Contacts of the helix formed by residues 222 - 235 (chain A) in PDB entry 3BSH
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 GLN 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A MET* 2.9 29.6 - - + +
211A ALA* 3.4 30.0 + - - +
218A PRO* 4.2 1.0 - - + +
219A ASN* 3.1 34.8 + - - +
220A TYR 3.3 3.8 + - - +
221A ASP* 1.3 73.1 + - - +
223A ASP* 1.3 56.0 + - - +
224A ALA* 3.1 3.6 - - - -
225A HIS* 2.7 39.8 + - - +
226A ARG* 3.2 11.9 + - - +
249A THR* 4.0 9.4 - - + -
253A ILE* 3.5 40.6 - - + +
273A PRO 5.2 1.3 - - - +
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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
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221A ASP* 3.2 32.1 + - - +
222A GLN* 1.3 78.1 + - - +
224A ALA* 1.3 57.3 + - - +
226A ARG* 3.8 22.1 + - - +
227A GLN* 2.9 31.8 + - - +
267A ASP* 5.3 4.0 - - - +
268A PRO* 5.7 1.7 - - - +
278A TRP* 3.1 32.5 - - + -
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Residues in contact with ALA 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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221A ASP* 4.8 2.0 + - - +
222A GLN 2.9 1.2 + - - -
223A ASP* 1.3 75.3 - - - +
225A HIS* 1.3 68.0 + - - +
227A GLN* 3.3 7.5 + - - +
228A ASN* 3.2 27.4 + - - +
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Residues in contact with HIS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL 6.1 0.4 - - - -
207A TRP* 5.7 0.4 - - - -
208A ASP* 2.9 44.0 + - + +
209A ASN 3.2 18.7 + - - +
210A MET* 3.6 21.0 - - + +
211A ALA 5.6 0.4 - - - +
222A GLN* 2.7 34.4 + - + +
224A ALA* 1.3 77.1 - - - +
226A ARG* 1.3 57.7 + - - +
228A ASN* 3.5 16.1 + - - +
229A LEU* 3.9 11.9 + - + +
248A PHE* 4.1 10.8 - - + +
249A THR* 3.4 41.3 + - + -
299A TRP* 5.8 0.8 - + - -
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Residues in contact with ARG 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 GLN 3.7 7.2 - - - +
223A ASP* 3.5 24.6 + - - +
225A HIS* 1.3 75.3 - - - +
227A GLN* 1.3 60.6 + - - +
228A ASN 3.0 2.2 - - - -
229A LEU* 2.9 17.6 + - - +
230A VAL* 3.0 17.3 + - - +
249A THR* 3.3 24.0 - - + +
267A ASP* 3.1 31.5 + - - +
272A ALA 3.1 12.9 + - - -
273A PRO* 3.0 22.4 + - - +
274A GLY 3.0 22.0 + - - -
275A VAL* 4.0 11.0 - - + +
277A GLY 4.3 0.6 - - - -
278A TRP* 3.3 66.6 - - + +
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Residues in contact with GLN 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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223A ASP 2.9 20.8 + - - +
224A ALA* 3.3 7.8 + - - +
226A ARG* 1.3 76.9 - - - +
228A ASN* 1.3 58.1 + - - +
229A LEU 3.1 0.4 - - - -
230A VAL* 3.4 20.3 - - - +
231A ASN* 2.9 57.3 + - - +
278A TRP* 3.8 19.6 - - + -
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Residues in contact with ASN 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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183A ARG* 4.1 20.4 + - - +
208A ASP* 4.1 19.6 - - - +
224A ALA* 3.2 12.9 + - - +
225A HIS* 3.6 13.7 - - - +
226A ARG 3.0 0.8 - - - -
227A GLN* 1.3 82.5 + - - +
229A LEU* 1.3 63.2 + - - +
231A ASN* 4.1 10.7 - - - +
232A TRP* 3.7 17.3 + - - +
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Residues in contact with LEU 229 (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* 3.5 47.1 - - + +
208A ASP* 5.0 2.9 - - - +
