Contacts of the helix formed by residues 221 - 242 (chain A) in PDB entry 4Y5U
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ILE* 6.0 0.7 - - + -
204A TRP* 3.5 43.5 - - + +
219A GLU 4.3 0.2 + - - -
220A SER* 1.3 73.4 + - - +
222A ALA* 1.3 57.8 + - - +
223A PRO 3.4 1.1 - - - -
224A LEU* 3.5 18.9 + - + +
225A GLN* 3.1 26.2 + - - +
274A LEU* 3.9 24.9 - - + -
276A GLU* 3.7 32.5 - - + +
294A ARG* 3.5 36.0 - - + +
296A LEU* 4.0 9.3 - - + +
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Residues in contact with ALA 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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220A SER* 3.4 10.5 + - - +
221A LEU* 1.3 75.5 - - - +
223A PRO* 1.3 73.2 - - + +
225A GLN* 3.4 9.0 + - - +
226A GLU* 3.1 28.6 + - + +
294A ARG* 3.9 11.0 - - - +
354A ASN* 6.1 2.9 - - - +
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Residues in contact with PRO 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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220A SER* 3.6 20.9 - - - +
222A ALA* 1.3 98.7 - - + +
224A LEU* 1.3 59.3 + - + +
226A GLU* 3.4 6.9 + - + +
227A ARG* 3.1 36.3 + - - +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 4.4 14.8 - - + -
200A ARG* 3.7 62.1 - - + +
201A ILE* 4.3 13.5 - - + +
204A TRP* 4.5 16.4 - - + -
220A SER 4.8 6.1 - - - +
221A LEU* 3.5 17.9 + - + +
223A PRO* 1.3 80.5 - - + +
225A GLN* 1.3 59.7 + - - +
227A ARG* 3.5 13.9 + - - +
228A CYS* 3.1 31.2 + - - -
296A LEU* 4.2 11.0 - - + -
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Residues in contact with GLN 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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221A LEU 3.1 13.2 + - - +
222A ALA* 3.6 12.3 + - - +
224A LEU* 1.3 74.0 - - - +
226A GLU* 1.3 61.8 + - + +
228A CYS* 3.2 6.8 + - - +
229A GLU* 3.0 41.8 + - - +
294A ARG* 2.8 25.1 + - - +
295A PHE 4.4 1.7 - - - +
296A LEU* 3.3 39.1 - - + +
299A LEU* 3.9 17.1 - - - +
354A ASN* 3.1 30.1 + - - +
355A CYS* 4.3 4.7 - - - -
356A CYS 4.9 0.2 + - - -
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Residues in contact with GLU 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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131A LYS* 6.6 0.2 - - - -
222A ALA 3.1 16.4 + - - +
223A PRO* 3.9 7.4 - - + +
224A LEU 3.4 0.2 - - - -
225A GLN* 1.3 74.4 + - + +
227A ARG* 1.3 66.6 + - + +
229A GLU* 3.4 21.0 - - - +
230A SER* 3.1 27.9 + - - -
354A ASN* 4.9 10.6 + - - -
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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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130A PHE* 3.3 44.3 - - - +
131A LYS* 4.9 21.2 - - - +
134A LEU* 5.7 3.8 - - + +
196A LEU* 4.8 5.7 + - - +
197A VAL* 4.3 25.1 - - + +
200A ARG* 3.3 39.4 - - - +
223A PRO* 3.1 24.8 + - - +
224A LEU* 3.5 14.7 - - + +
226A GLU* 1.3 78.7 - - + +
228A CYS* 1.3 59.8 + - - +
230A SER* 3.8 5.5 - - - -
231A LEU* 3.4 26.0 + - - +
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Residues in contact with CYS 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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197A VAL* 3.8 22.4 - - - -
201A ILE* 4.8 3.4 - - - -
224A LEU 3.1 18.3 + - - +
225A GLN* 3.2 9.6 + - - +
227A ARG* 1.3 74.6 - - - +
229A GLU* 1.3 64.0 + - - +
