Contacts of the strand formed by residues 201 - 210 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136J GLU* 5.0 2.2 + - + +
137J TYR 3.3 18.4 - - - +
138J THR* 3.7 17.5 + - - +
195J ALA* 3.9 1.4 - - - +
196J GLU* 2.9 44.3 + - + +
197J VAL 3.8 1.4 + - - -
198J MET* 3.0 41.0 + - + +
199J PRO 3.1 0.4 - - - -
200J ALA* 1.3 79.9 + - - +
202J TRP* 1.3 68.9 + - - +
242J PRO* 5.5 1.0 - - - +
248J ASN* 3.8 15.2 + - - +
249J GLY 3.1 32.2 + - - +
250J ALA* 4.0 9.1 - - - +
601J P3S 4.5 2.0 + - - -
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Residues in contact with TRP 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J GLU* 3.4 7.3 - - - +
137J TYR* 2.9 52.9 + - + +
139J LEU* 3.9 17.3 - - + +
170J ALA* 4.1 6.5 - - + -
171J TYR 2.9 38.6 + - - +
172J GLY 4.5 0.4 - - - -
173J ARG* 3.9 49.8 - - + -
176J VAL* 3.3 34.1 - - + -
194J ASN* 3.7 9.2 - - - -
195J ALA* 3.3 43.3 - - + -
196J GLU* 4.1 5.0 - - - +
200J ALA* 3.6 16.1 - - - +
201J GLN* 1.3 79.1 + - - +
203J GLU* 1.3 64.1 + - - +
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Residues in contact with GLU 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J GLU* 2.7 13.0 - - + +
135J GLN 3.4 13.7 - - - +
136J GLU* 3.3 9.5 - - + +
137J TYR* 3.9 3.3 + - - -
176J VAL* 5.3 1.7 - - - +
193J THR* 3.2 24.8 - - - +
194J ASN* 3.0 32.1 + - - +
196J GLU* 3.0 8.8 - - + +
202J TRP* 1.3 79.4 - - - +
204J PHE* 1.3 70.8 + - - +
205J GLN* 3.2 7.0 + - - +
401J MN 2.1 34.2 + - - -
403J MN 2.3 26.0 + - - -
501J ADP 3.2 5.7 + - - -
601J P3S 3.2 0.3 + - - -
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Residues in contact with PHE 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J MET 3.7 0.3 - - - +
134J GLU* 3.6 1.4 - - - -
135J GLN* 2.8 63.6 + - + -
137J TYR* 3.7 22.0 - + - -
179J HIS* 3.5 29.2 - + + +
190J ILE* 3.9 9.2 - - + -
192J GLY 3.3 10.8 - - - +
193J THR* 3.8 11.2 - - + +
203J GLU* 1.3 74.2 - - - +
205J GLN* 1.3 64.0 + - - +
206J ILE* 3.5 23.6 - - + -
218J LEU* 4.0 3.1 - - + -
221J ALA* 3.5 36.1 - - + -
222J ARG* 4.5 4.7 - - - -
225J LEU* 4.1 11.9 - - + -
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Residues in contact with GLN 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LYS* 6.3 0.4 - - - +
44I THR 4.5 1.2 - - - +
60I TRP* 5.2 5.4 - - - -
133J MET 3.3 4.3 - - - +
134J GLU* 3.9 13.2 - - + -
190J ILE* 3.4 1.7 - - - +
191J ALA* 2.6 37.6 + - + +
192J GLY* 3.0 35.3 + - - +
193J THR* 3.7 3.5 + - - +
194J ASN* 3.1 26.3 + - - -
203J GLU* 3.2 15.6 + - - +
204J PHE* 1.3 75.3 - - - +
206J ILE* 1.3 63.0 + - - +
501J ADP 3.3 49.1 + - - +
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Residues in contact with ILE 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J GLY* 3.2 2.3 - - - -
133J MET 2.8 33.0 + - - +
183J CYS* 5.6 0.2 - - - -
188J VAL* 4.0 13.5 - - + -
189J LYS 3.4 9.4 - - - +
190J ILE* 3.8 16.8 - - + -
204J PHE* 3.5 33.2 - - + -
205J GLN* 1.3 82.1 - - - +
207J GLY* 1.3 60.8 + - - +
209J CYS* 4.0 4.5 - - - -
214J MET* 3.5 21.7 - - + +
217J HIS* 3.6 30.7 - - + -
218J LEU* 3.9 14.1 - - + +
221J ALA* 4.0 5.8 - - + -
501J ADP 4.0 2.7 - - - -
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Residues in contact with GLY 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J PHE 3.7 1.8 - - - -
132J GLY* 4.1 0.7 - - - -
189J LYS* 2.9 27.4 + - - +
191J ALA* 3.4 13.0 - - - +
205J GLN 4.0 1.8 + - - -
206J ILE* 1.3 75.6 - - - +
208J PRO* 1.3 77.3 - - - +
209J CYS* 3.7 7.6 - - - -
501J ADP 3.4 12.4 + - - -
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Residues in contact with PRO 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J TRP* 4.1 31.9 - - + -
131J PHE 3.1 9.2 - - - +
189J LYS* 3.4 26.0 - - - +
191J ALA* 5.3 0.2 - - + -
207J GLY* 1.3 82.4 - - - +
209J CYS* 1.3 58.9 + - - +
210J GLU 4.2 0.5 + - - -
501J ADP 3.3 46.2 - - + +
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Residues in contact with CYS 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J TRP* 3.4 3.4 - - - -
131J PHE* 2.7 35.7 + - - +
189J LYS* 4.5 8.1 - - - -
206J ILE* 4.0 25.6 - - - -
207J GLY* 4.0 6.3 - - - -
208J PRO* 1.3 76.8 - - - +
210J GLU* 1.3 62.8 + - - +
211J GLY 3.5 1.4 + - - -
213J SER* 3.4 14.4 - - - +
214J MET* 3.4 27.8 - - + -
217J HIS* 4.0 20.0 - - - -
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Residues in contact with GLU 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J SER* 4.1 7.1 - - - +
128J HIS* 2.5 47.5 + - - -
129J PRO* 3.4 14.2 - - + +
130J TRP* 3.6 19.8 + - + +
208J PRO 4.2 0.6 + - - -
209J CYS* 1.3 70.3 - - - +
211J GLY* 1.3 70.9 + - - +
212J ILE* 3.3 0.7 + - - +
213J SER* 3.0 22.9 + - - +
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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