Contacts of the helix formed by residues 234 - 242 (chain A) in PDB entry 2BS3
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 GLY 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A THR* 5.7 3.7 + - - -
217A GLY 5.6 1.1 - - - -
218A GLY 3.6 8.8 + - - -
219A TYR* 3.8 15.7 - - - -
232A CYS 3.5 3.0 - - - -
233A GLU* 1.3 78.4 - - - +
235A THR* 1.3 60.4 + - - +
236A GLY 3.2 3.6 - - - -
237A THR* 3.1 19.8 + - - -
238A ALA* 3.0 22.1 + - - +
526A MET* 6.1 0.4 - - - -
529A VAL* 3.6 9.4 - - - +
1656A FAD 6.0 0.2 + - - -
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Residues in contact with THR 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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36A LEU* 5.2 2.8 - - - +
180A GLU* 4.2 7.4 + - - +
181A ALA 5.2 1.6 - - - -
231A VAL 5.8 0.2 + - - -
233A GLU* 4.6 15.8 - - + +
234A GLY* 1.3 75.3 - - - +
236A GLY* 1.3 60.9 + - - +
238A ALA* 3.2 7.5 + - - +
239A ILE* 2.9 34.0 + - - +
522A ARG* 4.0 34.1 - - + +
525A MET* 4.1 20.4 - - + -
526A MET* 5.1 0.2 - - + -
1656A FAD 2.9 37.3 + - - -
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Residues in contact with GLY 236 (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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214A ILE* 3.8 13.4 - - - +
216A THR* 3.2 37.1 + - - -
234A GLY 3.2 0.8 - - - -
235A THR* 1.3 81.4 + - - +
237A THR* 1.3 62.0 + - - +
239A ILE* 3.2 27.2 - - - +
240A ALA* 3.4 4.5 + - - +
375A ILE* 4.0 0.7 - - - +
1656A FAD 4.2 3.0 + - - -
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Residues in contact with THR 237 (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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216A THR* 4.1 3.0 + - - -
217A GLY 4.8 8.0 + - - -
219A TYR* 4.4 9.3 - - + -
234A GLY* 3.1 20.9 + - - -
236A GLY* 1.3 76.3 - - - +
238A ALA* 1.3 57.9 + - - +
240A ALA* 3.2 5.7 + - - +
241A LEU* 3.0 25.7 + - - +
248A LEU* 3.6 34.5 - - + +
251A MET* 3.9 20.9 - - + -
374A GLY* 4.9 6.2 - - - -
375A ILE* 4.4 11.9 - - + -
394A ALA* 5.0 6.3 + - - +
529A VAL* 4.2 5.6 - - + -
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Residues in contact with ALA 238 (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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234A GLY 3.0 11.5 + - - +
235A THR 3.2 8.3 + - - +
237A THR* 1.3 74.4 - - - +
239A ILE* 1.3 61.2 + - - +
241A LEU* 3.1 10.5 + - + +
242A GLU* 2.7 38.8 + - + +
525A MET* 3.6 46.7 - - + +
528A LYS* 5.7 0.9 - - + -
529A VAL* 4.0 6.2 - - + +
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Residues in contact with ILE 239 (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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11A ILE* 4.5 3.8 - - + -
181A ALA* 3.9 35.7 - - + +
182A ILE* 3.5 30.1 - - - +
183A ALA* 4.2 11.7 - - - +
184A LEU* 3.8 28.8 + - + +
214A ILE* 4.1 9.2 - - + -
235A THR 2.9 20.8 + - - +
236A GLY* 3.2 24.5 - - - +
238A ALA* 1.3 73.3 - - - +
240A ALA* 1.3 61.2 + - - +
242A GLU* 3.5 14.0 + - - +
243A THR* 3.3 19.1 + - - +
525A MET* 4.3 10.3 - - - -
1656A FAD 5.3 0.2 - - - +
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Residues in contact with ALA 240 (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 LEU* 3.8 11.2 - - - -
214A ILE* 4.3 6.7 - - + -
236A GLY 3.4 1.8 + - - +
237A THR 3.2 8.9 + - - +
238A ALA 3.2 0.2 - - - -
239A ILE* 1.3 81.4 - - - +
241A LEU* 1.3 60.7 + - - +
243A THR* 2.7 27.9 + - - -
246A ALA* 3.5 22.2 - - + +
248A LEU* 4.8 1.8 - - + -
375A ILE* 3.7 32.8 - - + -
388A LEU* 4.4 4.7 - - + -
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Residues in contact with LEU 241 (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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237A THR 3.0 14.1 + - - +
238A ALA* 3.4 13.5 - - + +
240A ALA* 1.3 78.6 - - - +
242A GLU* 1.3 57.5 + - + +
244A GLY* 3.1 20.4 + - - -
246A ALA 4.5 7.5 - - - +
248A LEU* 4.0 27.1 - - + +
528A LYS* 4.1 21.8 - - + +
529A VAL* 4.7 1.8 - - + +
532A CYS* 3.8 26.9 - - - -
566A ALA 4.3 0.9 - - - +
567A SER* 3.9 33.2 - - - -
568A TRP* 3.9 27.6 + - + +
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Residues in contact with GLU 242 (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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182A ILE 4.7 9.7 - - - +
183A ALA* 6.0 0.2 - - - -
186A HIS* 5.1 0.7 + - - -
238A ALA* 2.7 25.1 + - + +
239A ILE* 4.1 8.8 - - - +
240A ALA 3.3 0.6 - - - -
241A LEU* 1.3 70.6 - - + +
243A THR* 1.3 61.9 + - - +
244A GLY* 3.1 2.2 + - - -
524A PRO 5.8 0.2 - - - -
525A MET* 4.2 23.7 - - - +
528A LYS* 3.0 45.0 + - + +
568A TRP* 5.3 5.1 - - - +
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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