Contacts of the helix formed by residues 219 - 233 (chain A) in PDB entry 2YWB
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A SER* 3.2 14.6 + - - -
218A GLY* 1.3 79.3 - - - +
220A VAL* 1.3 61.6 + - - -
221A ASP* 3.2 3.9 + - - -
222A SER* 3.5 3.6 + - - -
223A SER* 2.9 29.1 + - - -
378A ARG* 5.2 4.9 - - - -
380A PRO* 6.5 0.7 - - - -
381A PHE* 6.3 1.3 - - - -
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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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218A GLY 3.8 1.2 + - - -
219A GLY* 1.3 71.1 - - - -
221A ASP* 1.3 60.0 + - - +
223A SER* 4.2 4.9 - - - -
224A THR* 2.6 47.9 + - - +
359A LYS* 4.4 17.9 - - + +
362A VAL* 4.8 2.0 - - + -
363A ARG* 3.8 44.6 - - + +
366A ALA* 4.1 15.0 - - + -
371A LEU* 4.2 8.3 - - + -
375A LEU 4.2 12.3 + - - +
376A ARG* 3.9 14.6 - - - +
378A ARG* 5.4 3.9 - - + +
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Residues in contact with ASP 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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219A GLY* 3.2 2.4 - - - -
220A VAL* 1.3 87.0 - - + +
222A SER* 1.3 59.1 + - - +
224A THR* 3.1 2.6 + - - -
225A LEU* 2.9 24.4 + - - +
315A GLY* 2.7 44.3 - - - +
317A LEU* 3.3 24.2 - - - +
354A PHE* 3.5 11.8 - - - -
359A LYS* 4.9 11.4 - - + +
362A VAL* 4.1 10.8 - - + -
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Residues in contact with SER 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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214A LEU* 4.4 1.7 - - - +
215A ALA 3.6 22.9 - - - -
216A VAL* 3.6 8.0 - - - +
217A SER* 3.2 30.2 + - - -
218A GLY 3.9 1.2 + - - -
219A GLY 3.5 8.7 + - - -
221A ASP* 1.3 80.7 + - - +
223A SER* 1.3 64.7 + - - +
225A LEU* 3.6 11.5 - - - +
226A ALA* 3.1 23.2 + - - +
315A GLY* 5.7 2.5 - - - -
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.9 1.0 - - - +
218A GLY* 3.8 17.4 + - - -
219A GLY 2.9 19.5 + - - -
220A VAL* 3.8 7.9 - - - -
222A SER* 1.3 77.5 + - - +
224A THR* 1.3 63.5 + - - +
226A ALA* 3.3 4.8 + - - +
227A LEU* 3.1 30.0 + - - +
254A VAL* 5.0 1.4 - - - +
258A LEU* 4.0 28.9 - - - +
371A LEU* 4.3 16.0 - - - +
375A LEU* 5.4 5.1 - - - +
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Residues in contact with THR 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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220A VAL* 2.6 26.5 + - - +
221A ASP 3.6 3.1 - - - -
223A SER* 1.3 73.8 - - - +
225A LEU* 1.3 62.0 + - - +
227A LEU* 3.3 9.6 + - - +
228A LEU* 2.9 27.2 + - - +
354A PHE* 4.1 6.7 - - + -
362A VAL* 3.7 19.1 - - + +
365A LEU* 3.9 10.8 - - + -
366A ALA* 3.2 45.9 - - - +
369A LEU* 3.8 9.5 - - + +
371A LEU* 4.5 1.0 - - - +
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Residues in contact with LEU 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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214A LEU* 4.0 13.5 - - + -
221A ASP 2.9 13.8 + - - +
222A SER* 3.6 13.2 - - - +
223A SER 3.2 0.2 - - - -
224A THR* 1.3 77.6 - - - +
226A ALA* 1.3 62.6 + - - +
228A LEU* 3.1 15.7 + - + +
229A LEU* 3.1 23.4 + - + +
313A ALA* 4.0 9.6 - - + +
314A GLN* 3.3 46.0 - - - +
315A GLY* 3.5 7.4 - - - +
353A PRO* 3.9 28.7 - - + -
354A PHE* 3.8 18.1 - - + -
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.0 17.9 - - + +
