Contacts of the helix formed by residues 201 - 209 (chain A) in PDB entry 5F2R
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 GLU 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP* 4.3 3.3 - - - +
35A LEU 4.1 3.5 - - - +
96A LYS* 2.7 27.8 + - - -
171A THR* 3.6 20.4 + - - +
172A VAL* 2.8 20.5 + - - +
173A PRO* 3.3 28.3 - - + +
200A ASN* 1.3 70.5 - - - +
202A PRO* 1.3 71.0 - - + +
204A ALA* 3.1 5.0 + - - +
205A ALA* 3.0 18.5 + - - +
224A ASP* 4.2 9.0 - - - +
231A ASP* 5.4 2.3 - - - +
394A VAL* 3.7 28.4 - - + +
501A ACP 3.6 19.8 + - - -
502A MG 4.1 4.2 - - - -
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Residues in contact with PRO 202 (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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173A PRO* 5.1 0.2 - - + -
174A ALA* 3.9 21.3 - - + +
200A ASN* 3.6 6.7 - - + -
201A GLU* 1.3 94.7 - - + +
203A THR* 1.3 57.1 + - - +
205A ALA* 3.5 5.7 - - + +
206A ALA* 3.1 25.6 + - - +
222A VAL* 3.7 41.3 - - + +
224A ASP* 6.0 1.3 - - + +
233A SER* 3.5 26.7 - - - +
235A LEU* 3.8 13.6 - - + +
362A VAL* 5.4 1.1 - - + -
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Residues in contact with THR 203 (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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199A ILE* 5.6 4.7 - - + -
200A ASN* 3.1 29.8 + - - +
202A PRO* 1.3 77.3 - - - +
204A ALA* 1.3 60.3 + - - +
206A ALA* 3.1 4.2 + - - +
207A ILE* 2.9 38.3 + - + +
235A LEU* 3.6 22.6 - - - +
242A PHE* 3.5 38.3 - - + +
244A VAL* 4.7 1.9 - - - +
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Residues in contact with ALA 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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171A THR* 3.9 10.1 - - + -
199A ILE* 3.9 19.0 - - + +
200A ASN 2.9 12.5 + - - +
201A GLU 3.5 7.6 - - - +
203A THR* 1.3 77.6 - - - +
205A ALA* 1.3 56.2 + - - +
207A ILE* 3.2 11.2 + - - +
208A ALA* 2.9 25.8 + - - +
393A ALA 4.2 1.3 - - - -
394A VAL* 3.5 22.0 - - - +
397A GLY* 3.2 11.5 - - - -
398A ALA 4.1 3.1 - - - +
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Residues in contact with ALA 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 GLU 3.0 11.3 + - - +
202A PRO* 3.5 11.0 - - + +
204A ALA* 1.3 74.9 - - - +
206A ALA* 1.3 62.0 + - - +
208A ALA* 3.2 12.8 + - - +
209A TYR* 3.2 18.7 + - - -
222A VAL* 4.8 0.2 - - + -
360A VAL* 4.0 11.2 - - + -
362A VAL* 3.5 32.1 - - + -
393A ALA* 4.0 19.9 + - + -
394A VAL* 4.3 4.2 - - + +
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Residues in contact with ALA 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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202A PRO 3.1 10.7 + - - +
203A THR* 3.1 9.2 + - - +
205A ALA* 1.3 77.4 - - - +
207A ILE* 1.3 62.4 + - - +
209A TYR* 3.2 3.7 + - - +
210A GLY 3.2 3.5 + - - -
211A LEU* 3.0 48.1 + - + +
220A ILE* 4.5 9.2 - - + -
222A VAL* 5.4 0.2 - - + -
235A LEU* 4.6 3.8 - - + -
242A PHE* 3.8 24.0 - - + -
360A VAL* 4.8 5.1 - - + +
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Residues in contact with ILE 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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199A ILE* 4.6 4.3 - - + -
203A THR* 2.9 36.0 + - + +
204A ALA* 3.2 11.2 + - - +
206A ALA* 1.3 71.7 - - - +
208A ALA* 1.3 58.8 + - - +
210A GLY* 2.7 24.9 + - - -
212A ASP* 4.0 21.7 - - - +
242A PHE* 3.7 20.4 - - + -
397A GLY 4.0 7.2 - - - +
400A VAL* 3.8 35.2 - - + +
401A GLN* 3.5 34.3 - - + +
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Residues in contact with ALA 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 ALA 2.9 7.5 + - - +
205A ALA 3.3 10.3 - - - +
207A ILE* 1.3 77.1 - - - +
209A TYR* 1.3 58.4 + - + +
210A GLY 3.2 0.9 + - - -
388A ILE* 3.2 24.5 - - + +
393A ALA* 3.4 28.3 - - + +
396A TYR* 3.6 33.1 - - + -
397A GLY* 3.6 4.9 - - - +
400A VAL* 4.7 1.6 - - - -
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Residues in contact with TYR 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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205A ALA 3.2 19.5 + - - +
206A ALA 3.8 6.7 - - - +
207A ILE 3.1 1.2 - - - -
208A ALA* 1.3 76.2 - - - +
210A GLY* 1.3 63.6 + - - +
211A LEU* 3.1 20.1 + - + +
214A ARG* 4.5 6.4 + - - -
360A VAL* 4.0 19.1 - - + -
361A LEU 5.0 6.2 + - - -
385A SER* 3.8 29.9 + - - +
386A ARG* 3.3 30.7 - - - -
387A GLY 3.5 4.7 + - - -
388A ILE* 3.0 52.4 + - + -
390A PRO* 6.5 0.2 - - + -
393A ALA* 4.7 9.9 - - + -
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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