Contacts of the helix formed by residues 203 - 215 (chain C) in PDB entry 4CEV
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 MET 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C TYR* 3.7 27.4 - - + +
172C ILE* 4.5 10.5 - - + -
198C VAL* 4.1 12.6 + - + +
202C GLY* 1.3 69.8 - - - -
204C THR* 1.3 56.2 + - - +
206C VAL* 3.3 8.5 + - - +
207C MET* 2.9 55.5 + - + +
246C LEU* 3.7 31.0 - - + -
250C GLU* 3.7 45.0 + - + +
253C LEU* 4.2 13.9 - - + -
254C ALA* 4.5 1.3 - - + -
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Residues in contact with THR 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASP 3.5 3.5 + - - -
200A ARG* 3.1 45.0 + - + +
202C GLY* 3.1 1.5 + - - -
203C MET* 1.3 78.4 - - - +
205C ARG* 1.3 58.3 + - - +
208C GLU* 2.9 52.3 + - - +
253C LEU* 3.4 21.7 - - - +
257C MET* 3.8 12.1 - - + +
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Residues in contact with ARG 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C LEU* 3.6 58.0 + - + +
202C GLY 3.1 2.7 + - - +
204C THR* 1.3 76.1 - - - +
206C VAL* 1.3 61.2 + - - +
208C GLU* 3.7 15.6 - - - +
209C GLU* 2.6 59.4 + - - +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ILE* 4.2 24.2 - - + -
193C TYR* 3.6 52.1 - - + -
197C GLU 4.1 5.4 - - - +
198C VAL* 4.1 24.7 - - + +
201C LEU* 4.3 5.2 - - + -
202C GLY 3.1 13.9 + - - +
203C MET* 3.6 15.3 - - - +
205C ARG* 1.3 75.6 - - - +
207C MET* 1.3 55.2 + - - +
209C GLU* 3.9 1.6 - - - +
210C THR* 2.8 36.6 + - - -
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Residues in contact with MET 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 5.0 2.5 - - + -
121C TYR* 5.3 2.2 - - - -
172C ILE* 3.8 28.0 - - + -
203C MET* 2.9 41.0 + - + +
206C VAL* 1.3 75.4 - - - +
208C GLU* 1.3 64.9 + - - +
210C THR* 3.7 5.1 - - + -
211C ILE* 2.9 39.1 + - + +
254C ALA* 3.9 30.5 - - + +
257C MET* 3.7 21.8 - - + -
258C LEU* 3.6 39.7 - - + -
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Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ARG* 5.0 6.9 + - - +
204C THR* 2.9 39.3 + - - +
205C ARG* 3.7 18.2 - - - +
207C MET* 1.3 77.2 - - - +
209C GLU* 1.3 58.2 + - + +
211C ILE* 3.5 4.9 + - - +
212C ALA* 3.0 31.5 + - - +
257C MET* 3.8 14.8 - - + +
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Residues in contact with GLU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS* 4.6 5.3 + - - +
193C TYR* 2.5 43.9 + - + +
201C LEU* 4.2 4.8 - - - +
205C ARG* 2.6 63.2 + - + +
206C VAL 3.9 0.9 - - - +
208C GLU* 1.3 78.9 - - + +
210C THR* 1.3 55.2 + - - +
212C ALA* 3.6 5.0 + - - +
213C TYR* 3.0 30.0 + - - +
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Residues in contact with THR 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 4.0 28.9 - - + -
170C VAL* 3.3 38.2 - - + +
172C ILE* 3.8 13.9 - - + +
191C LYS* 5.1 0.7 - - - +
193C TYR* 3.4 9.1 + - - -
206C VAL 2.8 22.2 + - - -
207C MET* 3.7 10.5 - - + -
208C GLU 3.3 0.2 - - - -
209C GLU* 1.3 74.3 - - - +
211C ILE* 1.3 66.0 + - - +
213C TYR* 3.3 5.1 + - - +
214C LEU* 3.1 27.2 + - + +
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Residues in contact with ILE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C MET* 2.9 30.2 + - + +
208C GLU* 3.9 5.2 - - - +
210C THR* 1.3 76.6 - - + +
212C ALA* 1.3 59.3 + - - +
214C LEU* 4.4 0.5 - - - +
215C LYS* 2.9 47.3 + - - +
257C MET* 3.5 39.7 - - + +
258C LEU* 3.8 24.0 - - + -
261C ALA* 3.5 22.7 - - + -
263C ILE* 3.8 14.2 - - + +
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Residues in contact with ALA 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C GLU 3.0 18.9 + - - +
209C GLU* 3.9 5.4 - - - +
211C ILE* 1.3 79.5 - - - +
213C TYR* 1.3 62.2 + - - +
215C LYS* 4.0 6.8 - - - +
216C GLU* 3.2 28.2 + - - +
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Residues in contact with TYR 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C GLU* 2.7 39.8 + - - +
169C VAL 4.5 2.9 - - - -
170C VAL* 3.8 15.5 - - + -
191C LYS* 3.8 40.5 + - + +
209C GLU 3.0 18.7 + - - +
210C THR 3.5 4.3 - - - +
212C ALA* 1.3 79.9 - - - +
214C LEU* 1.3 78.8 + - + +
216C GLU* 3.4 6.0 + - - +
217C ARG* 3.0 63.1 + - - +
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLY* 4.5 0.7 - - - -
118C VAL 4.3 5.8 - - - +
119C ILE* 3.4 35.7 - - + -
168C HIS* 3.3 32.3 - - - +
170C VAL* 3.9 15.3 - - + -
210C THR* 3.1 16.1 + - + +
211C ILE 4.4 1.3 - - - +
213C TYR* 1.3 92.8 - - + +
215C LYS* 1.3 63.8 + - - +
217C ARG* 3.0 2.5 + - + -
218C THR* 2.6 46.5 + - + +
221C VAL* 4.0 22.0 - - + -
263C ILE* 5.1 3.6 - - + -
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ILE* 2.9 35.6 + - - +
212C ALA* 4.0 5.6 - - - +
214C LEU* 1.3 76.0 - - - +
216C GLU* 1.3 60.7 + - - +
217C ARG 3.4 0.9 + - - -
218C THR* 4.2 11.4 - - - +
261C ALA* 3.3 26.3 + - - +
263C ILE* 3.7 23.9 - - + +
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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