Contacts of the strand formed by residues 130 - 140 (chain F) 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 TRP 130 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128F HIS* 3.2 13.7 + - - +
129F PRO* 1.3 78.4 - - - +
131F PHE* 1.3 63.2 + - - +
208F PRO* 4.0 26.9 - - + -
209F CYS 3.5 3.8 - - - +
210F GLU* 3.4 33.7 + - + +
256F PHE* 3.4 9.0 - - - -
257F SER* 3.0 37.9 + - - +
262F ARG* 3.3 45.4 - - - +
501F ADP 4.0 17.5 - + - +
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Residues in contact with PHE 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F MET* 4.1 17.7 - - + -
129F PRO* 4.1 20.4 - - + -
130F TRP* 1.3 74.7 - - - +
132F GLY* 1.3 59.1 + - - +
207F GLY* 3.8 0.2 - - - -
208F PRO* 3.0 4.0 - - - +
209F CYS 2.6 42.7 + - - -
211F GLY 4.3 4.3 - - - -
214F MET* 3.4 30.7 - - + +
254F THR* 3.9 17.0 - - + -
255F ASN 3.3 6.3 - - - +
256F PHE* 3.5 32.3 - + - -
352F THR* 3.6 42.2 - - + -
355F LEU* 3.8 15.3 - - + -
356F ILE* 4.0 9.0 - - + -
501F ADP 3.9 5.4 - - - -
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Residues in contact with GLY 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F PHE* 1.3 75.0 - - - +
133F MET* 1.3 61.1 + - - -
206F ILE 3.2 10.1 - - - -
207F GLY* 4.3 0.2 - - - -
254F THR* 3.6 0.5 - - - -
255F ASN* 2.7 45.9 + - - -
501F ADP 3.6 28.1 + - - -
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Residues in contact with MET 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLY* 1.3 78.9 - - - +
134F GLU* 1.3 63.3 + - - +
135F GLN* 3.7 1.3 + - - -
204F PHE 3.7 1.4 - - - +
205F GLN* 3.3 2.8 - - - -
206F ILE* 2.8 39.2 + - - +
214F MET* 3.6 40.1 - - + +
218F LEU* 3.8 16.6 - - + -
252F CYS* 3.7 25.4 - - - -
253F HIS 3.3 3.8 - - - +
254F THR* 3.4 35.4 - - + +
346F CYS* 4.1 8.3 - - - -
348F PRO* 3.8 27.1 - - + -
351F VAL* 4.5 3.6 - - + -
352F THR* 4.4 4.9 - - - -
501F ADP 5.0 0.4 - - - -
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Residues in contact with GLU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F MET* 1.3 73.7 - - - +
135F GLN* 1.3 61.9 + - - +
136F GLU* 3.2 9.5 + - + +
203F GLU* 2.9 13.1 - - - +
204F PHE 3.6 5.8 - - - -
205F GLN* 4.2 3.8 - - + +
251F GLY 3.5 1.6 - - - +
252F CYS* 3.3 19.6 - - - -
253F HIS* 2.9 24.4 + - + +
255F ASN* 3.1 18.4 + - - +
338F GLU* 2.9 5.7 - - - +
401F MN 3.9 0.2 + - - -
402F MN 2.4 30.6 + - - -
403F MN 2.1 27.5 + - - -
501F ADP 2.7 32.2 + - - +
601F P3S 2.5 2.3 + - - -
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Residues in contact with GLN 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F MET 3.7 1.6 - - - +
134F GLU* 1.3 70.9 - - - +
136F GLU* 1.3 82.4 + - - +
137F TYR* 3.7 4.6 - - + -
203F GLU* 3.2 3.3 - - - -
204F PHE* 2.8 70.4 + - + -
218F LEU* 3.7 14.5 - - + +
222F ARG* 3.0 34.5 + - - +
238F PHE* 3.4 19.7 - - + -
252F CYS* 3.8 8.6 - - - -
344F ALA* 2.9 25.4 + - - +
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Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLU* 3.2 6.1 + - - +
135F GLN* 1.3 93.4 + - - +
137F TYR* 1.3 61.7 + - - +
196F GLU* 2.8 19.9 - - + +
201F GLN* 4.5 4.5 - - - +
202F TRP 3.4 5.2 - - - +
203F GLU* 3.9 12.3 - - + +
238F PHE* 4.0 0.2 - - - -
250F ALA* 4.1 8.3 - - + -
251F GLY* 3.0 31.3 + - - +
253F HIS* 4.4 4.0 + - - -
344F ALA* 3.3 10.6 - - - +
401F MN 2.2 37.9 + - - +
601F P3S 2.6 39.1 + - - +
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Residues in contact with TYR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F GLN* 3.7 10.8 - - + -
136F GLU* 1.3 76.5 - - - +
138F THR* 1.3 72.0 + - - +
139F LEU* 3.8 25.4 - - + -
175F ILE* 4.7 0.9 - - - +
176F VAL* 3.5 21.8 - - - +
179F HIS* 5.7 1.0 + - - +
201F GLN* 3.3 6.6 - - - +
202F TRP* 3.0 66.8 + - + +
203F GLU 3.8 2.7 + - - -
204F PHE* 3.6 27.1 - + - +
225F LEU* 3.8 34.7 - - + +
236F ALA* 4.4 2.5 - - + -
237F THR 3.4 15.7 - - - +
238F PHE* 3.6 15.3 - - + -
250F ALA* 4.5 5.5 - - - +
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Residues in contact with THR 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F TYR* 1.3 80.0 + - - +
139F LEU* 1.3 75.1 + - - +
140F MET* 3.8 17.0 + - - -
146F PRO* 4.3 4.7 - - + -
198F MET* 3.3 35.4 - - + +
200F ALA 3.5 7.0 - - - +
201F GLN* 3.8 12.3 + - - +
235F ILE 3.7 0.7 - - - +
236F ALA* 3.6 1.0 - - - -
237F THR* 2.9 46.7 + - + +
242F PRO* 3.9 11.9 - - + +
250F ALA* 5.3 1.4 - - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F TYR* 3.8 23.6 - - + -
138F THR* 1.3 75.9 - - - +
140F MET* 1.3 55.7 + - - +
146F PRO* 3.4 5.9 - - - +
147F PHE* 2.7 37.6 + - + +
171F TYR 3.8 16.6 - - - +
172F GLY* 3.7 27.6 - - - +
175F ILE* 3.9 14.8 - - + -
176F VAL* 5.2 0.4 - - + -
200F ALA* 2.9 15.9 + - + +
202F TRP* 3.9 12.1 - - + -
229F CYS* 3.6 31.4 - - - -
234F VAL* 4.2 9.9 - - + -
235F ILE 3.4 3.6 - - - +
236F ALA* 4.8 0.7 - - - -
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Residues in contact with MET 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F THR* 3.9 25.4 - - - +
139F LEU* 1.3 74.3 - - - +
141F GLY* 1.3 70.6 + - - +
144F GLY* 3.0 33.2 - - - +
145F HIS 3.6 4.0 - - - +
146F PRO* 3.9 22.0 - - + -
147F PHE* 4.0 4.5 - - - -
234F VAL* 3.4 7.6 - - - +
235F ILE* 2.9 46.0 + - + +
237F THR* 4.1 20.4 - - + -
242F PRO* 5.1 11.9 - - + +
243F ILE* 5.5 3.6 - - + -
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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