225A HIS* 4.1 11.9 - - + +
226A ARG 2.9 8.4 + - - +
228A ASN* 1.3 80.9 - - + +
230A VAL* 1.3 65.0 + - - +
231A ASN 2.9 5.1 + - - -
232A TRP* 3.1 4.4 + - + +
233A VAL* 3.0 27.2 + - - +
245A VAL* 4.1 16.7 - - + +
246A PHE 3.7 21.8 - - - +
248A PHE* 4.1 14.1 - - + +
249A THR* 3.8 21.8 - - - +
275A VAL* 3.9 14.4 - - + -
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Residues in contact with VAL 230 (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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226A ARG 3.0 15.8 + - - +
227A GLN* 3.4 29.2 - - - +
229A LEU* 1.3 75.4 - - - +
231A ASN* 1.3 61.2 + - - +
233A VAL* 3.7 7.4 + - - -
234A ASP* 2.9 24.4 + - - +
275A VAL* 3.6 28.7 - - + -
278A TRP* 4.2 20.6 - - + -
279A TRP* 3.7 32.0 - - + -
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Residues in contact with ASN 231 (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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227A GLN* 2.9 48.7 + - - +
228A ASN* 4.3 13.1 - - - +
229A LEU 2.9 0.8 - - - -
230A VAL* 1.3 79.2 - - - +
232A TRP* 1.3 58.1 + - - +
233A VAL 3.0 1.6 - - - -
234A ASP* 2.7 30.1 + - - +
235A LYS* 2.8 24.7 + - + +
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Residues in contact with TRP 232 (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* 4.6 5.2 - - + -
182A ALA* 4.4 14.9 + - + -
183A ARG* 4.7 12.1 - - - +
185A TYR* 4.6 2.3 + + - -
187A PRO* 3.6 43.7 - - + +
190A ALA* 3.8 27.4 - - + -
194A ILE* 4.6 3.4 - - + -
202A ALA 5.5 0.4 - - - -
204A ALA* 3.4 25.8 - - + -
206A VAL* 3.9 27.2 - - + +
228A ASN 3.7 13.8 + - - +
229A LEU* 3.1 9.1 + - - +
231A ASN* 1.3 78.8 - - - +
233A VAL* 1.3 67.7 + - + +
235A LYS* 3.6 1.7 + - - -
236A VAL* 3.6 33.5 + - + +
243A GLY* 5.4 0.4 - - - -
244A MET 4.2 9.4 - - - -
245A VAL* 3.4 26.0 - - + -
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Residues in contact with VAL 233 (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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229A LEU 3.0 19.8 + - - +
230A VAL* 3.7 6.7 - - - +
231A ASN 3.0 0.2 - - - -
232A TRP* 1.3 80.4 - - + +
234A ASP* 1.3 68.6 + - - +
236A VAL* 2.9 23.7 - - + +
238A GLY* 3.2 12.1 + - - -
243A GLY 4.6 2.7 - - - +
244A MET* 4.5 3.4 - - - -
245A VAL* 3.5 38.6 - - + +
275A VAL* 6.5 0.4 - - + -
279A TRP* 3.6 27.8 - - + -
282A LYS* 4.1 22.4 - - + -
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Residues in contact with ASP 234 (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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230A VAL 2.9 17.6 + - - +
231A ASN* 2.7 24.4 + - - +
233A VAL* 1.3 78.5 - - - +
235A LYS* 1.3 61.9 + - + +
236A VAL 2.9 6.9 + - - -
237A GLY* 3.4 8.7 + - - -
238A GLY* 3.8 3.6 + - - +
279A TRP* 4.4 13.6 - - + -
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Residues in contact with LYS 235 (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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187A PRO* 3.5 34.1 - - + +
188A GLU* 3.6 28.3 + - - +
191A LYS* 4.2 9.7 - - - +
231A ASN* 2.8 24.0 + - + +
232A TRP* 4.0 1.1 - - - -
233A VAL 3.3 0.2 - - - -
234A ASP* 1.3 76.5 - - - +
236A VAL* 1.3 57.5 + - - +
237A GLY 3.6 0.9 - - - -
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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