Contacts of the helix formed by residues 205 - 211 (chain A) in PDB entry 2J6U
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 LEU 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A PHE* 4.2 20.0 - - + -
156A ILE* 6.0 0.7 - - + -
177A LEU 5.0 0.4 - - - +
178A ILE* 3.4 28.1 + - + +
181A LEU* 3.9 16.1 + - + +
183A ILE* 3.6 12.9 - - + +
186A VAL* 4.0 22.2 - - + -
204A LYS* 1.3 71.1 - - - +
206A VAL* 1.3 64.6 + - - +
207A ASP 3.0 1.4 + - - -
208A THR* 2.9 26.2 + - - -
228A LEU* 3.7 38.6 - - + +
231A LEU* 3.9 30.3 - - + +
232A ALA* 3.7 5.4 - - - +
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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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178A ILE* 2.7 30.5 + - + +
179A ARG* 3.9 39.3 - - + +
204A LYS* 3.6 21.8 - - + -
205A LEU* 1.3 73.3 - - - +
207A ASP* 1.3 72.8 + - - +
209A LEU* 3.0 35.7 + - + +
210A SER* 4.2 1.7 + - - -
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Residues in contact with ASP 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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201A GLY 3.9 10.3 - - - +
202A ILE* 3.7 19.1 - - - -
203A ASN* 3.1 11.2 + - - +
204A LYS* 3.0 39.1 + - - +
206A VAL* 1.3 86.3 - - - +
208A THR* 1.3 58.7 + - - +
209A LEU 3.0 0.9 - - - -
210A SER* 2.9 26.4 + - - +
211A ILE* 3.6 12.8 - - - +
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Residues in contact with THR 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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183A ILE* 4.7 2.2 - - + -
197A LEU* 5.4 0.2 - - + -
202A ILE* 3.9 28.7 - - + -
205A LEU 2.9 17.3 + - - +
207A ASP* 1.3 76.4 - - - +
209A LEU* 1.3 62.4 + - - +
211A ILE* 3.7 18.1 + - - +
216A LEU* 5.3 14.4 - - + +
228A LEU* 3.8 31.3 + - + -
229A ILE* 4.1 23.9 - - - +
232A ALA* 3.3 16.8 - - - +
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Residues in contact with LEU 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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178A ILE* 5.4 1.3 - - + -
206A VAL* 3.0 29.9 + - + +
207A ASP 3.0 0.8 - - - -
208A THR* 1.3 79.4 - - - +
210A SER* 1.3 58.4 + - - +
211A ILE 3.4 5.4 + - - +
229A ILE* 4.6 5.6 - - + +
232A ALA* 3.7 32.5 - - + +
233A ARG* 3.6 35.9 - - + +
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Residues in contact with SER 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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206A VAL 4.5 0.9 + - - -
207A ASP* 2.9 26.2 + - - +
209A LEU* 1.3 77.1 - - - +
211A ILE* 1.3 66.8 + - - +
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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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200A LEU* 3.9 21.3 - - + +
201A GLY* 5.5 3.4 - - - +
202A ILE* 3.7 21.8 - - + -
207A ASP 3.6 15.7 - - - +
208A THR* 3.7 16.1 + - - +
209A LEU 3.4 5.8 - - - +
210A SER* 1.3 88.7 - - - +
212A GLU* 1.3 90.6 + - - +
213A PHE 3.7 1.9 + - - -
215A LYS* 4.4 23.6 - - + +
216A LEU* 4.4 17.3 - - + +
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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