Contacts of the helix formed by residues 207 - 213 (chain A) in PDB entry 5ABT
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 ASP 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ILE* 3.9 2.6 - - - +
206A GLY* 1.3 80.8 - - - +
208A ILE* 1.3 64.9 + - - +
209A ASP* 3.2 17.3 + - - +
210A ASP* 3.0 38.9 + - - +
211A ILE* 3.6 3.1 + - - +
232A LYS* 4.8 3.1 - - + +
233A PHE* 3.5 19.1 - - - -
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Residues in contact with ILE 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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207A ASP* 1.3 75.0 - - - +
209A ASP* 1.3 69.1 + - - +
211A ILE* 3.1 12.5 + - + +
212A ALA* 3.1 18.0 + - + -
233A PHE* 3.6 37.6 - - + -
237A GLU* 3.9 11.4 - - + +
238A ALA* 3.8 29.6 - - - +
241A CYS* 3.8 20.4 - - + -
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Residues in contact with ASP 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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207A ASP* 3.2 15.2 + - - +
208A ILE* 1.3 81.6 - - - +
210A ASP* 1.3 59.3 + - - +
212A ALA* 3.3 10.9 + - - +
213A ALA* 2.9 29.5 + - - +
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Residues in contact with ASP 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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179A LEU 4.3 1.7 - - - +
180A ALA 4.6 0.6 - - - -
181A GLY* 3.5 25.9 + - - -
182A SER* 4.9 2.5 + - - +
184A VAL* 5.4 0.7 - - - +
205A ILE* 3.7 24.7 - - + +
206A GLY* 2.8 26.7 + - - +
207A ASP* 3.0 28.5 + - - +
209A ASP* 1.3 74.9 - - - +
211A ILE* 1.3 66.6 + - - +
213A ALA* 3.5 17.1 + - - +
214A LEU* 3.7 9.0 - - - +
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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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2A ILE* 4.0 17.9 - - + -
205A ILE* 3.9 25.1 - - + -
207A ASP 3.6 2.2 + - - +
208A ILE* 3.1 13.6 + - + +
210A ASP* 1.3 76.0 - - - +
212A ALA* 1.3 67.3 + - - +
214A LEU* 2.9 23.1 + - - +
222A VAL* 4.6 6.7 - - + -
224A VAL* 4.4 4.3 - - + -
233A PHE* 3.8 20.9 - - + -
238A ALA* 3.7 32.3 - - + +
241A CYS* 3.9 15.3 - - + -
242A TRP* 3.7 26.1 - - + -
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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 ILE* 3.1 9.8 + - + +
209A ASP* 3.5 14.1 - - - +
211A ILE* 1.3 76.5 - - - +
213A ALA* 1.3 62.8 + - - +
214A LEU 3.1 1.4 + - - -
215A ARG* 3.1 50.0 + - - +
241A CYS* 3.7 20.4 - - - -
245A VAL* 4.2 8.7 - - + -
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Residues in contact with ALA 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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184A VAL* 3.7 33.3 - - + +
209A ASP 2.9 16.4 + - - +
210A ASP* 3.6 13.2 - - - +
211A ILE 3.1 0.2 - - - -
212A ALA* 1.3 76.4 - - - +
214A LEU* 1.3 59.5 + - - +
215A ARG* 3.4 1.6 + - - +
216A GLY 4.8 1.9 + - - -
217A THR* 4.5 1.0 - - - +
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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