Contacts of the strand formed by residues 201 - 210 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136I GLU* 5.0 2.2 - - + -
137I TYR 3.4 17.7 - - - +
138I THR* 3.7 14.5 + - - +
195I ALA* 4.0 1.2 - - - +
196I GLU* 2.8 50.4 + - + +
198I MET* 3.0 40.3 + - + +
199I PRO 3.1 0.6 - - - -
200I ALA* 1.3 77.7 + - - +
202I TRP* 1.3 70.8 + - - +
242I PRO* 5.5 1.2 - - - +
248I ASN* 3.7 15.2 + - - +
249I GLY 2.9 33.5 + - - +
250I ALA* 3.9 10.5 - - - +
601I P3S 4.2 2.1 + - - -
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Residues in contact with TRP 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I GLU* 3.3 6.9 - - - +
137I TYR* 2.9 53.4 + - + +
139I LEU* 4.1 15.7 - - + +
170I ALA* 4.0 21.1 - - + -
171I TYR 2.9 28.7 + - - +
172I GLY 4.5 0.4 - - - -
173I ARG* 3.9 45.5 - - + -
176I VAL* 3.3 30.5 - - + -
194I ASN* 3.6 7.9 - - - -
195I ALA* 3.3 45.3 - - + -
196I GLU* 4.0 5.3 - - - +
200I ALA* 3.6 16.0 - - - +
201I GLN* 1.3 78.4 + - - +
203I GLU* 1.3 65.0 + - - +
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Residues in contact with GLU 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I GLU* 2.8 13.7 - - + +
135I GLN 3.3 13.0 - - - +
136I GLU* 3.4 7.2 - - + +
137I TYR* 4.1 3.0 + - - -
176I VAL* 5.1 1.9 - - - +
193I THR* 3.2 9.5 - - - +
194I ASN* 2.9 47.0 + - - +
196I GLU* 3.0 8.3 - - + +
202I TRP* 1.3 79.7 - - - +
204I PHE* 1.3 70.6 + - - +
205I GLN* 2.9 14.3 + - - +
401I MN 2.0 34.7 + - - -
403I MN 2.2 28.4 + - - -
501I ADP 3.1 0.2 + - - -
601I P3S 3.2 0.5 + - - -
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Residues in contact with PHE 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I MET 3.7 0.5 - - - +
134I GLU 3.6 0.5 - - - -
135I GLN* 2.8 65.8 + - + -
137I TYR* 3.9 15.5 - + - -
179I HIS* 3.4 32.1 - + + +
190I ILE* 4.0 8.5 - - + -
192I GLY 3.4 6.3 - - - +
193I THR* 3.7 18.2 - - + +
203I GLU* 1.3 76.3 - - - +
205I GLN* 1.3 60.4 + - - +
206I ILE* 3.6 31.4 - - + -
218I LEU* 4.2 3.8 - - + -
221I ALA* 3.7 22.4 - - + -
222I ARG* 4.6 4.7 - - - -
225I LEU* 4.2 17.5 - - + -
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Residues in contact with GLN 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LYS* 6.2 0.8 - - - +
44H THR 4.5 1.7 - - - +
60H TRP* 5.2 4.9 - - - -
133I MET 3.3 4.5 - - - -
134I GLU* 3.8 9.6 - - + -
190I ILE* 3.5 7.1 - - - +
191I ALA* 2.6 38.8 + - + -
192I GLY* 3.0 33.6 + - - +
193I THR* 3.6 2.1 + - - +
194I ASN* 3.1 18.0 + - - -
203I GLU* 2.9 28.1 + - - +
204I PHE* 1.3 73.5 - - - +
206I ILE* 1.3 58.5 + - - +
501I ADP 3.0 51.7 + - - +
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Residues in contact with ILE 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I GLY* 3.2 2.6 - - - -
133I MET 3.0 29.7 + - - +
183I CYS* 5.5 0.2 - - - -
188I VAL* 3.5 27.8 - - + -
189I LYS 3.3 6.3 - - - +
190I ILE* 3.9 15.9 - - + -
204I PHE* 3.6 25.4 - - + -
205I GLN* 1.3 76.6 - - - +
207I GLY* 1.3 60.0 + - - +
209I CYS* 4.1 4.3 - - - -
214I MET* 3.6 25.7 - - + +
217I HIS* 3.9 22.4 - - + -
218I LEU* 4.3 9.2 - - + +
221I ALA* 3.8 14.4 - - + -
501I ADP 3.9 2.2 - - - -
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Residues in contact with GLY 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I PHE 4.0 1.3 - - - -
132I GLY* 4.3 0.2 - - - -
189I LYS* 2.8 28.4 + - - +
191I ALA* 3.6 14.7 - - - +
206I ILE* 1.3 75.2 - - - +
208I PRO* 1.3 76.1 - - - +
209I CYS* 3.8 6.3 - - - -
501I ADP 3.3 11.1 + - - -
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Residues in contact with PRO 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I TRP* 4.1 29.6 - - + -
131I PHE 3.3 8.7 - - - +
189I LYS* 3.1 26.5 - - - +
207I GLY* 1.3 81.3 - - - +
209I CYS* 1.3 61.2 + - - +
210I GLU 4.1 0.9 + - - -
501I ADP 3.3 46.4 - - + +
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Residues in contact with CYS 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I TRP* 3.4 3.0 - - - -
131I PHE* 2.7 37.4 + - - +
189I LYS* 4.3 11.2 - - - -
206I ILE* 4.1 16.2 - - - -
207I GLY* 4.1 6.3 - - - -
208I PRO* 1.3 77.2 - - - +
210I GLU* 1.3 61.3 + - - +
211I GLY 3.5 1.2 + - - -
213I SER* 3.4 27.4 - - - +
214I MET* 3.5 20.6 - - - +
217I HIS* 4.1 20.9 - - - -
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Residues in contact with GLU 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I SER* 4.1 8.3 - - - +
128I HIS* 2.7 46.2 + - - +
129I PRO* 3.2 14.7 - - + +
130I TRP* 3.5 22.1 + - + +
208I PRO 4.1 1.4 + - - -
209I CYS* 1.3 70.1 - - - +
211I GLY* 1.3 68.9 + - - +
212I ILE* 3.5 0.7 + - - +
213I SER* 2.8 28.5 + - - +
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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