Contacts of the helix formed by residues 182 - 187 (chain E) in PDB entry 3ECS
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 ALA 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D ILE* 4.1 20.0 - - + -
214D GLN* 3.3 1.3 - - - -
269D GLU* 6.0 0.9 - - + +
271D PRO* 4.9 8.3 - - + -
178E VAL* 4.2 16.8 - - + -
179E LEU* 3.0 20.8 + - + +
181E ALA* 1.3 78.2 - - - +
183E VAL* 1.3 63.2 + - - +
184E GLY 3.4 1.3 - - - -
185E TYR* 3.1 14.1 + - + +
186E ILE* 2.9 25.9 + - - +
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Residues in contact with VAL 183 (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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214D GLN* 2.4 26.2 - - - +
126E LEU* 4.4 2.2 - - + -
153E THR* 3.3 34.1 - - + -
178E VAL* 5.3 0.2 - - + -
179E LEU 4.1 0.4 + - - +
180E ASP 3.5 10.5 - - - +
182E ALA* 1.3 68.9 - - - +
184E GLY* 1.3 63.1 + - - +
185E TYR 3.0 0.2 + - - -
186E ILE* 3.2 9.7 + - + +
187E MSE 3.0 48.5 + - + +
211E GLY 6.1 0.7 - - - +
214E GLN* 5.0 3.4 - - + +
215E MSE 3.6 33.9 - - + +
218E CYS* 4.6 4.5 - - + -
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Residues in contact with GLY 184 (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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213D ASN* 3.0 30.5 + - - -
214D GLN* 2.8 30.2 - - - +
243D GLN* 5.0 2.4 + - - +
181E ALA 5.7 0.2 - - - -
183E VAL* 1.3 72.4 - - - +
185E TYR* 1.3 56.7 - - - +
187E MSE 3.9 10.9 + - - +
188E GLU* 4.9 0.7 + - - +
218E CYS* 3.7 15.7 - - - +
222E GLN* 4.1 7.1 - - - +
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Residues in contact with TYR 185 (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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210D ILE* 3.8 18.8 - - + -
213D ASN* 3.8 3.2 - - - +
243D GLN* 3.2 57.0 - - + +
251D LYS* 3.1 36.0 + - - +
252D TYR* 3.8 8.5 + - - -
269D GLU* 4.7 7.9 + - + -
271D PRO* 3.6 37.1 - - + +
273D VAL 4.3 2.7 - - - -
274D ASP* 3.9 15.0 + - + +
181E ALA 5.3 0.8 + - - -
182E ALA* 3.2 14.8 - - + +
184E GLY* 1.3 76.7 - - - +
186E ILE* 1.3 79.5 + - + +
187E MSE 3.8 0.2 + - - -
188E GLU* 3.9 8.2 - - - +
189E LYS* 5.6 7.7 + - - +
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Residues in contact with ILE 186 (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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269D GLU* 3.8 15.0 - - + +
126E LEU* 4.4 21.5 - - + -
151E TYR* 3.4 50.7 - - + +
178E VAL* 4.7 13.9 - - + -
182E ALA* 2.9 22.2 + - + +
183E VAL* 3.4 13.0 - - - +
185E TYR* 1.3 82.9 - - + +
187E MSE 1.3 62.8 + - - +
188E GLU 3.3 2.9 - - - -
189E LYS* 2.8 43.6 + - + +
190E ALA* 3.8 3.2 + - - +
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Residues in contact with MSE 187 (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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126E LEU* 3.7 26.7 - - + -
183E VAL* 3.0 28.3 + - + +
184E GLY 3.9 5.8 - - - +
185E TYR 3.4 0.8 - - - -
186E ILE* 1.3 77.7 - - - +
188E GLU* 1.3 63.6 + - - +
189E LYS 3.0 1.6 + - - -
190E ALA* 3.0 18.0 + - - +
193E VAL* 4.1 14.4 - - + -
215E MSE 3.5 28.0 - - + +
218E CYS* 3.5 23.3 - - + +
219E ALA* 3.8 17.5 - - + +
222E GLN* 3.6 19.7 - - - +
224E LYS* 3.6 23.4 - - + -
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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