230A SER 3.3 0.2 - - - -
231A LEU* 3.4 6.4 + - - +
232A VAL* 3.3 27.0 + - - +
268A LEU* 4.0 15.1 - - + +
272A CYS* 3.8 22.2 - - - -
296A LEU* 4.4 7.9 - - + -
297A LEU* 3.7 18.8 - - + -
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Residues in contact with GLU 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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225A GLN* 3.0 37.7 + - + +
226A GLU* 3.4 36.9 - - - +
227A ARG 3.3 0.2 - - - -
228A CYS* 1.3 77.4 - - - +
230A SER* 1.3 61.1 + - - +
232A VAL* 3.7 2.4 + - - +
233A ASP* 3.3 8.3 + - - +
296A LEU 4.8 2.0 - - - +
297A LEU* 4.2 9.4 - - + -
299A LEU* 4.2 20.3 - - - +
300A ARG* 3.1 47.6 + - + +
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Residues in contact with SER 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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134A LEU* 4.2 29.4 - - - +
138A GLN* 5.0 4.8 + - - -
226A GLU 3.1 16.0 + - - -
227A ARG* 3.8 7.4 - - - -
229A GLU* 1.3 79.0 - - - +
231A LEU* 1.3 60.9 + - - +
233A ASP* 3.3 11.6 + - - +
234A ILE* 3.2 25.9 + - - +
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Residues in contact with LEU 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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134A LEU* 4.0 22.2 - - + -
137A LEU* 4.4 4.3 - - + -
190A LEU* 3.7 21.4 - - + +
193A ALA* 4.0 38.8 - - + +
194A LYS* 4.0 19.7 - - + +
197A VAL* 4.3 10.8 - - + -
227A ARG 3.4 18.3 + - - +
228A CYS 3.4 6.2 + - - +
229A GLU 3.3 0.4 - - - -
230A SER* 1.3 78.1 - - - +
232A VAL* 1.3 60.0 + - - +
233A ASP 3.1 0.4 - - - -
234A ILE* 3.6 5.6 + - + +
235A TYR* 3.2 23.2 + - - +
264A VAL* 5.5 2.2 - - + +
268A LEU* 4.5 18.2 - - + -
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Residues in contact with VAL 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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228A CYS 3.3 14.4 - - - +
229A GLU* 3.7 8.5 - - - +
231A LEU* 1.3 73.0 - - - +
233A ASP* 1.3 60.0 + - - +
235A TYR* 3.5 9.0 - - + +
236A SER* 3.0 29.8 + - - +
265A LEU* 4.4 13.7 - - + -
268A LEU* 4.0 9.0 - - + -
297A LEU* 3.7 29.2 - - + -
300A ARG* 3.4 28.7 - - - +
301A PHE* 3.9 21.3 - - + -
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Residues in contact with ASP 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 GLU* 3.3 8.8 + - - +
230A SER* 3.3 14.1 + - - +
231A LEU 3.1 0.4 - - - -
232A VAL* 1.3 78.9 - - - +
234A ILE* 1.3 64.1 + - + +
236A SER* 3.5 3.5 + - - -
237A GLN* 3.3 31.6 + - - +
300A ARG* 1.8 48.0 + - - +
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Residues in contact with ILE 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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134A LEU* 4.6 3.8 - - + -
137A LEU* 3.6 44.4 - - + +
138A GLN* 3.9 34.5 - - + +
141A VAL* 4.1 13.7 - - + -
190A LEU* 4.1 10.1 - - + -
230A SER 3.2 15.9 + - - +
231A LEU* 3.7 9.4 - - + +
233A ASP* 1.3 75.4 - - - +
235A TYR* 1.3 66.1 + - - +
237A GLN* 3.3 13.0 + - - +
238A LEU* 3.0 31.1 + - + +
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Residues in contact with TYR 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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190A LEU* 4.2 14.6 - - + -
231A LEU 3.2 12.6 + - - +
232A VAL* 3.3 14.6 + - + +
