Contacts of the helix formed by residues 203 - 215 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.6 25.6 - - + +
172A ILE* 4.5 5.6 - - + -
198A VAL* 4.1 10.6 + - + +
202A GLY* 1.3 70.6 - - - -
204A THR* 1.3 57.1 + - - +
206A VAL* 3.6 14.4 - - - +
207A MET* 2.9 59.4 + - + +
246A LEU* 3.6 34.3 - - + -
250A GLU* 3.6 45.5 + - + +
253A LEU* 4.4 13.0 - - + -
254A ALA* 4.6 1.6 - - + -
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLY* 3.1 1.9 + - - -
203A MET* 1.3 78.7 - - - +
205A ARG* 1.3 57.8 + - - +
208A GLU* 2.9 52.5 + - - +
253A LEU* 3.4 8.9 - - - +
257A MET* 3.7 16.2 - - + +
199B ASP 3.5 3.5 + - - -
200B ARG* 3.0 54.1 + - + +
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Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.5 57.3 + - + +
202A GLY 3.2 2.6 + - - +
204A THR* 1.3 76.6 - - - +
206A VAL* 1.3 60.9 + - - +
208A GLU* 3.7 14.0 - - - +
209A GLU* 2.8 62.7 + - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 4.2 20.9 - - + -
193A TYR* 3.6 52.2 - - + -
197A GLU 4.1 17.5 - - - +
198A VAL* 4.2 10.3 - - + +
201A LEU* 4.3 4.7 - - + -
202A GLY 3.1 16.5 + - - +
203A MET* 3.6 13.9 - - - +
205A ARG* 1.3 76.2 - - - +
207A MET* 1.3 58.9 + - - +
209A GLU* 3.5 2.1 + - - +
210A THR* 2.8 35.9 + - - +
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 5.1 1.3 - - + -
121A TYR* 5.3 1.8 - - - -
172A ILE* 3.9 28.0 - - + -
203A MET* 2.9 33.8 + - + +
206A VAL* 1.3 75.1 - - - +
208A GLU* 1.3 59.2 + - - +
210A THR* 4.1 5.2 - - + -
211A ILE* 2.8 45.1 + - + +
254A ALA* 3.9 35.7 - - + +
257A MET* 3.8 21.3 - - + -
258A LEU* 3.6 40.8 - - + -
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A THR* 2.9 37.1 + - - +
205A ARG* 3.7 15.2 - - - +
207A MET* 1.3 77.0 - - - +
209A GLU* 1.3 58.6 + - + +
211A ILE* 4.0 4.8 - - - +
212A ALA* 3.0 31.8 + - - +
257A MET* 3.7 16.3 - - + +
200B ARG* 5.0 7.3 + - - +
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS* 4.6 3.0 + - - -
193A TYR* 2.8 40.6 + - - +
201A LEU* 4.3 4.7 - - - +
205A ARG* 2.8 60.9 + - + +
206A VAL 3.8 0.9 - - - +
208A GLU* 1.3 77.3 - - + +
210A THR* 1.3 58.1 + - - +
212A ALA* 3.9 4.6 - - - +
213A TYR* 3.0 31.6 + - - +
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 4.1 28.9 - - + -
170A VAL* 3.4 33.9 - - + +
172A ILE* 3.7 15.8 - - + +
191A LYS* 5.1 0.4 - - - +
193A TYR* 3.4 9.7 - - - -
206A VAL 2.8 21.8 + - - -
207A MET* 3.6 10.3 - - + +
208A GLU 3.3 0.2 - - - -
209A GLU* 1.3 77.6 - - - +
211A ILE* 1.3 65.3 + - + +
213A TYR* 3.4 6.1 + - - +
214A LEU* 3.1 26.3 + - + +
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A MET* 2.8 30.6 + - + +
208A GLU* 4.0 4.5 - - - +
210A THR* 1.3 74.7 - - + +
212A ALA* 1.3 67.2 + - - +
214A LEU* 4.2 0.7 - - - +
215A LYS* 2.9 41.4 + - - +
257A MET* 3.5 35.7 - - + +
258A LEU* 3.7 28.5 - - + -
261A ALA* 3.5 22.4 - - + -
263A ILE* 3.9 14.0 - - + +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLU 3.0 18.7 + - - +
209A GLU* 3.9 4.7 - - - +
211A ILE* 1.3 80.4 - - - +
213A TYR* 1.3 63.1 + - - +
215A LYS* 3.9 7.1 - - - +
216A GLU* 3.1 27.3 + - - +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 2.6 41.3 + - - +
169A VAL 4.6 3.5 + - - -
170A VAL* 3.8 16.6 - - + -
189A GLY 5.5 1.6 + - - -
191A LYS* 3.7 46.4 + - + +
209A GLU 3.0 19.5 + - - +
210A THR* 3.5 4.3 - - - +
212A ALA* 1.3 78.1 - - - +
214A LEU* 1.3 71.2 + - + +
216A GLU* 3.4 5.7 + - - +
217A ARG* 2.9 66.3 + - - +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLY* 4.3 1.1 - - - -
118A VAL 4.2 4.9 - - - +
119A ILE* 3.5 34.8 - - + -
168A HIS* 3.5 30.5 - - - +
170A VAL* 3.9 23.6 - - + -
210A THR* 3.1 16.3 + - + +
211A ILE 4.3 1.8 - - - +
213A TYR* 1.3 81.9 - - + +
215A LYS* 1.3 65.8 + - - +
216A GLU 3.0 2.0 - - - -
217A ARG* 2.9 13.4 + - + -
218A THR* 2.8 32.7 + - + -
221A VAL* 4.0 26.0 - - + -
263A ILE* 5.1 4.5 - - + -
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 2.9 33.6 + - - +
212A ALA* 3.9 6.1 - - - +
214A LEU* 1.3 77.1 - - - +
216A GLU* 1.3 60.2 + - - +
217A ARG 3.4 0.7 + - - -
218A THR* 4.3 11.3 - - - +
221A VAL* 6.0 0.2 - - - -
261A ALA* 3.3 26.0 + - - +
262A GLN 5.4 0.2 + - - -
263A ILE* 3.8 24.9 - - + +
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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