Contacts of the helix formed by residues 228 - 240 (chain A) in PDB entry 1BWC
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 SER 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A LYS* 6.4 0.9 - - - -
226A PHE 3.4 4.6 + - - -
227A ASP* 1.3 78.5 + - - +
229A MET* 1.3 58.0 + - - +
231A SER* 3.7 7.9 - - - -
232A THR* 2.9 37.1 + - - -
385A ASP* 6.0 3.1 - - - -
420A LYS* 4.8 4.3 + - - -
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Residues in contact with MET 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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227A ASP* 3.1 13.8 + - - +
228A SER* 1.3 80.3 + - - +
230A ILE* 1.3 78.4 + - + +
232A THR* 3.9 3.6 - - - -
233A ASN* 2.9 33.2 + - + +
400A SER* 4.6 7.0 - - - -
401A THR 5.0 1.3 - - - +
418A VAL* 3.7 28.9 - - + +
419A MET 3.9 9.2 - - - +
420A LYS* 3.6 43.7 - - + +
434A HIS* 3.6 17.0 - - + +
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Residues in contact with ILE 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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223A LEU* 4.7 3.4 - - + -
226A PHE* 4.2 19.3 - - + -
227A ASP* 2.9 13.9 + - + +
229A MET* 1.3 94.2 - - + +
231A SER* 1.3 69.8 + - - +
233A ASN* 4.7 1.6 - - - -
234A CYS* 2.8 29.0 + - - +
377A ILE* 3.7 38.1 - - + -
378A GLY 5.5 0.2 - - - +
379A THR* 5.8 1.3 - - - -
418A VAL* 4.6 2.0 - - + -
434A HIS* 3.9 20.0 - - + +
435A MET 3.7 31.0 - - - +
436A GLN* 4.1 8.7 - - + +
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Residues in contact with SER 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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221A LYS* 3.4 20.4 - - - +
222A VAL 2.6 27.9 + - - +
223A LEU* 3.5 18.5 + - - -
224A ARG* 4.0 7.3 - - - +
226A PHE 4.5 2.0 - - - -
227A ASP 3.0 10.8 + - - -
228A SER* 3.7 13.9 - - - -
230A ILE* 1.3 79.7 - - - +
232A THR* 1.3 56.9 + - - +
234A CYS* 4.1 1.1 - - - +
235A THR* 2.7 31.4 + - - -
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Residues in contact with THR 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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221A LYS* 2.8 39.1 + - - +
228A SER* 2.9 20.4 + - - -
229A MET* 3.9 4.0 - - - -
231A SER* 1.3 75.5 - - - +
233A ASN* 1.3 63.0 + - - +
235A THR* 3.2 5.0 + - - -
236A GLU* 3.1 40.3 + - - +
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Residues in contact with ASN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A MET* 2.9 20.6 + - + +
230A ILE* 4.1 1.8 - - - +
232A THR* 1.3 79.3 - - - +
234A CYS* 1.3 57.3 + - - +
236A GLU* 3.4 11.7 + - - +
237A GLU* 2.9 37.9 + - - +
416A LYS* 3.5 37.9 + - - +
418A VAL* 3.7 28.9 - - + +
436A GLN* 3.1 31.2 + - - +
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Residues in contact with CYS 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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200A VAL* 4.0 21.8 - - - -
222A VAL* 4.0 17.9 - - + -
223A LEU* 4.0 4.7 - - + -
230A ILE 2.8 18.7 + - - +
231A SER 4.1 2.5 - - - +
233A ASN* 1.3 75.4 - - - +
235A THR* 1.3 65.5 + - - +
237A GLU* 3.9 1.1 - - - +
238A LEU* 3.0 27.8 + - - +
373A SER* 4.4 2.9 - - - -
377A ILE* 3.9 23.8 - - + -
436A GLN* 3.5 23.8 + - - +
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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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220A ASP 3.9 20.0 - - - +
221A LYS* 3.4 11.8 - - + +
222A VAL* 3.1 27.6 + - + +
231A SER 2.7 22.3 + - - -
232A THR 3.2 5.4 + - - -
234A CYS* 1.3 77.2 - - - +
236A GLU* 1.3 60.5 + - + +
238A LEU* 3.6 5.6 + - - +
239A GLU* 3.0 32.8 + - - +
245A VAL* 4.5 14.7 - - + +
247A LYS* 4.1 16.6 - - - +
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Residues in contact with GLU 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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232A THR* 3.1 33.5 + - + +
233A ASN* 3.6 16.3 - - - +
235A THR* 1.3 75.7 - - + +
237A GLU* 1.3 60.3 + - + +
239A GLU* 3.3 14.0 + - - +
240A ASN* 2.9 37.7 + - - +
416A LYS* 4.8 11.6 + - - +
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Residues in contact with GLU 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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233A ASN* 2.9 36.5 + - - +
234A CYS* 3.3 5.8 + - - +
236A GLU* 1.3 75.0 - - + +
238A LEU* 1.3 58.9 + - - +
240A ASN* 3.7 22.5 + - - +
241A ALA* 3.0 30.5 + - - +
374A HIS 4.1 16.6 - - - +
375A PRO* 3.7 15.4 - - + +
414A LYS 4.4 2.6 - - - +
415A THR* 3.3 21.7 - - - +
416A LYS* 3.2 37.1 + - + +
436A GLN* 4.6 3.1 - - - +
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Residues in contact with LEU 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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200A VAL* 4.4 27.1 - - + +
203A ALA* 4.7 4.0 - - + -
204A GLY* 4.9 6.1 - - - +
215A LEU* 3.8 24.7 - - + -
222A VAL* 4.1 20.6 - - + -
234A CYS* 3.0 25.4 + - - +
235A THR* 3.7 7.0 - - - +
236A GLU 3.2 0.2 - - - -
237A GLU* 1.3 75.4 - - - +
239A GLU* 1.3 61.7 + - - +
241A ALA* 3.3 5.5 + - + -
242A GLY 3.2 4.5 + - - -
243A VAL* 2.9 52.9 + - + +
245A VAL* 4.3 10.5 - - + -
373A SER* 6.0 2.5 - - - -
374A HIS 6.2 0.7 - - - +
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Residues in contact with GLU 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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235A THR* 3.0 20.6 - - - +
236A GLU* 3.3 13.6 + - - +
238A LEU* 1.3 76.1 - - - +
240A ASN* 1.3 59.8 + - - +
242A GLY* 3.0 19.2 + - - -
243A VAL 3.5 10.9 + - - +
245A VAL* 4.2 20.2 + - + +
247A LYS* 3.1 33.5 + - - -
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Residues in contact with ASN 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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236A GLU* 2.9 27.3 + - - +
237A GLU* 3.7 24.0 + - - +
238A LEU 3.3 0.4 - - - -
239A GLU* 1.3 78.2 - - - +
241A ALA* 1.3 60.8 + - - +
242A GLY* 3.1 1.4 + - - -
414A LYS 5.7 4.4 + - - +
416A LYS* 6.1 2.8 - - - +
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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