Contacts of the helix formed by residues 203 - 222 (chain C) in PDB entry 5LSW
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 TYR 203 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C THR* 1.3 75.5 - - - +
204C GLU* 1.3 78.5 + - - +
206C PHE* 4.2 26.5 - + - -
207C SER* 2.7 43.1 + - - -
244C ARG* 3.7 16.5 - - - +
248C ALA* 4.8 10.7 - - + +
303C SO4 3.4 21.8 + - - +
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C THR* 3.2 19.7 - - + +
203C TYR* 1.3 101.6 + - + +
205C ARG* 1.3 65.1 + - - +
207C SER* 3.7 6.9 - - - -
208C HIS* 3.0 24.6 + - - +
303C SO4 4.7 6.4 + - - -
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Residues in contact with ARG 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ILE* 5.8 5.8 - - + -
198C TYR* 2.7 88.7 + - - -
199C ILE* 3.6 15.3 - - + +
201C GLN* 3.9 14.3 + - - +
202C THR* 3.3 29.3 + - - +
204C GLU* 1.3 80.2 - - - +
206C PHE* 1.3 62.5 + - - +
208C HIS* 3.4 6.0 + - - +
209C VAL* 3.3 23.5 + - + +
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Residues in contact with PHE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ILE* 3.2 16.9 + - + +
200C CYS* 4.5 8.5 - - + +
202C THR 3.0 16.7 + - - +
203C TYR* 3.8 22.7 - + - +
205C ARG* 1.3 75.5 - - - +
207C SER* 1.3 69.0 + - - +
209C VAL* 3.1 4.0 + - + +
210C ALA* 2.9 41.2 + - + +
239C LEU* 4.2 26.7 - - + -
244C ARG* 5.4 3.8 - - - +
245C ALA* 3.4 38.8 - - + -
248C ALA* 3.6 31.9 - - + -
249C LEU* 4.2 9.9 - - + -
252C CYS* 5.0 2.7 - - - -
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Residues in contact with SER 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR* 2.7 43.7 + - - -
204C GLU* 3.7 8.7 - - - -
205C ARG 3.3 0.4 - - - -
206C PHE* 1.3 79.1 - - - +
208C HIS* 1.3 57.6 + - - +
210C ALA* 4.0 3.5 - - - +
211C MET* 2.9 51.3 + - - +
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Residues in contact with HIS 208 (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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165C PRO* 5.3 10.5 - - + +
168C LEU* 3.6 23.8 - - + +
204C GLU 3.0 16.9 + - - +
205C ARG* 3.7 7.2 - - - +
206C PHE 3.2 0.4 - - - -
207C SER* 1.3 77.8 - - - +
209C VAL* 1.3 61.7 + - - +
211C MET* 3.8 17.1 - - + +
212C ILE* 3.2 44.1 + - + +
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ILE* 4.9 5.4 - - + -
168C LEU* 4.2 24.6 - - + +
186C LEU* 4.1 19.1 - - + -
190C LEU* 5.0 2.9 - - + -
199C ILE* 3.6 31.0 - - + -
205C ARG* 3.3 14.3 + - + +
206C PHE* 3.1 7.5 + - + +
208C HIS* 1.3 77.8 - - - +
210C ALA* 1.3 57.9 + - - +
212C ILE* 3.2 3.5 + - - +
213C LEU* 2.8 48.4 + - + +
239C LEU* 4.2 13.2 - - + -
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Residues in contact with ALA 210 (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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206C PHE* 2.9 42.0 + - + +
207C SER* 4.0 3.8 - - - +
209C VAL* 1.3 77.2 - - - +
211C MET* 1.3 56.2 + - + +
213C LEU* 3.7 8.3 - - - +
214C GLY* 2.7 33.6 + - - -
236C TYR* 4.0 4.3 + - + -
239C LEU* 5.5 1.1 - - + -
249C LEU* 4.8 5.4 - - + -
252C CYS* 4.6 15.7 - - - -
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Residues in contact with MET 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C SER* 2.9 37.6 + - - +
208C HIS* 3.8 21.3 - - + +
210C ALA* 1.3 77.0 - - + +
212C ILE* 1.3 65.8 + - + +
214C GLY* 3.2 2.2 + - - -
215C LYS* 3.0 32.2 + - + +
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Residues in contact with ILE 212 (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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168C LEU* 3.5 51.1 - - + +
169C ARG* 5.5 0.2 - - - -
171C MET* 4.2 3.4 - - + -
172C GLU* 4.3 30.5 - - + +
208C HIS* 3.2 45.0 + - + +
209C VAL 3.8 2.0 - - - +
211C MET* 1.3 75.4 - - + +
213C LEU* 1.3 65.0 + - - +
215C LYS* 3.3 9.0 + - + +
216C MET* 3.1 42.6 + - + +
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Residues in contact with LEU 213 (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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171C MET* 3.8 14.8 - - + -
186C LEU* 4.9 0.2 - - + -
209C VAL* 2.8 39.5 + - + +
210C ALA* 3.7 3.6 - - - +
212C ILE* 1.3 76.2 - - - +
