Contacts of the helix formed by residues 203 - 215 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E TYR* 3.6 24.9 - - + +
172E ILE* 4.5 11.7 - - + -
198E VAL* 4.1 10.6 + - + +
202E GLY* 1.3 69.7 - - - -
204E THR* 1.3 62.5 + - - +
206E VAL* 3.3 8.8 + - - +
207E MET* 2.9 54.9 + - + +
246E LEU* 3.5 34.8 - - + -
250E GLU* 3.6 45.2 + - + +
253E LEU* 4.3 13.5 - - + -
254E ALA* 4.4 2.2 - - + -
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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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202E GLY* 3.1 1.9 + - - -
203E MET* 1.3 79.4 - - - +
205E ARG* 1.3 58.9 + - - +
207E MET 3.3 0.5 + - - -
208E GLU* 2.9 51.5 + - - +
253E LEU* 3.5 6.8 - - - +
257E MET* 3.8 16.7 - - + +
199F ASP 3.6 3.6 + - - -
200F ARG* 2.9 54.2 + - + +
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Residues in contact with ARG 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* 3.5 44.3 + - + +
202E GLY 3.1 2.6 + - - +
204E THR* 1.3 76.7 - - - +
206E VAL* 1.3 61.3 + - - +
208E GLU* 3.7 19.9 + - - +
209E GLU* 2.9 56.8 + - - +
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Residues in contact with VAL 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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172E ILE* 4.2 23.8 - - + -
193E TYR* 3.5 53.1 - - + -
197E GLU 4.0 17.7 - - - +
198E VAL* 4.2 13.0 - - + -
201E LEU* 4.2 5.8 - - + -
202E GLY 3.1 14.5 + - - +
203E MET* 3.7 13.2 - - - +
205E ARG* 1.3 75.6 - - - +
207E MET* 1.3 58.8 + - - +
209E GLU* 3.9 1.4 - - - +
210E THR* 2.9 33.3 + - - -
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Residues in contact with MET 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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119E ILE* 4.9 2.0 - - + -
121E TYR* 5.4 1.3 - - - -
172E ILE* 3.7 29.8 - - + -
203E MET* 2.9 36.6 + - + +
204E THR 3.8 2.5 - - - +
206E VAL* 1.3 76.1 - - - +
208E GLU* 1.3 60.3 + - - +
210E THR* 4.2 5.2 - - + -
211E ILE* 2.8 46.2 + - + +
254E ALA* 3.9 32.8 - - + +
257E MET* 3.9 16.2 - - + -
258E LEU* 3.6 40.2 - - + -
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Residues in contact with GLU 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* 2.9 36.0 + - - +
205E ARG* 3.3 26.2 + - + +
207E MET* 1.3 77.1 - - - +
209E GLU* 1.3 60.2 + - + +
211E ILE* 3.9 4.4 - - - +
212E ALA* 3.0 31.8 + - - +
257E MET* 3.8 15.1 - - + +
200F ARG* 5.1 5.7 + - - +
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Residues in contact with GLU 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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191E LYS* 4.6 4.3 + - - +
193E TYR* 2.8 41.6 + - - +
201E LEU* 4.1 9.3 - - - +
205E ARG* 2.9 47.2 + - + +
206E VAL 3.9 1.1 - - - +
208E GLU* 1.3 77.5 - - + +
210E THR* 1.3 58.1 + - - +
212E ALA* 3.9 4.2 - - - +
213E TYR* 2.9 32.5 + - - +
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Residues in contact with THR 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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119E ILE* 3.8 32.1 - - + -
170E VAL* 3.2 36.4 - - + +
172E ILE* 3.8 12.2 - - + +
191E LYS* 5.0 0.4 - - - +
193E TYR* 3.3 11.4 - - - -
206E VAL 2.9 22.6 + - - -
207E MET* 3.7 10.1 - - + +
209E GLU* 1.3 77.4 - - - +
211E ILE* 1.3 62.8 + - - +
213E TYR* 3.4 5.5 + - - +
214E LEU* 3.1 26.4 + - + +
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Residues in contact with ILE 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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207E MET* 2.8 35.9 + - + +
208E GLU* 4.0 4.3 - - - +
210E THR* 1.3 73.2 - - + +
212E ALA* 1.3 57.6 + - - +
214E LEU* 4.3 0.3 - - - +
215E LYS* 2.9 47.3 + - - +
257E MET* 3.5 34.5 - - + +
258E LEU* 3.7 29.2 - - + -
261E ALA* 3.4 22.7 - - + -
263E ILE* 3.8 14.9 - - + +
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Residues in contact with ALA 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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208E GLU 3.0 19.1 + - - +
209E GLU* 3.9 4.5 - - - +
211E ILE* 1.3 78.4 - - - +
213E TYR* 1.3 62.7 + - - +
215E LYS* 3.9 6.0 - - - +
216E GLU* 3.1 28.5 + - - +
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Residues in contact with TYR 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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167E GLU* 2.8 40.3 + - - +
169E VAL 4.5 2.5 - - - -
170E VAL* 3.8 22.7 - - + -
191E LYS* 3.7 40.8 + - + +
209E GLU 2.9 19.1 + - - +
210E THR 3.6 3.6 - - - +
211E ILE 3.3 0.2 - - - -
212E ALA* 1.3 78.8 - - - +
214E LEU* 1.3 72.1 + - + +
216E GLU* 3.4 5.7 + - - +
217E ARG* 2.9 65.1 + - - +
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Residues in contact with LEU 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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117E GLY* 4.2 1.3 - - - -
118E VAL 4.3 4.0 - - - +
119E ILE* 3.5 35.7 - - + -
168E HIS* 3.3 34.1 - - - +
170E VAL* 4.0 15.0 - - + -
210E THR* 3.1 14.9 + - + +
211E ILE 4.3 1.1 - - - +
213E TYR* 1.3 88.6 - - + +
215E LYS* 1.3 59.0 + - - +
217E ARG* 2.9 18.8 + - + -
218E THR* 2.7 39.3 + - + +
221E VAL* 3.9 21.5 - - + -
263E ILE* 5.1 4.5 - - + -
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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
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211E ILE* 2.9 33.9 + - - +
212E ALA* 3.9 5.8 - - - +
214E LEU* 1.3 76.9 - - - +
216E GLU* 1.3 59.9 + - - +
217E ARG 3.4 0.9 + - - -
218E THR* 4.2 10.9 - - - +
261E ALA* 3.2 26.5 + - - +
262E GLN 5.3 0.4 + - - -
263E ILE* 3.6 25.4 - - + +
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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