Contacts of the helix formed by residues 216 - 233 (chain C) in PDB entry 5Y3R
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 LYS 216 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ASP* 4.3 25.7 + - - +
171C LEU* 4.6 11.9 - - + -
207C GLN* 3.0 15.3 + - - +
215C PRO* 1.3 79.1 + - - +
217C LEU* 1.3 54.1 + - - +
218C PRO 3.3 1.1 - - - -
219C VAL* 2.6 51.2 + - + +
220C LEU 3.0 5.2 + - - -
257C ARG* 3.1 38.3 - - - +
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Residues in contact with LEU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C PRO* 3.9 15.0 + - + +
216C LYS* 1.3 66.3 - - - +
218C PRO* 1.3 68.5 - - + +
219C VAL 3.0 0.9 - - - -
220C LEU* 3.5 30.9 - - + +
221C ALA* 2.8 24.8 + - - +
248C ILE 6.1 0.4 - - - +
251C PHE* 5.6 6.1 - - + +
252C VAL* 5.4 10.8 - - + -
256C ILE* 3.9 36.6 - - + -
257C ARG* 4.3 5.6 - - + +
263C LYS* 4.0 3.3 - - - -
264C ARG* 3.3 50.3 - - - +
267C VAL* 4.1 11.4 - - + +
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Residues in contact with PRO 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ASP 4.7 13.2 - - - +
169C THR 5.6 3.4 - - - +
171C LEU* 5.1 6.5 - - + -
172C GLU* 5.4 9.0 - - - +
216C LYS* 3.5 1.6 - - + -
217C LEU* 1.3 91.9 - - + +
219C VAL* 1.3 61.8 + - + +
221C ALA* 3.2 3.7 + - + +
222C GLY* 3.0 23.9 + - - -
257C ARG* 3.1 28.0 - - - +
259C GLN* 3.2 16.2 - - - +
263C LYS* 3.0 28.0 - - - +
264C ARG* 3.7 0.2 - - - +
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 3.5 33.2 - - + -
174C VAL* 5.2 2.7 - - + -
175C TYR* 3.3 33.3 - - + -
204C LEU* 3.2 33.4 - - + +
207C GLN* 3.5 6.7 - - - +
216C LYS* 2.6 39.3 + - + +
218C PRO* 1.3 72.9 - - + +
220C LEU* 1.3 57.7 + - - +
222C GLY 3.5 0.9 + - - -
223C CYS 2.9 20.6 + - - -
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Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 3.6 33.7 - - + -
207C GLN* 4.0 3.8 - - - +
208C MET* 4.4 13.0 - - + -
215C PRO* 3.4 35.0 - - + -
216C LYS 3.0 7.9 + - - +
217C LEU* 3.5 20.6 - - + +
218C PRO 3.4 0.2 - - - -
219C VAL* 1.3 74.6 - - - +
221C ALA* 1.3 65.5 + - - +
222C GLY 3.1 0.2 - - - -
223C CYS* 2.9 2.1 + - + -
224C LEU* 2.9 30.2 + - - +
248C ILE* 3.6 45.3 - - + +
251C PHE* 6.1 1.8 - - + -
267C VAL* 4.6 3.6 - - + -
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Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU 2.8 19.7 + - - +
218C PRO* 3.3 9.2 - - + +
220C LEU* 1.3 74.2 - - - +
222C GLY* 1.3 50.9 + - - +
224C LEU* 4.6 1.2 - - - +
225C LYS* 2.4 41.9 + - + +
263C LYS* 4.4 9.6 - - + -
267C VAL* 3.9 27.9 - - + +
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Residues in contact with GLY 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLU* 5.4 4.5 - - - -
175C TYR* 3.4 28.2 - - - +
197C PHE* 4.8 0.3 - - - -
218C PRO 3.0 13.5 + - - -
219C VAL 3.8 1.3 - - - -
220C LEU 3.1 0.2 - - - -
221C ALA* 1.3 75.6 - - - +
223C CYS* 1.3 60.9 + - - +
225C LYS* 2.6 25.9 + - - -
226C GLY* 2.9 12.1 + - - -
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Residues in contact with CYS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 3.2 17.0 - - + -
197C PHE* 3.3 29.3 - - - -
200C PHE 3.8 8.5 - - - -
201C LEU* 3.6 17.5 - - - -
204C LEU* 3.3 36.3 - - + -
219C VAL 2.9 6.9 + - - +
220C LEU* 2.9 8.1 + - + +
222C GLY* 1.3 71.7 - - - +
224C LEU* 1.3 53.4 + - - +
227C LEU* 2.5 38.6 + - - +
248C ILE* 5.5 6.1 - - + -
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU 2.9 16.9 + - - +
221C ALA* 4.6 1.6 - - - +
223C CYS* 1.3 75.4 - - - +
225C LYS* 1.3 69.1 + - - +
227C LEU* 3.0 24.3 - - + +
228C SER* 2.8 22.9 + - - +
231C LEU* 5.2 6.3 - - + -
245C SER* 5.7 4.3 - - - -