214C GLY* 1.3 61.8 + - - +
216C MET* 3.2 31.8 + - + +
217C VAL* 3.2 14.6 + - - +
232C VAL* 4.2 21.1 - - + +
235C CYS* 4.1 25.6 - - + -
236C TYR* 3.1 30.5 + - + +
239C LEU* 3.8 20.2 - - + -
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Residues in contact with GLY 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ALA 2.7 19.8 + - - -
211C MET* 3.2 2.4 + - - -
213C LEU* 1.3 73.0 - - - +
215C LYS* 1.3 60.1 + - - +
217C VAL* 3.3 15.5 + - - +
218C LEU* 3.3 17.4 + - - +
236C TYR* 3.0 12.0 + - - -
252C CYS 5.6 2.2 - - - -
254C PRO* 4.6 11.2 - - - +
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLU* 4.1 28.8 + - + +
211C MET* 3.0 22.6 + - - +
212C ILE* 3.8 7.0 - - + +
213C LEU 3.3 0.2 - - - -
214C GLY* 1.3 73.3 - - - +
216C MET* 1.3 66.1 + - - +
218C LEU* 3.1 21.3 + - + +
219C GLN* 3.1 24.5 + - - +
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Residues in contact with MET 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C MET* 3.4 61.2 - - + +
172C GLU* 5.3 1.6 - - - -
179C LYS* 5.1 0.9 - - + -
183C THR* 4.0 10.1 - - - -
212C ILE* 3.1 37.5 + - + +
213C LEU* 3.2 22.4 + - + +
215C LYS* 1.3 77.1 - - - +
217C VAL* 1.3 58.1 + - - +
219C GLN* 3.3 14.3 + - - +
220C LEU* 2.8 35.2 + - + +
228C LEU* 4.8 14.3 - - + +
232C VAL* 4.1 20.0 - - + -
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Residues in contact with VAL 217 (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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213C LEU 3.2 14.9 + - - +
214C GLY 3.5 7.6 - - - +
215C LYS 3.2 0.6 - - - -
216C MET* 1.3 76.9 - - - +
218C LEU* 1.3 61.3 + - - +
220C LEU* 3.1 11.0 + - + +
221C SER* 3.0 24.4 + - - -
229C LEU* 5.6 0.4 - - + -
232C VAL* 4.0 10.8 - - + -
236C TYR* 4.0 15.9 - - + -
254C PRO* 3.6 35.4 - - + -
256C GLN* 3.9 20.9 - - + +
257C LEU* 4.0 13.9 - - + -
262C PHE* 4.0 10.4 - - + -
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Residues in contact with LEU 218 (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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214C GLY 3.3 11.9 + - - +
215C LYS* 3.1 24.8 + - + +
217C VAL* 1.3 78.6 - - - +
219C GLN* 1.3 62.4 + - + +
221C SER* 3.2 21.1 + - - -
222C LYS* 3.4 21.1 + - - +
254C PRO* 5.3 3.8 - - + -
256C GLN* 3.4 29.6 - - - +
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Residues in contact with GLN 219 (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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172C GLU 4.2 10.5 + - - +
179C LYS* 2.4 35.0 + - - +
215C LYS 3.1 12.9 + - - +
216C MET* 3.6 17.2 - - - +
218C LEU* 1.3 76.7 - - + +
220C LEU* 1.3 52.0 + - + +
222C LYS* 2.8 11.7 + - + +
223C GLU* 2.7 57.5 + - - +
228C LEU* 6.1 0.5 - - - +
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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
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216C MET* 2.8 27.9 + - + +
217C VAL* 3.1 9.6 + - - +
219C GLN* 1.3 75.6 - - + +
221C SER* 1.3 61.0 + - - +
222C LYS 3.4 0.3 + - - -
223C GLU 3.6 29.7 - - - +
224C PRO* 3.7 8.2 - - + +
225C SER* 3.8 30.1 - - - +
228C LEU* 4.0 19.5 - - + -
229C LEU* 3.9 31.6 - - + +
232C VAL* 4.1 16.6 - - + -
262C PHE* 3.4 23.4 - - + -
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Residues in contact with SER 221 (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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217C VAL 3.0 14.5 + - - -
218C LEU* 3.3 11.9 + - - -
219C GLN 3.1 0.4 - - - -
220C LEU* 1.3 75.7 - - - +
222C LYS* 1.3 61.8 + - - +
224C PRO* 5.0 5.2 - - - +
256C GLN* 3.2 34.0 + - - +
261C THR* 4.6 10.3 - - - +
262C PHE* 3.9 7.1 - - - -
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Residues in contact with LYS 222 (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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218C LEU* 3.4 26.0 + - - +
219C GLN* 2.8 8.2 + - + +
221C SER* 1.3 83.9 - - - +
223C GLU* 1.3 77.2 + - - +
224C PRO* 3.2 11.3 - - - +
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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
------------------------------------------------------------
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