Contacts of the strand formed by residues 201 - 210 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLU* 5.0 1.8 - - + -
137A TYR 3.3 17.7 - - - +
138A THR* 3.7 14.6 + - - +
195A ALA* 4.1 0.7 - - - +
196A GLU* 2.9 41.4 + - + +
197A VAL 3.9 1.0 + - - -
198A MET* 2.9 46.9 + - + +
199A PRO 3.1 0.6 - - - -
200A ALA* 1.3 77.8 + - - +
202A TRP* 1.3 68.7 + - - +
242A PRO* 5.4 1.2 - - - +
248A ASN* 3.8 12.1 + - - +
249A GLY 3.0 35.1 + - - +
250A ALA* 3.8 13.5 - - - +
601A P3S 4.4 1.8 + - - -
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Residues in contact with TRP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLU* 3.3 6.2 - - - +
137A TYR* 2.9 53.6 + + + +
139A LEU* 4.0 17.2 - - + +
170A ALA* 4.1 9.6 - - + -
171A TYR 2.7 39.1 + - - +
172A GLY 4.4 0.2 - - - -
173A ARG* 3.8 48.0 - - + -
176A VAL* 3.3 30.7 - - + -
194A ASN* 3.6 9.2 - - - -
195A ALA* 3.3 44.2 - - + -
196A GLU* 4.0 4.3 - - - +
200A ALA* 3.4 15.3 - - - +
201A GLN* 1.3 88.7 + - - +
203A GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLU* 3.1 12.4 - - - +
135A GLN 3.3 13.0 - - - +
136A GLU* 4.0 6.3 - - + -
137A TYR* 3.8 2.8 + - - -
176A VAL* 5.3 1.7 - - - +
193A THR* 3.3 7.3 - - - +
194A ASN* 3.0 46.6 + - - +
196A GLU* 2.8 11.6 - - + +
202A TRP* 1.3 80.6 - - - +
204A PHE* 1.3 73.0 + - - +
205A GLN* 2.9 13.6 + - - +
401A MN 2.0 35.9 + - - -
403A MN 2.2 28.3 + - - -
501A ADP 2.9 1.7 + - - -
601A P3S 3.1 0.9 + - - -
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A MET 3.7 0.3 - - - +
134A GLU 3.5 0.9 - - - -
135A GLN* 2.7 65.7 + - + -
137A TYR* 3.7 17.0 - + - -
179A HIS* 3.5 30.1 - + + +
190A ILE* 4.1 7.4 - - + -
192A GLY 3.4 11.9 - - - +
193A THR* 3.9 11.7 - - + -
203A GLU* 1.3 75.8 - - - +
205A GLN* 1.3 61.2 + - - +
206A ILE* 3.7 22.9 - - + -
218A LEU* 3.9 4.9 - - + -
221A ALA* 3.7 32.5 - - + -
222A ARG* 4.6 2.0 - - - -
225A LEU* 3.8 25.4 - - + -
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Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A MET 3.2 4.7 - - - +
134A GLU* 4.0 5.6 - - + -
190A ILE* 3.5 6.8 - - - +
191A ALA* 2.8 31.8 + - + +
192A GLY* 3.0 35.9 + - - +
193A THR* 3.7 2.7 + - - +
194A ASN* 3.0 18.4 + - - -
203A GLU* 2.9 29.5 + - - +
204A PHE* 1.3 75.1 - - - +
206A ILE* 1.3 63.7 + - - +
501A ADP 3.4 50.6 + - - +
44E THR 4.6 1.2 - - - +
60E TRP* 5.0 5.9 - - - -
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY* 3.3 1.4 - - - -
133A MET 2.9 31.5 + - - +
183A CYS* 5.2 0.4 - - - -
188A VAL* 3.5 26.7 - - + -
189A LYS 3.3 7.2 - - - +
190A ILE* 3.7 13.7 - - + -
204A PHE* 3.7 25.1 - - + -
205A GLN* 1.3 82.7 - - - +
207A GLY* 1.3 61.0 + - - +
209A CYS* 4.1 2.7 - - - -
214A MET* 3.5 27.3 - - + +
217A HIS* 3.8 24.0 - - + -
218A LEU* 4.3 10.8 - - + +
221A ALA* 3.8 13.5 - - + -
501A ADP 4.1 2.4 + - - -
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PHE 3.5 5.4 - - - -
132A GLY* 4.1 1.1 - - - -
189A LYS* 2.9 23.7 + - - +
191A ALA* 3.5 12.6 - - - +
206A ILE* 1.3 76.5 - - - +
208A PRO* 1.3 77.6 - - - +
209A CYS* 3.6 6.5 - - - -
501A ADP 3.4 12.2 + - - -
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Residues in contact with PRO 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TRP* 3.9 36.2 - - + -
131A PHE 3.1 8.1 - - - +
189A LYS* 3.2 30.2 - - - +
207A GLY* 1.3 83.1 - - - +
209A CYS* 1.3 60.7 + - - +
210A GLU 4.2 0.7 + - - -
501A ADP 3.3 40.4 - - + +
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Residues in contact with CYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TRP* 3.6 2.3 - - - -
131A PHE* 2.8 31.8 + - - -
189A LYS* 4.3 7.9 - - - -
206A ILE* 4.1 8.7 - - - -
207A GLY* 3.9 13.2 - - - -
208A PRO* 1.3 78.5 - - - +
210A GLU* 1.3 61.5 + - - +
211A GLY 3.6 1.4 + - - -
213A SER* 3.5 9.9 - - - +
214A MET* 3.5 28.1 - - + +
217A HIS* 4.0 37.7 - - - -
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A SER* 4.2 4.5 - - - +
128A HIS* 2.6 44.1 + - - -
129A PRO* 3.3 14.1 - - + +
130A TRP* 3.2 28.4 + - + +
208A PRO 4.1 1.0 + - - -
209A CYS* 1.3 70.7 - - - +
211A GLY* 1.3 68.8 + - - +
212A ILE* 3.5 0.5 + - - +
213A SER* 2.7 26.7 + - - +
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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