Contacts of the helix formed by residues 207 - 212 (chain A) in PDB entry 3BRW
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A SER* 1.3 75.8 - - - +
208A GLU* 1.3 58.8 + - + +
210A LEU* 2.9 27.4 + - - +
211A PHE* 3.1 27.5 + - + -
280A GLN* 4.9 10.6 - - - +
285A LYS* 3.6 26.6 + - - +
308A MET 3.1 23.6 + - - +
309A ILE* 3.8 8.3 - - + -
310A ALA* 3.2 34.3 + - - +
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Residues in contact with GLU 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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206A SER* 3.7 3.4 + - - +
207A GLU* 1.3 76.5 - - + +
209A GLU* 1.3 65.3 + - - +
210A LEU 3.2 0.9 + - - -
211A PHE* 4.4 5.8 - - - +
212A SER* 3.3 36.7 + - - +
277A GLY 5.3 0.9 - - - +
278A ASP 3.3 17.8 - - - +
279A ALA* 3.1 39.6 - - - +
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Residues in contact with GLU 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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201A LYS* 4.2 28.4 + - - +
202A LEU* 5.9 1.6 - - - +
203A GLY 4.5 2.9 - - - +
204A ALA* 3.6 28.5 - - + +
205A THR* 2.7 37.3 + - - -
206A SER* 3.2 21.6 + - - +
207A GLU 3.2 0.2 - - - -
208A GLU* 1.3 77.5 - - - +
210A LEU* 1.3 59.0 + - - +
212A SER* 5.0 0.5 - - - -
213A THR* 3.2 18.5 + - - -
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Residues in contact with LEU 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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198A ILE* 4.0 21.7 - - + +
199A TYR 4.0 7.0 + - - +
200A GLN* 3.7 43.5 - - + +
204A ALA* 3.8 14.8 - - + -
205A THR 5.3 0.4 - - - +
206A SER 3.4 21.5 - - - +
207A GLU 2.9 6.9 + - - +
209A GLU* 1.3 74.3 - - - +
211A PHE* 1.3 59.2 + - + +
212A SER 2.9 11.4 + - - -
213A THR* 3.1 22.9 + - - -
269A SER* 4.8 5.9 + - - -
304A PHE* 4.4 13.0 - - + -
308A MET* 4.9 4.7 - - + -
309A ILE* 4.1 31.0 - - + -
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Residues in contact with PHE 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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198A ILE* 5.0 8.1 - - + -
207A GLU* 3.1 30.1 + - - +
208A GLU* 3.6 5.6 + - - -
210A LEU* 1.3 83.6 - - + +
212A SER* 1.3 57.6 + - - +
213A THR 3.6 0.4 - - - -
269A SER* 5.1 8.3 - - - -
280A GLN 4.5 5.6 - - - +
281A GLN* 3.5 17.3 - - + +
284A ARG* 3.4 45.9 + - + -
285A LYS* 3.7 37.5 - - + -
288A ILE* 4.2 37.2 - - + -
289A GLY* 5.7 0.4 - - - -
309A ILE* 4.0 39.7 - - + -
314A LEU* 5.9 0.2 - - + -
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Residues in contact with SER 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 GLU* 3.3 36.0 + - - +
209A GLU 5.2 0.7 - - - -
210A LEU 3.1 1.0 - - - -
211A PHE* 1.3 76.6 - - - +
213A THR* 1.3 66.4 + - - +
214A ASN* 3.1 15.9 + - - +
274A TYR* 4.0 21.8 + - - -
278A ASP 4.7 0.2 + - - -
281A GLN* 3.4 17.0 + - - +
284A ARG* 4.6 1.6 - - - -
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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