Contacts of the helix formed by residues 211 - 222 (chain E) in PDB entry 4CQM
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 PRO 211 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-3B HIS 3.7 26.9 - - - +
-1B HIS 3.4 17.9 - - - +
1B MET* 3.5 25.1 - - + -
28B ARG* 5.9 0.2 - - - +
49B ASP* 3.4 20.2 - - - +
209E LYS 3.8 0.7 - - - +
210E VAL* 1.3 89.3 - - + +
212E GLN* 1.3 60.2 + - - +
213E LYS* 4.3 6.3 - - + +
214E VAL* 2.9 21.0 + - + +
215E VAL* 2.8 25.5 + - - +
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Residues in contact with GLN 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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28B ARG* 5.9 1.2 - - - +
49B ASP* 4.7 5.4 + - - -
210E VAL 3.5 1.8 + - - -
211E PRO* 1.3 70.7 - - - +
213E LYS* 1.3 56.3 + - - +
215E VAL* 4.1 19.8 - - - +
216E ASP* 2.9 66.1 + - - +
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Residues in contact with LYS 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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211E PRO* 4.2 7.4 - - + +
212E GLN* 1.3 75.8 - - + +
214E VAL* 1.3 62.4 + - + +
216E ASP* 3.1 11.5 + - + +
217E LYS* 2.9 27.8 + - - +
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Residues in contact with VAL 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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-3B HIS 4.3 6.5 - - - +
-2B HIS* 4.1 42.6 - - + +
-1B HIS* 5.4 0.7 - - - -
210E VAL* 3.7 17.9 - - + -
211E PRO* 2.9 29.2 + - + +
213E LYS* 1.3 76.2 - - + +
215E VAL* 1.3 53.3 + - - +
217E LYS* 3.2 8.9 + - + +
218E ILE* 2.8 51.3 + - + +
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Residues in contact with VAL 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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207E THR* 4.2 13.2 - - + +
210E VAL* 3.5 28.7 - - + +
211E PRO 2.8 18.2 + - - +
212E GLN* 3.6 25.8 - - - +
214E VAL* 1.3 77.1 - - - +
216E ASP* 1.3 57.9 + - - +
218E ILE* 3.1 11.7 + - + +
219E THR* 2.8 31.9 + - - +
227E LEU* 3.9 30.3 - - + -
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Residues in contact with ASP 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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212E GLN* 2.9 48.6 + - - +
213E LYS* 3.5 11.1 - - + +
215E VAL* 1.3 77.2 - - - +
217E LYS* 1.3 61.7 + - - +
219E THR* 3.6 10.6 + - - +
220E GLU* 3.2 32.6 + - - +
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Residues in contact with LYS 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 LYS 2.9 13.0 + - - +
214E VAL* 3.2 13.4 + - + +
216E ASP* 1.3 77.6 - - - +
218E ILE* 1.3 61.5 + - + +
220E GLU* 3.4 13.7 + - - +
221E MET* 3.2 28.3 + - - +
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Residues in contact with ILE 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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201E PHE* 3.5 62.8 - - + -
207E THR* 6.0 0.4 - - + -
210E VAL* 4.4 9.2 - - + -
214E VAL* 2.8 36.2 + - + +
215E VAL* 3.1 10.7 + - + +
217E LYS* 1.3 75.5 - - + +
219E THR* 1.3 59.4 + - - +
221E MET* 2.8 31.8 + - + +
222E ILE* 2.8 27.2 + - + +
227E LEU* 4.6 3.8 - - + -
259E LEU* 4.6 2.2 - - + -
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Residues in contact with THR 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 VAL* 2.8 24.5 + - - +
216E ASP* 3.6 12.9 + - - +
218E ILE* 1.3 72.5 - - - +
220E GLU* 1.3 64.3 + - + +
222E ILE* 3.3 15.3 + - - +
225E GLY* 3.2 46.4 - - - +
226E HIS* 4.1 2.0 - - - +
227E LEU* 4.3 21.5 + - - +
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Residues in contact with GLU 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 ASP* 3.2 19.4 + - - +
217E LYS* 3.5 13.2 - - - +
219E THR* 1.3 80.2 - - + +
221E MET* 1.3 60.2 + - + +
168F ARG* 3.0 22.8 + - - +
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Residues in contact with MET 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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217E LYS* 3.2 17.7 + - + +
218E ILE* 2.8 21.8 + - + +
220E GLU* 1.3 77.5 - - + +
222E ILE* 1.3 64.7 + - - +
223E PRO* 3.2 10.2 - - - +
259E LEU* 3.8 15.4 - - + +
260E PHE* 4.1 32.8 - - + -
168F ARG* 5.0 0.2 + - - -
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Residues in contact with ILE 222 (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 PHE* 4.4 11.0 - - + +
218E ILE* 2.8 35.6 + - + +
219E THR* 3.6 7.6 + - - +
220E GLU 3.5 0.2 - - - -
221E MET* 1.3 73.8 - - - +
223E PRO* 1.3 65.1 - - + +
224E MET* 3.7 7.4 - - + +
225E GLY* 2.8 24.6 + - - +
226E HIS 3.4 31.4 - - - +
227E LEU* 4.3 11.9 - - + -
256E THR 3.7 13.7 - - - +
257E GLY* 3.6 19.7 - - - +
259E LEU* 3.8 20.6 - - + -
168F ARG* 3.0 13.9 + - - -
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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