Contacts of the helix formed by residues 212 - 225 (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 TYR 212 (chain E).
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Specific contacts
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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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Residues in contact with PHE 213 (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* 4.9 1.8 - - + -
208E LEU* 2.8 43.6 + - + +
209E VAL* 3.2 37.5 - - + +
212E TYR* 1.3 100.8 - + - +
214E GLY* 1.3 65.5 + - - +
216E LEU* 5.0 1.8 - - - -
217E CYS* 2.9 39.3 + - - +
273F THR* 5.9 1.3 - - + -
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Residues in contact with GLY 214 (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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209E VAL* 2.8 21.4 + - - +
210E LEU 4.7 0.2 - - - -
213E PHE* 1.3 72.2 - - - +
215E PRO* 1.3 57.1 - - - +
217E CYS* 4.0 2.1 - - - +
218E PHE* 2.8 39.2 + - - +
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Residues in contact with PRO 215 (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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125C ILE* 3.3 25.4 - - + -
126C PHE* 3.5 20.0 - - + -
129C VAL* 3.5 17.3 - - + -
210E LEU 2.9 24.9 - - - +
211E GLN 3.1 19.7 - - - +
212E TYR 3.3 7.0 - - - +
214E GLY* 1.3 87.6 - - - +
216E LEU* 1.3 56.4 + - - +
218E PHE* 3.5 2.5 - - + +
219E ILE* 2.8 37.4 + - - +
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Residues in contact with LEU 216 (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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125C ILE* 3.4 33.0 - - + -
212E TYR* 2.9 65.6 + - + +
213E PHE* 4.1 2.0 - - - +
215E PRO* 1.3 73.6 - - - +
217E CYS* 1.3 59.3 + - - +
219E ILE* 3.1 5.7 + - + +
220E PHE* 2.9 67.1 + - + -
258F VAL* 5.2 2.9 - - + -
261F PHE* 4.9 4.7 - - + -
262F ALA* 4.1 22.9 - - + -
266F LEU* 4.6 4.7 - - + -
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Residues in contact with CYS 217 (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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213E PHE* 2.9 31.1 + - - +
214E GLY* 4.0 2.2 - - - +
216E LEU* 1.3 73.9 - - - +
218E PHE* 1.3 57.4 + - - +
220E PHE* 3.3 16.9 + - - +
221E ILE* 2.9 42.5 + - + +
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Residues in contact with PHE 218 (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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129C VAL* 3.4 34.3 - - + -
132C ALA* 3.7 10.8 - - + -
133C VAL* 3.2 36.3 - - + -
214E GLY 2.8 25.1 + - - +
215E PRO* 3.5 3.1 - - + +
217E CYS* 1.3 73.3 - - - +
219E ILE* 1.3 58.4 + - + +
221E ILE* 4.9 2.5 - - + -
222E CYS* 2.8 62.7 + - + +
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Residues in contact with ILE 219 (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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125C ILE* 3.5 23.3 - - + +
128C LEU* 3.4 28.7 - - + +
129C VAL* 3.5 27.1 - - + +
132C ALA* 3.9 16.7 - - + +
215E PRO 2.8 29.2 + - - +
216E LEU* 3.6 5.2 - - - +
218E PHE* 1.3 71.1 - - - +
220E PHE* 1.3 55.7 + - + +
222E CYS* 3.8 0.3 - - - +
223E TYR* 2.8 37.6 + - - +
255F LEU* 4.1 15.7 - - + -
258F VAL* 3.6 29.4 - - + -
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Residues in contact with PHE 220 (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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216E LEU* 2.9 62.1 + - + -
217E CYS* 3.4 17.3 - - - +
219E ILE* 1.3 82.0 - - + +
221E ILE* 1.3 60.3 + - + +
223E TYR* 3.2 5.1 - + - +
224E PHE* 2.9 59.2 + + + -
255F LEU* 6.5 0.4 - - + -
258F VAL* 5.1 9.4 - - + -
262F ALA* 5.4 6.5 - - + -
266F LEU* 6.0 4.3 - - + -
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Residues in contact with ILE 221 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217E CYS* 2.9 28.2 + - + +
218E PHE* 4.1 3.1 - - + +
220E PHE* 1.3 70.7 - - + +
222E CYS* 1.3 66.0 + - - +
224E PHE* 3.2 25.8 + - + +
225E LYS* 2.9 38.5 + - + +
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Residues in contact with CYS 222 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C ALA* 3.4 19.7 - - + -
133C VAL* 4.2 0.9 - - - -
135C ARG* 2.6 34.2 + - - -
136C HIS* 3.3 22.8 - - - -
218E PHE* 2.8 56.7 + - + +
219E ILE 3.8 2.0 - - - +
221E ILE* 1.3 73.0 - - - +
223E TYR* 1.3 57.1 + - - +
225E LYS* 2.9 19.0 + - - +
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Residues in contact with TYR 223 (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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132C ALA* 5.0 2.4 - - + +
135C ARG* 2.7 38.3 + - - +
219E ILE* 2.8 25.9 + - + +
220E PHE* 3.2 5.4 - + - +
222E CYS* 1.3 71.1 - - - +
224E PHE* 1.3 81.4 + + - +
225E LYS* 3.0 2.4 - - - +
251F ASN* 5.2 8.5 - - + -
252F ILE* 5.1 10.7 - - - +
255F LEU* 3.3 52.6 - - + +
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Residues in contact with PHE 224 (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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220E PHE* 2.9 52.9 + + + -
221E ILE* 3.4 25.6 - - + +
223E TYR* 1.3 91.8 - + - +
225E LYS* 1.3 63.9 + - + +
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Residues in contact with LYS 225 (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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135C ARG* 3.5 8.5 + - - -
136C HIS* 3.2 32.9 + - + +
139C ILE* 4.0 9.4 - - - +
221E ILE* 2.9 29.3 + - + +
222E CYS* 2.9 19.5 + - - +
223E TYR 3.0 9.2 - - - +
224E PHE* 1.3 80.0 - - + +
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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