Contacts of the helix formed by residues 211 - 228 (chain A) in PDB entry 1BRW
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A THR* 3.6 15.0 + - + +
209A LYS 4.1 0.8 + - - -
210A LYS* 1.3 70.9 - - - +
212A ASP* 1.3 60.9 + - - +
214A ALA* 3.2 3.5 + - - +
215A ARG* 3.0 51.5 + - - +
236A ILE* 3.9 22.7 - - + -
429A TYR* 3.7 47.3 - - + -
430A GLU* 5.0 1.6 - - - +
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Residues in contact with ASP 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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210A LYS* 3.2 5.5 - - + +
211A LEU* 1.3 82.6 - - - +
213A GLU* 1.3 59.0 - - + +
215A ARG* 3.3 31.3 + - - +
216A ARG* 3.2 35.5 + - - +
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Residues in contact with GLU 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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175A ASN* 4.9 1.6 - - - +
177A ILE* 3.5 19.4 - - + +
207A PHE 4.5 2.1 - - - +
208A MET* 3.6 28.7 - - + +
209A LYS* 3.6 10.6 + - - +
210A LYS* 3.0 50.0 + - + +
212A ASP* 1.3 75.8 - - + +
214A ALA* 1.3 62.3 + - - +
216A ARG* 3.4 15.7 + - - +
217A LEU* 3.1 25.1 + - - +
6002A MES 5.8 3.2 - - - -
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Residues in contact with ALA 214 (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 VAL* 3.7 14.9 - - + +
202A THR* 3.6 31.4 - - - +
208A MET* 4.0 15.6 - - + +
210A LYS 3.2 1.9 + - - +
211A LEU 3.2 8.9 + - - +
213A GLU* 1.3 77.3 - - - +
215A ARG* 1.3 58.9 + - - +
217A LEU* 3.3 0.6 + - - -
218A ALA* 3.0 30.1 + - - +
236A ILE* 3.9 16.5 - - + +
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Residues in contact with ARG 215 (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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211A LEU* 3.0 41.9 + - - +
212A ASP* 3.3 39.8 + - - +
214A ALA* 1.3 76.8 - - - +
216A ARG* 1.3 61.6 + - + +
218A ALA* 3.5 1.6 + - - +
219A ARG* 3.1 31.2 + - + +
236A ILE* 3.6 14.3 - - + +
430A GLU* 3.2 39.3 + - - +
432A ILE* 4.2 6.1 - - + +
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Residues in contact with ARG 216 (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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52A GLU* 5.1 0.7 - - - +
177A ILE* 3.7 33.5 - - + +
212A ASP* 3.2 23.4 + - - +
213A GLU* 3.7 19.4 - - - +
214A ALA 3.3 0.4 - - - -
215A ARG* 1.3 78.9 - - + +
217A LEU* 1.3 60.9 + - - +
219A ARG* 4.0 5.9 - - - +
220A VAL* 3.3 24.9 + - - +
6002A MES 2.8 35.9 + - - -
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 4.0 26.2 - - + -
177A ILE* 3.9 31.4 - - + +
180A ILE* 4.1 17.3 - - + -
181A ALA* 4.0 20.4 - - + +
200A VAL* 4.0 4.3 - - + -
207A PHE* 6.3 0.2 - - + -
208A MET* 3.5 30.3 - - + -
213A GLU 3.1 17.0 + - - +
214A ALA 3.7 5.4 - - - +
215A ARG 3.2 0.4 - - - -
216A ARG* 1.3 76.3 - - - +
218A ALA* 1.3 64.9 + - - +
220A VAL* 3.3 7.0 - - - +
221A MET* 3.2 35.5 + - + +
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Residues in contact with ALA 218 (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 VAL* 3.7 26.2 - - + +
214A ALA 3.0 16.6 + - - +
215A ARG 4.0 0.9 - - - +
217A LEU* 1.3 76.0 - - - +
219A ARG* 1.3 58.3 + - - +
221A MET* 3.4 4.4 + - - +
222A VAL* 3.0 34.5 + - - +
234A ALA* 4.1 12.1 - - + +
236A ILE* 4.3 9.0 - - + -
432A ILE* 3.8 20.6 - - + -
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Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.8 23.7 + - - +
215A ARG* 3.1 22.1 + - + +
216A ARG* 4.0 7.2 - - - +
218A ALA* 1.3 77.9 - - - +
220A VAL* 1.3 61.8 + - - +
222A VAL* 3.4 5.9 + - - +
223A ASP* 3.0 22.8 + - + +
432A ILE* 3.9 18.5 - - + +
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Residues in contact with VAL 220 (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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52A GLU* 3.5 37.2 - - + +
55A THR* 4.0 28.7 - - + +
177A ILE* 4.5 9.0 - - + -
181A ALA* 3.9 19.7 - - + -