234A ILE* 1.3 78.7 - - - +
236A SER* 1.3 70.6 + - - +
238A LEU* 3.6 4.1 - - - +
239A GLN* 2.9 50.7 + - + +
261A LEU* 2.8 44.3 - - + +
262A ASP* 2.9 19.2 + - - -
264A VAL* 4.7 7.6 - - + -
265A LEU* 3.9 41.2 - - + +
301A PHE* 6.1 1.1 - + - -
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Residues in contact with SER 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 VAL* 3.0 17.5 + - - +
233A ASP* 3.7 7.4 - - - -
234A ILE 3.1 0.2 - - - -
235A TYR* 1.3 92.0 - - - +
237A GLN* 1.3 57.8 + - - +
239A GLN* 3.4 5.9 + - - +
240A GLN* 3.1 27.1 + - - +
300A ARG* 4.4 10.6 + - - -
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Residues in contact with GLN 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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138A GLN* 5.9 1.4 + - - +
141A VAL* 3.8 23.8 - - + +
233A ASP* 3.3 20.6 + - - +
234A ILE* 3.3 18.9 + - - +
236A SER* 1.3 73.8 - - - +
238A LEU* 1.3 67.8 + - - +
239A GLN 3.0 1.1 - - - -
240A GLN* 3.1 9.7 + - - +
241A GLU* 2.8 29.1 + - + +
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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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141A VAL* 3.3 40.8 - - + -
144A ILE* 5.7 4.5 - - + -
184A GLN* 6.1 0.7 - - + +
186A THR* 3.8 23.8 - - + +
187A THR* 3.9 24.2 - - + -
190A LEU* 4.1 23.6 - - + -
234A ILE* 3.0 19.8 + - + +
235A TYR 3.6 0.7 - - - +
237A GLN* 1.3 78.1 - - - +
239A GLN* 1.3 62.4 + - - +
241A GLU* 3.1 20.3 + - + +
242A VAL* 3.3 14.4 + - - +
261A LEU* 3.6 17.7 - - + -
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Residues in contact with GLN 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 TYR* 2.9 36.4 + - + +
236A SER* 3.6 8.5 - - - +
237A GLN 3.0 0.4 - - - -
238A LEU* 1.3 78.1 - - - +
240A GLN* 1.3 61.7 + - - +
242A VAL* 3.1 26.4 + - - +
243A GLY 3.8 2.4 + - - -
258A THR* 3.1 36.0 - - - +
261A LEU* 2.8 40.7 - - - +
262A ASP* 5.0 2.0 - - - +
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Residues in contact with GLN 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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148A ARG* 5.0 3.8 + - - +
236A SER 3.1 15.0 + - - +
237A GLN* 3.5 9.8 - - - +
239A GLN* 1.3 78.8 - - - +
241A GLU* 1.3 69.9 + - - +
243A GLY* 3.1 21.5 + - - -
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Residues in contact with GLU 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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141A VAL* 5.0 7.2 - - + +
144A ILE* 3.4 40.4 - - + +
145A HIS* 4.1 13.9 - - - +
148A ARG* 3.2 54.1 + - - +
237A GLN* 2.8 17.4 + - + +
238A LEU* 3.3 17.0 - - + +
239A GLN 2.9 0.4 - - - -
240A GLN* 1.3 83.1 - - - +
242A VAL* 1.3 60.5 + - + +
243A GLY 3.0 12.5 + - - +
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Residues in contact with VAL 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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184A GLN* 5.8 5.4 - - - +
238A LEU 3.5 14.6 - - - +
239A GLN* 3.1 20.4 + - - +
241A GLU* 1.3 77.9 - - + +
243A GLY* 1.3 55.5 + - - +
254A ARG* 3.5 63.8 + - + +
257A LEU* 5.2 19.5 - - + -
258A THR* 4.5 10.8 - - + +
261A LEU* 5.6 3.4 - - + -
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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