Contacts of the strand formed by residues 201 - 210 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136G GLU* 5.0 2.2 - - + -
137G TYR 3.2 17.9 - - - +
138G THR* 3.7 17.4 + - - +
195G ALA* 4.1 0.9 - - - +
196G GLU* 2.9 44.2 + - + +
197G VAL 3.9 1.2 + - - -
198G MET* 3.1 39.1 + - + +
199G PRO 3.1 1.8 - - - -
200G ALA* 1.3 76.7 + - - +
202G TRP* 1.3 72.3 + - - +
242G PRO* 5.3 1.4 - - - +
248G ASN* 3.7 16.7 + - - +
249G GLY 3.2 31.3 + - - +
250G ALA* 3.9 9.4 - - - +
601G P3S 4.3 2.7 + - - -
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Residues in contact with TRP 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G GLU* 3.4 6.2 - - - +
137G TYR* 2.7 52.4 + - + +
139G LEU* 3.9 18.3 - - + +
170G ALA* 4.0 17.3 - - + -
171G TYR 2.9 39.0 + - - +
172G GLY 4.5 0.2 - - - -
173G ARG* 3.8 39.7 - - - -
176G VAL* 3.3 30.7 - - + -
194G ASN* 3.6 9.0 - - - -
195G ALA* 3.4 41.3 - - + -
196G GLU* 4.1 4.9 - - - +
200G ALA* 3.6 15.8 - - - +
201G GLN* 1.3 81.0 + - - +
203G GLU* 1.3 66.2 + - - +
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Residues in contact with GLU 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G GLU* 3.0 13.2 - - - +
135G GLN 3.3 13.5 - - - +
136G GLU* 3.5 4.9 - - + +
137G TYR* 3.8 3.9 + - - -
176G VAL* 5.2 1.7 - - - +
193G THR* 3.2 9.2 - - - +
194G ASN* 2.8 45.3 + - - +
196G GLU* 2.9 9.0 - - + +
202G TRP* 1.3 79.3 - - - +
204G PHE* 1.3 69.1 + - - +
205G GLN* 2.7 19.9 + - - +
401G MN 2.1 33.3 + - - -
403G MN 2.1 30.0 + - - -
501G ADP 3.0 0.9 + - - -
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Residues in contact with PHE 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G MET 3.8 0.2 - - - +
135G GLN* 2.7 69.7 + - + -
137G TYR* 3.7 23.1 - + - +
179G HIS* 3.7 31.9 - + + +
190G ILE* 4.1 8.7 - - + -
192G GLY 3.3 12.3 - - - +
193G THR* 3.9 11.0 - - + -
203G GLU* 1.3 75.4 - - - +
205G GLN* 1.3 60.9 + - - +
206G ILE* 3.7 21.3 - - + -
218G LEU* 4.0 3.6 - - + -
221G ALA* 3.7 32.1 - - + -
222G ARG* 4.6 3.1 - - - -
225G LEU* 4.1 12.8 - - + -
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Residues in contact with GLN 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F THR 4.8 1.0 - - - +
60F TRP* 5.4 4.2 - - - -
133G MET 3.2 4.0 - - - +
134G GLU* 3.8 13.5 - - + -
190G ILE* 3.5 9.7 - - - +
191G ALA* 2.8 29.8 + - + +
192G GLY* 2.9 34.5 + - - +
193G THR 3.8 1.1 + - - -
194G ASN* 3.3 10.5 + - - -
203G GLU* 2.7 37.4 + - - +
204G PHE* 1.3 75.5 - - - +
206G ILE* 1.3 61.7 + - - +
403G MN 4.0 0.2 + - - -
501G ADP 3.4 49.5 + - - +
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Residues in contact with ILE 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G GLY* 3.3 1.9 - - - -
133G MET 2.9 32.0 + - - +
183G CYS* 5.5 0.4 - - - -
188G VAL* 3.5 29.4 - - + -
189G LYS 3.5 10.8 - - - +
190G ILE* 3.9 7.0 - - + -
204G PHE* 3.7 22.7 - - + -
205G GLN* 1.3 80.5 - - - +
207G GLY* 1.3 60.6 + - - +
209G CYS* 4.0 4.7 - - - -
214G MET* 3.3 27.1 - - + +
217G HIS* 3.8 22.4 - - + -
218G LEU* 4.0 12.8 - - + +
221G ALA* 3.8 10.5 - - + -
501G ADP 3.9 2.5 - - - -
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Residues in contact with GLY 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G PHE 3.6 3.1 - - - -
132G GLY* 4.0 1.6 - - - -
189G LYS* 3.1 23.4 + - - +
191G ALA* 3.4 13.0 - - - +
205G GLN 4.1 0.2 - - - -
206G ILE* 1.3 76.8 - - - +
208G PRO* 1.3 77.5 - - - +
209G CYS* 3.6 7.8 - - - -
501G ADP 3.3 12.5 + - - -
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Residues in contact with PRO 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G TRP* 4.0 30.7 - - + -
131G PHE 3.3 7.0 - - - +
189G LYS* 3.1 29.8 - - - +
191G ALA* 5.3 0.2 - - + -
207G GLY* 1.3 80.7 - - - +
209G CYS* 1.3 60.3 + - - +
210G GLU 4.2 0.5 + - - -
501G ADP 3.3 44.9 - - + +
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Residues in contact with CYS 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G TRP* 3.5 3.4 - - - -
131G PHE* 2.8 31.5 + - - +
189G LYS* 4.3 12.6 - - - -
206G ILE* 4.0 18.4 - - - -
207G GLY* 4.0 13.0 - - - -
208G PRO* 1.3 78.7 - - - +
210G GLU* 1.3 62.1 + - - +
211G GLY 3.5 1.6 + - - -
213G SER* 3.6 20.4 - - - +
214G MET* 3.5 26.6 - - + +
217G HIS* 4.1 11.7 - - - -
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Residues in contact with GLU 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G SER* 4.4 4.9 - - - +
128G HIS* 2.7 42.0 + - - +
129G PRO* 3.3 13.6 - - + +
130G TRP* 3.2 26.1 + - + +
208G PRO 4.2 1.0 + - - -
209G CYS* 1.3 71.1 - - - +
211G GLY* 1.3 67.4 + - - +
212G ILE* 3.3 0.9 + - - +
213G SER* 2.7 28.4 + - - +
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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