216A ARG 3.3 13.9 + - - +
217A LEU* 3.3 15.9 - - - +
219A ARG* 1.3 78.9 - - - +
221A MET* 1.3 60.6 + - - +
223A ASP* 3.4 1.8 + - - +
224A ILE* 2.9 40.1 + - + +
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Residues in contact with MET 221 (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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84A THR* 4.2 10.1 - - + -
181A ALA* 3.8 32.1 - - + -
184A ILE* 4.1 28.5 - - + -
185A MET* 3.3 30.1 - - + +
198A LEU* 3.8 26.7 - - + -
200A VAL* 3.8 29.6 - - + -
217A LEU* 3.2 28.1 + - + +
218A ALA* 3.9 2.0 - - - +
220A VAL* 1.3 74.2 - - - +
222A VAL* 1.3 64.4 + - - +
224A ILE* 3.3 2.2 + - - +
225A GLY 3.2 17.2 + - - -
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Residues in contact with VAL 222 (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 LEU* 4.6 0.9 - - + -
218A ALA 3.0 21.0 + - - +
219A ARG 3.8 3.6 - - - +
221A MET* 1.3 74.8 - - - +
223A ASP* 1.3 64.1 + - - +
225A GLY* 3.2 3.5 + - - -
226A LYS* 3.2 40.8 + - + +
232A THR* 3.8 28.2 - - + +
233A MET* 4.1 11.9 - - - -
234A ALA* 3.8 25.8 - - + +
432A ILE* 4.2 23.3 - - + +
433A VAL* 4.5 3.4 - - - +
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.6 35.0 - - - +
219A ARG* 3.0 18.8 + - + +
220A VAL 3.6 4.6 - - - +
222A VAL* 1.3 79.0 - - - +
224A ILE* 1.3 62.9 + - - +
226A LYS* 3.5 8.2 + - - +
227A ARG* 3.0 61.4 + - - +
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Residues in contact with ILE 224 (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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52A GLU 5.4 0.2 - - - +
55A THR* 4.1 21.5 - - + +
56A ALA* 4.2 15.3 - - + -
59A THR* 3.5 33.4 - - + +
60A MET* 3.9 9.1 - - + +
181A ALA* 4.5 6.5 - - + -
185A MET* 3.8 30.1 - - + -
189A ILE* 4.0 8.3 - - + -
220A VAL* 2.9 33.8 + - + +
221A MET* 3.5 7.0 - - - +
222A VAL 3.2 0.2 - - - -
223A ASP* 1.3 79.2 - - - +
225A GLY* 1.3 61.6 + - - +
227A ARG* 3.4 20.4 + - - +
228A VAL* 3.6 9.4 - - - +
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Residues in contact with GLY 225 (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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185A MET* 3.8 11.9 - - - +
189A ILE* 4.9 1.1 - - - -
221A MET 3.2 8.3 + - - -
222A VAL 3.2 0.8 + - - -
224A ILE* 1.3 78.6 - - - +
226A LYS* 1.3 60.2 + - - +
228A VAL* 3.3 16.0 + - - +
230A ARG* 3.0 29.0 + - - +
232A THR* 3.3 24.0 - - - -
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Residues in contact with LYS 226 (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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222A VAL* 3.2 25.5 + - + +
223A ASP* 3.9 6.7 - - - +
225A GLY* 1.3 73.0 - - - +
227A ARG* 1.3 64.6 + - - +
229A GLY* 3.2 11.4 + - - -
230A ARG 3.7 15.7 - - - +
231A ARG* 6.0 0.7 - - - +
232A THR 3.6 25.1 - - - +
433A VAL* 2.7 34.1 + - - -
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Residues in contact with ARG 227 (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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52A GLU* 4.8 2.4 + - - +
53A GLU* 4.2 32.5 + - - +
56A ALA* 3.8 31.5 - - - +
60A MET* 4.9 5.2 - - + -
223A ASP* 3.0 49.8 + - - +
224A ILE* 3.6 11.9 - - - +
225A GLY 3.2 0.4 - - - -
226A LYS* 1.3 77.7 - - - +
228A VAL* 1.3 64.0 + - + +
229A GLY 3.4 0.6 + - - -
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Residues in contact with VAL 228 (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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60A MET* 3.6 29.2 - - + -
189A ILE* 3.7 27.1 - - + -
224A ILE 3.6 11.2 - - - +
225A GLY 3.5 11.4 - - - +
226A LYS 3.2 0.4 - - - -
227A ARG* 1.3 79.9 - - + +
229A GLY* 1.3 58.1 + - - +
230A ARG* 2.9 34.5 + - + +
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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
------------------------------------------------------------
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