Contacts of the helix formed by residues 182 - 187 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178F VAL* 4.3 9.9 - - + -
179F LEU* 2.8 27.0 + - + +
181F ALA* 1.3 77.3 - - - +
183F VAL* 1.3 57.9 + - - +
184F GLY 3.5 0.7 - - - -
185F TYR* 3.2 10.1 + - + +
186F ILE* 2.8 32.5 + - + +
210G ILE* 3.6 26.4 - - + +
269G GLU 5.5 0.2 - - - +
271G PRO* 5.0 9.4 - - + -
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Residues in contact with VAL 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 4.5 2.9 - - + -
128F HIS* 6.4 0.2 - - + -
153F THR* 3.2 32.5 - - + -
178F VAL* 5.3 0.7 - - + -
179F LEU 4.1 0.4 - - - +
180F ASP* 3.1 18.6 - - - +
182F ALA* 1.3 78.4 - - - +
184F GLY* 1.3 66.0 + - - +
186F ILE* 3.3 9.6 - - + +
187F MSE 3.0 32.5 + - + +
211F GLY 5.9 1.6 - - - +
214F GLN* 5.3 3.1 - - + +
215F MSE 4.0 42.6 - - + +
218F CYS* 4.8 3.6 - - + -
214G GLN* 3.0 9.0 + - - +
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Residues in contact with GLY 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F VAL* 1.3 73.5 - - - +
185F TYR* 1.3 58.7 + - - +
187F MSE 3.8 11.9 - - - +
218F CYS* 3.8 22.4 - - - -
222F GLN* 3.9 8.5 + - - -
213G ASN* 3.0 29.3 + - - -
214G GLN* 2.6 21.8 + - - +
243G GLN* 4.8 3.1 + - - +
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Residues in contact with TYR 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ALA 5.0 0.6 + - - -
182F ALA* 3.3 16.1 - - + +
183F VAL 3.0 0.4 - - - -
184F GLY* 1.3 77.5 - - - +
186F ILE* 1.3 81.1 + - + +
187F MSE 3.5 0.2 + - - -
188F GLU* 3.9 9.0 - - - +
189F LYS* 4.8 7.2 + - - +
210G ILE* 3.7 19.1 - - + -
213G ASN* 3.8 2.9 - - - +
243G GLN* 3.2 59.6 - - + +
251G LYS* 3.1 39.2 - - - +
252G TYR* 4.1 1.4 + - - -
269G GLU* 3.4 22.4 + - + -
271G PRO* 3.4 30.3 - - + +
273G VAL 4.2 4.7 - - - -
274G ASP* 3.8 15.5 + - + +
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Residues in contact with ILE 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 4.2 22.0 - - + -
151F TYR* 3.4 42.0 - - + -
178F VAL* 4.6 15.9 - - + -
182F ALA* 2.8 19.4 + - + +
183F VAL* 3.3 17.3 - - - +
185F TYR* 1.3 84.7 - - + +
187F MSE 1.3 68.7 + - - +
188F GLU 3.2 1.3 - - - -
189F LYS* 2.8 54.6 + - + +
190F ALA* 3.9 3.3 + - + +
269G GLU* 4.1 10.1 - - + +
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Residues in contact with MSE 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 3.6 29.2 - - + -
183F VAL* 3.0 17.4 + - + +
184F GLY* 3.8 6.5 - - - +
185F TYR 3.3 0.8 - - - -
186F ILE* 1.3 79.0 - - - +
188F GLU* 1.3 61.8 + - - +
190F ALA* 3.1 19.8 + - - +
193F VAL* 4.1 6.3 - - + -
215F MSE 3.4 17.5 - - + +
218F CYS* 3.7 18.4 - - + +
219F ALA* 3.3 37.7 - - + +
222F GLN* 3.3 27.1 - - - +
224F LYS* 3.6 24.7 - - + -
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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