216A VAL* 4.2 11.9 - - + -
222A SER 3.1 13.6 + - - +
223A SER* 3.5 10.1 - - - +
225A LEU* 1.3 77.8 - - - +
227A LEU* 1.3 57.3 + - + +
228A LEU 3.4 0.2 + - - -
229A LEU* 3.4 5.2 + - - +
230A ALA* 3.0 29.1 + - - +
236A HIS* 4.6 2.5 + - + -
238A ALA* 4.5 3.6 - - + -
258A LEU* 5.0 2.9 - - + -
263A VAL* 4.1 25.7 - - + +
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Residues in contact with LEU 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 SER 3.1 18.2 + - - +
224A THR* 3.7 12.1 - - - +
225A LEU 3.3 0.2 - - - -
226A ALA* 1.3 74.6 - - - +
228A LEU* 1.3 59.1 + - - +
230A ALA* 3.9 5.2 - - - +
231A LYS* 2.9 31.4 + - - +
258A LEU* 3.8 15.0 - - + -
261A LEU* 3.8 33.0 - - + +
263A VAL* 3.5 22.4 - - + -
366A ALA* 4.8 1.3 - - - +
369A LEU* 3.9 32.5 - - + +
371A LEU* 3.9 25.6 - - + -
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Residues in contact with LEU 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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196A LEU* 3.9 19.5 - - + -
199A LEU* 4.1 10.8 - - + -
200A LEU* 3.5 36.7 - - + +
203A VAL* 3.7 27.8 - - + -
224A THR 2.9 14.5 + - - +
225A LEU* 3.1 13.0 + - + +
227A LEU* 1.3 73.7 - - - +
229A LEU* 1.3 55.5 + - + +
231A LYS* 3.2 3.6 + - - +
232A ALA* 2.7 36.6 + - - +
353A PRO* 4.0 12.1 - - + -
354A PHE* 4.0 25.6 - - + -
365A LEU* 6.0 0.7 - - + -
369A LEU* 3.8 8.0 - - + +
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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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203A VAL* 3.4 30.5 - - + -
212A VAL* 4.0 16.2 - - + -
214A LEU* 3.9 33.9 - - + -
225A LEU* 3.1 22.8 + - + +
226A ALA* 3.7 4.9 - - - +
228A LEU* 1.3 75.5 - - + +
230A ALA* 1.3 63.8 + - - +
232A ALA* 3.1 3.8 + - - +
233A GLY 3.0 17.5 + - - -
234A VAL* 3.1 32.1 + - + +
236A HIS* 4.3 11.9 - - + -
313A ALA* 4.2 5.8 - - + -
351A LEU* 4.2 17.0 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.2 + - - +
227A LEU* 3.9 4.5 - - - +
229A LEU* 1.3 76.0 - - - +
231A LYS* 1.3 62.4 + - - +
233A GLY* 3.2 12.3 + - - -
234A VAL 5.0 0.7 - - - -
236A HIS* 3.8 17.1 - - + -
261A LEU 4.8 4.7 - - - +
262A GLY* 3.5 26.5 - - - +
263A VAL* 4.1 10.1 - - + -
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Residues in contact with LYS 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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200A LEU* 3.9 18.5 - - + +
204A ARG* 3.5 17.2 + - - +
227A LEU 2.9 20.3 + - - +
228A LEU 3.6 3.4 - - - +
230A ALA* 1.3 72.5 - - - +
232A ALA* 1.3 62.4 + - - +
233A GLY* 3.0 6.2 + - - -
369A LEU* 3.8 27.8 - - + +
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Residues in contact with ALA 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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200A LEU* 3.6 16.4 - - + +
203A VAL* 4.2 10.8 - - + -
204A ARG* 3.0 43.0 + - + +
228A LEU 2.7 18.1 + - - +
229A LEU 3.1 5.1 + - - +
231A LYS* 1.3 76.5 - - - +
233A GLY* 1.3 61.0 + - - +
234A VAL* 3.3 18.3 + - + +
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Residues in contact with GLY 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 3.2 + - - -
230A ALA* 3.2 9.8 + - - -
231A LYS 3.0 5.6 - - - -
232A ALA* 1.3 79.2 - - - +
234A VAL* 1.3 63.3 + - - +
235A ASP 3.8 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