + -
189E LYS 3.4 7.4 - - - +
190E ILE* 3.8 13.2 - - + -
204E PHE* 3.6 26.2 - - + -
205E GLN* 1.3 81.2 - - - +
207E GLY* 1.3 59.1 + - - +
209E CYS* 4.2 2.7 - - - -
214E MET* 3.5 26.5 - - + +
217E HIS* 3.9 23.3 - - + -
218E LEU* 4.1 9.4 - - + +
221E ALA* 3.7 14.4 - - + -
501E ADP 3.9 2.5 - - - -
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Residues in contact with GLY 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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131E PHE 3.7 1.3 - - - -
189E LYS* 2.9 26.3 + - - +
191E ALA* 3.5 16.8 - - - +
205E GLN 4.1 1.0 - - - -
206E ILE* 1.3 75.7 - - - +
208E PRO* 1.3 76.4 - - - +
209E CYS* 3.5 8.5 - - - -
501E ADP 3.4 9.3 + - - -
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Residues in contact with PRO 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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130E TRP* 4.1 32.4 - - + -
131E PHE 3.1 9.4 - - - +
189E LYS* 3.2 26.3 - - - +
191E ALA* 5.4 0.2 - - + -
207E GLY* 1.3 81.2 - - - +
209E CYS* 1.3 60.7 + - - +
210E GLU 4.1 0.9 + - - -
501E ADP 3.3 44.6 - - + +
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Residues in contact with CYS 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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130E TRP* 3.5 1.7 - - - -
131E PHE* 2.7 35.9 + - - +
189E LYS* 4.4 8.7 - - - -
206E ILE* 4.2 8.5 - - - -
207E GLY* 3.9 13.2 - - - -
208E PRO* 1.3 76.5 - - - +
210E GLU* 1.3 63.3 + - - +
211E GLY 3.7 1.4 + - - -
213E SER* 3.5 21.3 - - - +
214E MET* 3.4 27.1 - - + -
217E HIS* 4.0 22.7 - - - -
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Residues in contact with GLU 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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125E SER* 4.4 6.2 - - - +
128E HIS* 2.8 42.9 + - - +
129E PRO* 3.2 16.5 - - + +
130E TRP* 3.0 28.1 + - + +
208E PRO 4.1 1.8 + - - -
209E CYS* 1.3 72.7 - - - +
211E GLY* 1.3 68.1 + - - +
212E ILE 3.4 0.2 + - - -
213E SER* 2.6 28.2 + - - -
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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