Contacts of the helix formed by residues 211 - 222 (chain E) in PDB entry 4PEI
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 SER 211 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133E TYR* 3.5 12.4 - - - +
157E THR* 5.5 2.3 + - - -
181E ASP* 3.3 31.8 + - - -
182E TRP 2.7 10.1 + - - -
184E GLN* 2.8 20.8 + - - +
210E GLY* 1.3 71.2 - - - -
212E PRO* 1.3 61.9 - - - +
213E ILE* 3.2 11.6 + - - +
214E ASN* 3.0 27.6 + - - +
215E LYS 3.0 15.1 + - - -
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Residues in contact with PRO 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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133E TYR* 3.3 47.1 - - + +
184E GLN* 3.5 32.5 - - + +
210E GLY 3.4 9.4 - - - +
211E SER* 1.3 82.2 - - - +
213E ILE* 1.3 62.2 + - + +
215E LYS* 3.2 6.2 + - + +
216E VAL* 3.1 32.1 + - + +
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Residues in contact with ILE 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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129E VAL* 4.8 0.2 - - + -
133E TYR* 3.7 19.3 - - + -
138E GLU* 3.8 16.2 - - + +
157E THR* 3.6 32.3 - - + +
158E ARG 3.6 22.9 - - - +
159E ASN* 3.7 11.2 - - - +
161E VAL* 3.7 27.6 - - + -
162E ILE* 4.2 17.0 - - + +
211E SER* 3.2 7.5 + - - +
212E PRO* 1.3 77.7 - - + +
214E ASN* 1.3 66.2 + - - +
216E VAL* 3.4 2.1 + - - +
217E ILE* 3.1 35.1 + - + +
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Residues in contact with ASN 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 3.5 33.1 + - - +
131E GLY 5.2 1.0 + - - -
157E THR* 5.5 3.5 + - - -
179E SER* 3.3 16.5 - - - -
180E HIS 4.6 0.8 - - - +
181E ASP* 3.1 39.2 + - - +
183E PRO* 3.7 16.4 - - + +
211E SER* 3.0 18.6 + - - +
213E ILE* 1.3 80.5 - - - +
215E LYS* 1.3 57.3 + - - +
217E ILE* 4.5 0.8 - - - +
218E LEU* 3.0 28.9 + - - +
226E TRP* 3.6 18.1 - - + -
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Residues in contact with LYS 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E PRO* 4.0 10.0 - - + +
184E GLN* 3.6 41.4 + - + +
185E GLY* 5.6 1.8 - - - -
211E SER 3.0 13.0 + - - +
212E PRO* 3.2 13.0 - - + +
213E ILE 3.2 0.2 - - - -
214E ASN* 1.3 76.8 - - - +
216E VAL* 1.3 55.7 + - + +
218E LEU* 3.3 4.2 + - - +
219E ASN* 2.8 56.4 + - - +
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Residues in contact with VAL 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E ILE* 3.8 36.1 - - + -
212E PRO* 3.1 18.1 + - + +
213E ILE 3.8 4.0 - - - +
215E LYS* 1.3 77.2 - - + +
217E ILE* 1.3 55.7 + - - +
219E ASN* 3.6 9.6 - - - +
220E THR* 2.6 52.1 + - - +
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Residues in contact with ILE 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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127E VAL* 5.1 0.2 - - + -
129E VAL* 4.0 13.2 - - + -
161E VAL* 3.9 22.7 - - + -
162E ILE* 3.9 21.8 - - + +
165E LEU* 3.7 29.6 - - + -
177E SER* 4.9 1.1 - - - +
213E ILE* 3.1 23.7 + - + +
214E ASN* 4.5 0.9 - - - +
216E VAL* 1.3 77.2 - - - +
218E LEU* 1.3 54.6 + - - +
220E THR* 4.4 4.0 - - - -
221E LEU* 2.7 59.0 + - + +
226E TRP* 3.7 21.3 - - + -
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Residues in contact with LEU 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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183E PRO* 3.8 27.8 - - + -
186E ILE* 4.5 14.4 - - + -
214E ASN 3.0 17.8 + - - +
215E LYS* 3.5 4.7 - - - +
217E ILE* 1.3 77.9 - - - +
219E ASN* 1.3 61.1 + - - +
222E LYS* 2.7 34.8 + - + +
223E PRO* 4.2 2.7 - - + -
226E TRP* 3.4 36.2 - - + -
239E GLU* 3.8 28.0 - - + +
242E THR* 3.8 26.0 - - + +
244E PHE* 5.4 1.1 - - + -
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Residues in contact with ASN 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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215E LYS* 2.8 50.0 + - - +
216E VAL* 3.7 7.7 - - + +
218E LEU* 1.3 83.0 - - - +
220E THR* 1.3 61.7 - - - +
222E LYS* 3.1 36.3 + - - +
239E GLU* 4.5 13.5 - - - +
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Residues in contact with THR 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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162E ILE* 5.3 1.8 - - - +
166E SER* 3.6 41.3 - - - +
169E SER* 4.7 5.5 - - - -
216E VAL* 2.6 42.1 + - - +
217E ILE* 3.8 5.4 - - - -
219E ASN* 1.3 76.8 - - - +
221E LEU* 1.3 62.5 + - - +
222E LYS* 4.5 5.9 - - - +
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Residues in contact with LEU 221 (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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127E VAL* 4.2 27.1 - - + -
165E LEU* 3.5 33.2 - - + +
166E SER 3.6 15.7 - - - +
168E LEU* 4.0 3.8 - - + +
169E SER* 3.0 42.3 + - - +
173E GLN* 6.1 0.2 - - - +
174E ILE* 4.4 13.5 + - + +
177E SER* 5.5 1.8 - - - +
217E ILE* 2.7 40.8 + - + +
220E THR* 1.3 75.9 - - - +
222E LYS* 1.3 70.2 + - - +
223E PRO* 3.2 10.8 - - + +
226E TRP* 5.8 0.4 - - + -
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Residues in contact with LYS 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E GLN* 6.0 1.4 - - - +
174E ILE 5.0 0.3 + - - +
218E LEU* 2.7 21.3 + - + +
219E ASN* 3.1 32.4 + - - +
220E THR 4.5 4.5 - - - +
221E LEU* 1.3 75.0 - - - +
223E PRO* 1.4 72.1 - - - +
224E LYS* 5.7 0.9 - - - +
241E PRO* 4.2 31.4 - - + +
242E THR* 3.6 6.4 + - - +
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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