Contacts of the helix formed by residues 200 - 212 (chain E) in PDB entry 2F1U
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 ARG 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170D PRO* 2.7 26.3 + - - +
171D PHE* 4.9 1.0 - - - +
173D ILE* 2.7 31.0 + - - -
201E LEU* 1.3 71.1 + - + +
202E SER* 2.9 20.8 + - - +
203E TYR* 3.4 33.2 - - - +
204E THR* 2.8 30.2 + - - +
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Residues in contact with LEU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ARG* 1.3 78.9 - - + +
202E SER* 1.3 58.1 + - - +
204E THR* 3.0 15.2 - - + +
205E THR* 2.7 39.6 + - - +
276F ASP* 3.8 30.1 - - - +
277F TRP* 4.9 9.2 - - + +
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Residues in contact with SER 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ARG 2.9 17.5 + - - -
201E LEU* 1.3 73.5 - - - +
203E TYR* 1.3 56.5 + - - +
205E THR* 3.7 4.0 - - - -
206E LEU* 2.8 37.8 + - - +
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Residues in contact with TYR 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ALA 4.8 1.8 - - - -
167D SER 2.7 25.9 + - - -
170D PRO* 3.1 39.6 - - + +
171D PHE* 3.2 52.4 + + - -
200E ARG* 3.3 39.9 + - - +
202E SER* 1.3 79.2 + - - +
204E THR* 1.3 59.1 + - - +
206E LEU* 3.2 13.9 + - + +
207E LEU* 2.8 43.3 + - + +
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Residues in contact with THR 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ARG 2.8 13.2 + - - +
201E LEU* 3.0 40.2 - - + +
203E TYR* 1.3 73.9 - - - +
205E THR* 1.3 59.5 + - - +
207E LEU* 4.7 3.4 - - - -
208E LEU* 2.8 48.8 + - - +
273F THR* 5.4 0.2 - - - +
276F ASP* 2.7 43.7 + - - +
277F TRP* 5.2 0.4 - - - +
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Residues in contact with THR 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LEU* 2.7 24.9 + - - +
202E SER* 3.7 4.7 - - - -
204E THR* 1.3 78.2 - - - +
206E LEU* 1.3 58.7 + - - +
208E LEU* 3.5 5.2 - - - +
209E VAL* 2.8 48.8 + - + +
213E PHE* 5.9 1.6 - - + -
277F TRP* 4.7 15.0 - - + -
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Residues in contact with LEU 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ALA 6.0 2.2 - - - +
170D PRO* 6.0 3.6 - - + -
202E SER 2.8 19.1 + - - +
203E TYR* 3.3 15.7 - - + +
205E THR* 1.3 77.9 - - - +
207E LEU* 1.3 52.8 + - - +
209E VAL* 3.3 4.2 + - + +
210E LEU* 2.8 69.4 + - + +
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Residues in contact with LEU 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C CYS* 5.7 2.0 - - - -
167D SER* 3.3 37.9 - - - +
171D PHE* 3.8 19.7 - - + -
203E TYR* 2.8 35.9 + - + +
204E THR* 4.0 4.5 - - - +
206E LEU* 1.3 71.0 - - - +
208E LEU* 1.3 69.0 + - + +
211E GLN* 2.8 62.7 + - + +
212E TYR* 5.9 1.3 - - + -
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Residues in contact with LEU 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E THR* 2.8 40.8 + - - +
205E THR* 3.5 5.6 - - - +
207E LEU* 1.3 84.6 - - + +
209E VAL* 1.3 56.4 + - - +
212E TYR* 2.9 42.5 + - + +
213E PHE* 2.8 50.0 + - + -
269F THR* 3.7 19.3 - - + -
273F THR* 4.1 19.5 - - + -
276F ASP* 5.8 0.7 - - - +
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Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E THR* 2.8 36.8 + - + +
206E LEU* 3.7 5.2 - - + +
208E LEU* 1.3 71.9 - - - +
210E LEU* 1.3 70.6 + - + +
213E PHE* 3.2 25.1 - - + -
214E GLY* 2.8 31.3 + - - +
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Residues in contact with LEU 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 2.9 20.5 - - + -
163D LEU* 5.0 6.3 - - + -
166D ALA* 5.5 8.7 - - + +
206E LEU* 2.8 59.5 + - + +
209E VAL* 1.3 82.5 - - + +
211E GLN* 1.3 77.1 + - - +
214E GLY* 4.7 0.4 - - - -
215E PRO* 2.9 13.7 - - - +
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Residues in contact with GLN 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 6.1 3.0 - - + +
122C THR* 3.3 24.5 - - - +
125C ILE* 3.3 19.2 - - + +
126C PHE* 3.5 7.1 - - + -
163D LEU* 3.5 33.1 + - - +
166D ALA* 4.2 5.6 - - - +
167D SER* 3.5 27.9 - - - +
207E LEU* 2.8 58.4 + - + +
210E LEU* 1.3 94.5 - - - +
212E TYR* 1.3 55.2 + - + +
215E PRO* 3.1 17.1 - - - +
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Residues in contact with TYR 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 4.6 1.6 - - + +
208E LEU* 2.9 32.6 + - + +
211E GLN* 1.3 79.2 - - + +
213E PHE* 1.3 98.0 + + - +
214E GLY 3.4 0.9 - - - -
215E PRO* 3.3 0.7 - - - +
216E LEU* 2.9 60.7 + - + +
261F PHE* 6.2 1.1 - + - -
265F TRP* 6.6 0.2 - - + -
266F LEU* 3.3 44.7 + - + +
269F THR* 3.7 28.4 - - + +
270F ILE* 5.7 2.4 - - - +
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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