Contacts of the helix formed by residues 221 - 241 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B TRP* 3.2 61.8 - - + +
219B GLU 4.1 0.4 + - - -
220B SER* 1.3 73.7 + - - +
222B ALA* 1.3 63.1 + - - +
223B PRO 3.3 1.5 - - - -
224B LEU* 3.5 20.3 + - + +
225B GLN* 3.3 20.1 + - - +
274B LEU* 4.7 15.5 - - + -
276B GLU* 3.7 27.6 + - + +
294B ARG* 3.5 26.3 - - + +
296B LEU* 4.0 15.7 - - + +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER* 3.0 10.9 + - - +
221B LEU* 1.3 77.1 - - - +
223B PRO* 1.3 73.7 - - + +
225B GLN* 3.4 10.9 + - - +
226B GLU* 3.2 24.3 + - - +
294B ARG* 4.0 8.3 - - - +
354B ASN* 6.1 3.6 - - - +
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Residues in contact with PRO 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 5.5 7.4 - - - +
219B GLU* 5.9 0.7 - - - +
220B SER* 3.6 20.0 - - - +
222B ALA* 1.3 98.3 - - + +
224B LEU* 1.3 60.6 + - - +
226B GLU* 3.4 16.1 + - + +
227B ARG* 3.4 38.8 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 4.4 13.0 - - + +
200B ARG* 3.7 68.4 - - + +
201B ILE* 3.9 23.6 - - + -
204B TRP* 4.1 11.9 - - + -
220B SER 5.6 0.7 - - - +
221B LEU* 3.5 23.1 + - + +
222B ALA 3.4 0.2 - - - -
223B PRO* 1.3 76.5 - - - +
225B GLN* 1.3 63.8 + - - +
227B ARG* 3.8 9.8 + - - +
228B CYS* 3.3 26.9 + - - -
274B LEU* 6.1 0.7 - - + -
296B LEU* 4.0 9.6 - - + -
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Residues in contact with GLN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU 3.3 12.3 + - - +
222B ALA* 3.6 11.2 - - - +
223B PRO 3.3 0.2 - - - -
224B LEU* 1.3 75.5 - - - +
226B GLU* 1.3 63.0 + - + +
228B CYS* 3.3 4.1 + - - +
229B GLU* 3.0 50.9 + - - +
294B ARG* 3.0 21.5 + - - -
295B PHE 4.6 0.9 - - - +
296B LEU* 3.3 38.6 + - + +
299B LEU* 4.1 10.5 - - - +
354B ASN* 3.2 33.1 + - - +
355B CYS* 4.5 3.1 - - - +
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 4.6 17.6 - - - -
222B ALA 3.2 13.6 + - - +
223B PRO* 3.6 8.9 - - + +
224B LEU 3.4 0.2 - - - -
225B GLN* 1.3 83.9 - - + +
227B ARG* 1.3 63.0 + - + +
229B GLU* 3.7 8.7 + - - +
230B SER* 3.2 25.6 + - - -
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 3.6 35.9 - - - -
131B LYS* 5.7 13.9 - - + +
134B LEU* 5.2 2.3 - - + +
197B VAL* 4.5 20.0 - - + -
200B ARG* 4.5 21.9 - - - +
223B PRO* 3.6 33.0 + - - +
224B LEU* 3.9 10.7 - - - +
226B GLU* 1.3 82.9 + - + +
228B CYS* 1.3 61.5 + - - +
230B SER* 3.3 8.4 - - - -
231B LEU* 3.2 28.3 + - - +
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Residues in contact with CYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 4.0 23.1 - - - +
201B ILE* 4.9 2.0 - - - -
224B LEU 3.3 21.1 + - - +
225B GLN* 3.4 7.0 - - - +
227B ARG* 1.3 76.2 - - - +
229B GLU* 1.3 64.7 + - - +
231B LEU* 3.5 8.9 + - - +
232B VAL* 3.3 25.5 + - - +
268B LEU* 4.0 11.6 - - - +
272B CYS* 3.7 26.9 - - - -
296B LEU* 4.0 11.0 - - + -
297B LEU* 3.7 14.1 - - + +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLN* 3.0 43.0 + - - +
226B GLU* 3.9 8.6 - - - +
228B CYS* 1.3 77.9 - - - +
230B SER* 1.3 60.1 + - - +
232B VAL* 3.4 4.5 + - - +
233B ASP* 3.2 25.8 + - - -
296B LEU 3.4 17.6 - - - +
297B LEU* 3.7 9.8 - - + -
299B LEU* 3.8 17.2 - - - +
300B ARG* 3.6 51.0 + - + +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 4.2 18.2 + - - -
134B LEU* 3.7 23.1 - - - +
138B GLN* 5.4 2.4 + - - -
226B GLU 3.2 13.3 + - - -
227B ARG* 3.3 13.9 - - - -
228B CYS 3.2 0.2 - - - -
229B GLU* 1.3 78.4 - - - +
231B LEU* 1.3 62.9 + - - +
233B ASP* 3.5 11.0 + - - +
234B ILE* 3.3 23.9 + - - +
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 4.0 21.3 - - + -