248C ILE* 4.9 19.1 - - + +
249C PHE* 3.9 20.0 - - + -
267C VAL* 3.4 25.4 - - + +
271C GLY* 3.4 39.9 - - - +
275C PHE* 6.1 0.7 - - + -
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Residues in contact with LYS 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ARG* 4.1 33.5 - - - +
176C GLU 6.0 1.3 - - - +
221C ALA* 2.4 35.0 + - + +
222C GLY* 2.6 18.2 + - - +
224C LEU* 1.3 70.5 - - - +
226C GLY* 1.3 59.0 + - - +
228C SER* 2.3 33.1 + - - +
270C ALA* 6.1 6.1 - - + -
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Residues in contact with GLY 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR 5.3 4.3 + - - -
176C GLU 5.6 2.0 + - - -
178C LEU* 4.7 1.3 - - - -
179C GLY* 3.3 27.9 - - - -
180C LEU* 5.0 0.4 - - - -
197C PHE* 5.7 0.4 - - - -
222C GLY 2.9 7.8 + - - -
225C LYS* 1.3 76.2 - - - +
227C LEU* 1.3 54.3 + - - +
228C SER* 2.8 6.1 - - - -
229C SER* 2.7 25.6 + - - -
230C LEU* 3.0 20.0 + - - +
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C PHE* 4.4 2.8 - - + -
201C LEU* 4.2 29.2 - - + -
223C CYS* 2.5 23.1 + - - +
224C LEU* 3.0 32.3 - - + +
226C GLY* 1.3 75.8 - - - +
228C SER* 1.3 64.2 + - - +
230C LEU* 3.6 26.6 - - + +
231C LEU* 2.8 56.9 + - + +
244C THR* 5.1 9.6 - - + -
245C SER* 5.9 4.5 - - - +
248C ILE* 5.3 3.6 - - + -
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Residues in contact with SER 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 2.8 11.6 + - - +
225C LYS* 2.3 25.7 + - - +
226C GLY* 4.5 0.2 - - - -
227C LEU* 1.3 80.2 - - - +
229C SER* 1.3 64.3 + - - -
231C LEU* 3.1 7.3 + - - +
232C CYS* 2.9 27.2 + - - -
270C ALA* 5.5 4.0 + - - +
271C GLY* 6.0 1.0 - - - -
274C LEU* 4.0 34.5 - - - +
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Residues in contact with SER 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C GLY* 2.8 31.1 + - - -
182C GLY* 3.6 16.8 - - - -
183C GLU* 3.8 14.4 + - - +
226C GLY* 2.7 11.8 + - - -
228C SER* 1.3 78.0 - - - +
230C LEU* 1.3 65.3 + - - +
232C CYS* 3.0 15.9 + - - +
233C ASN* 3.0 23.5 + - - +
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C LEU* 3.2 31.6 - - + +
179C GLY* 3.9 1.8 - - - -
181C LEU* 5.4 1.6 - - + -
182C GLY* 5.7 1.3 - - - -
193C ALA* 5.3 1.8 - - + -
194C GLU* 2.7 43.2 - - + +
197C PHE* 3.3 47.3 - - + -
201C LEU* 5.1 2.9 - - + -
226C GLY 3.0 32.5 + - - +
227C LEU* 3.5 17.3 - - + +
229C SER* 1.3 76.4 - - - +
231C LEU* 1.3 54.6 + - - +
233C ASN* 2.6 23.6 + - - +
234C PHE* 3.1 8.7 + - - -
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 5.2 6.3 - - + -
227C LEU* 2.8 52.8 + - + +
228C SER* 3.4 6.1 - - - +
230C LEU* 1.3 70.6 - - - +
232C CYS* 1.3 57.5 + - - +
234C PHE* 2.7 39.2 + - + +
235C THR 4.5 0.7 + - - -
237C SER* 4.9 8.5 - - - +
241C ASP* 5.4 7.9 - - + +
245C SER* 6.2 3.4 - - - -
275C PHE* 3.5 33.2 - - + -
277C LEU* 3.3 39.0 - - + +
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Residues in contact with CYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C SER* 2.9 34.3 + - - -
229C SER* 3.0 16.4 - - - +
231C LEU* 1.3 75.1 - - - +
233C ASN* 1.3 63.7 + - - +
234C PHE 3.8 0.2 + - - -
235C THR 5.3 0.3 + - - -
274C LEU* 5.1 13.5 - - - -
277C LEU* 4.1 13.6 - - - +
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Residues in contact with ASN 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C GLY* 4.1 18.8 + - - +
190C ILE* 3.5 33.8 - - + +
194C GLU* 3.0 29.9 + - - +
229C SER* 3.2 12.5 + - - +
230C LEU 2.6 9.4 + - - -
232C CYS* 1.3 82.8 - - - +
234C PHE* 1.3 64.4 + - - +
235C THR* 3.5 5.4 + - - -
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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