137B LEU* 4.4 12.6 - - + -
190B LEU* 3.8 11.7 - - + +
193B ALA* 3.7 46.2 - - + +
194B LYS* 4.0 13.0 - - + +
197B VAL* 4.5 13.9 - - + -
227B ARG 3.2 12.9 + - - +
228B CYS* 3.8 8.3 - - - +
229B GLU 3.3 0.4 - - - -
230B SER* 1.3 78.6 - - - +
232B VAL* 1.3 58.7 + - - +
233B ASP 3.2 0.2 - - - -
234B ILE* 3.3 6.9 + - - +
235B TYR* 3.0 25.3 + - - +
264B VAL* 5.9 1.2 - - + +
268B LEU* 4.3 16.8 - - + -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B CYS 3.3 14.8 + - - +
229B GLU 3.6 7.9 - - - +
230B SER 3.4 0.2 - - - -
231B LEU* 1.3 72.6 - - - +
233B ASP* 1.3 64.9 + - - +
235B TYR* 3.1 9.7 + - + +
236B SER* 2.8 36.4 + - - +
265B LEU* 4.3 17.3 - - + -
268B LEU* 4.3 6.7 - - + -
297B LEU* 3.6 29.2 - - + -
300B ARG* 4.7 12.6 - - + -
301B PHE* 3.9 23.1 - - + -
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLU 3.2 9.1 + - - +
230B SER* 3.6 13.6 - - - +
232B VAL* 1.3 82.5 - - - +
234B ILE* 1.3 57.4 + - + +
236B SER* 3.6 5.6 + - - +
237B GLN* 2.9 38.4 + - - +
300B ARG* 3.1 33.5 + - - -
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 4.6 4.7 - - + -
137B LEU* 3.7 49.8 - - + +
138B GLN* 3.9 26.7 - - + +
141B VAL* 4.2 9.0 - - + -
190B LEU* 3.7 19.3 - - + -
230B SER 3.3 15.3 + - - +
231B LEU* 3.5 9.6 - - - +
232B VAL 3.2 0.2 - - - -
233B ASP* 1.3 79.9 - - + +
235B TYR* 1.3 62.1 + - - +
237B GLN* 3.6 15.1 + - - +
238B LEU* 3.2 28.8 + - + +
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LEU* 4.5 11.4 - - + -
231B LEU 3.0 14.3 + - - +
232B VAL* 3.1 14.3 + - + +
234B ILE* 1.3 75.6 - - - +
236B SER* 1.3 72.1 + - - +
238B LEU* 3.3 5.8 + - - +
239B GLN* 2.8 42.3 + - + +
261B LEU* 3.1 50.7 - - + -
262B ASP* 3.3 20.9 + - - -
264B VAL* 4.8 8.1 - - + -
265B LEU* 3.7 41.5 - - + +
301B PHE* 6.0 0.9 - + - -
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B VAL* 2.8 25.7 + - - +
233B ASP* 3.9 9.4 - - - -
234B ILE 3.4 0.2 - - - -
235B TYR* 1.3 84.1 - - - +
237B GLN* 1.3 56.1 + - - +
239B GLN* 3.4 5.6 + - - +
240B GLN* 2.8 38.8 + - - +
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLN* 6.0 0.2 - - - -
141B VAL* 3.6 30.6 - - + +
233B ASP* 2.9 26.1 + - - +
234B ILE* 3.6 19.9 - - - +
236B SER* 1.3 76.7 - - - +
238B LEU* 1.3 60.9 + - - +
239B GLN 3.3 0.2 - - - -
240B GLN* 4.3 4.4 - - - +
241B GLU* 3.1 32.7 + - - +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 3.8 32.1 - - + -
144B ILE* 4.6 13.0 - - + -
184B GLN* 5.4 6.9 + - - +
186B THR* 4.3 17.3 - - + +
187B THR* 3.8 38.8 - - + +
190B LEU* 4.9 5.2 - - + -
234B ILE* 3.2 22.9 + - + +
235B TYR* 3.6 6.3 - - - +
237B GLN* 1.3 78.6 - - - +
239B GLN* 1.3 56.5 + - - +
241B GLU* 2.4 25.8 - - - +
242B VAL* 3.3 14.6 - - + +
261B LEU* 3.9 15.7 - - + +
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TYR* 2.8 31.4 + - + +
236B SER* 3.5 9.0 - - - +
238B LEU* 1.3 73.2 - - - +
240B GLN* 1.3 63.2 + - - +
241B GLU 2.3 18.9 - - - +
242B VAL* 3.7 12.6 - - - +
258B THR* 3.4 26.7 + - - +
261B LEU* 2.6 34.8 - - - +
262B ASP* 2.5 33.5 + - - -
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 2.8 24.3 + - - +
237B GLN* 4.3 4.9 - - - +
238B LEU 3.5 0.2 - - - -
239B GLN* 1.3 75.4 - - - +
241B GLU* 1.3 70.9 + - - +
242B VAL 3.5 9.5 - - - +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 6.3 1.6 - - - -
144B ILE* 3.3 31.4 - - + -
145B HIS* 3.4 24.4 + - - +
148B ARG* 3.0 49.8 + - + +
237B GLN 3.1 19.6 + - - +
238B LEU 2.4 16.6 - - - +
239B GLN 2.3 19.9 - - - +
240B GLN* 1.3 76.9 - - - +
242B VAL* 1.3 57.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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