Contacts of the helix formed by residues 213 - 233 (chain L) in PDB entry 6PSS
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 ASP 213 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L SER* 6.0 2.9 - - - -
164L GLY* 5.8 1.6 - - - -
212L ILE* 1.4 113.8 + - + +
214L PRO* 1.3 71.7 - - + +
215L GLU* 4.1 10.5 - - + +
216L LEU* 4.2 18.6 - - + +
217L ALA* 3.3 19.2 + - - +
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Residues in contact with PRO 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L SER* 6.3 3.8 - - - -
212L ILE 4.7 2.7 - - - +
213L ASP* 1.3 84.6 - - + +
215L GLU* 1.3 73.3 + - + +
216L LEU 3.4 0.2 - - - -
217L ALA* 3.5 7.9 - - + -
218L ARG* 2.6 50.5 + - + +
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Residues in contact with GLU 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L ASP* 3.2 6.0 - - + -
214L PRO* 1.3 101.9 - - + +
216L LEU* 1.3 57.0 + - - +
218L ARG* 3.3 15.5 + - - +
219L GLU* 2.9 23.7 + - - +
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Residues in contact with LEU 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L PHE* 4.2 1.1 - - - -
167L ASP* 3.3 39.9 - - + +
212L ILE* 5.1 10.8 - - + -
213L ASP* 3.7 23.3 + - + +
214L PRO 3.4 0.2 - - - -
215L GLU* 1.3 75.3 - - - +
217L ALA* 1.3 60.4 + - - +
218L ARG 3.2 0.4 - - - -
219L GLU* 3.5 23.9 - - + +
220L LYS* 3.1 31.3 + - + +
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Residues in contact with ALA 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L LEU* 6.0 2.2 - - + -
159L SER* 6.3 3.8 - - - -
162L ILE* 5.7 3.4 - - + -
164L GLY* 5.2 9.4 - - - -
165L PHE* 3.5 24.6 - - + -
213L ASP 3.3 15.3 + - - +
214L PRO* 3.2 12.5 + - + +
216L LEU* 1.3 77.3 - - - +
218L ARG* 1.3 86.3 + - - +
220L LYS 4.2 0.2 - - - -
221L PHE* 3.4 16.1 + - - +
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Residues in contact with ARG 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L TYR* 3.3 17.1 + - - +
152L GLU* 3.1 28.5 + - - -
154L GLU* 5.8 1.4 + - - -
158L LEU* 3.3 26.9 - - - +
214L PRO* 2.6 53.0 + - + +
215L GLU* 3.3 18.6 + - - +
216L LEU 3.2 0.2 - - - -
217L ALA* 1.3 104.8 + - - +
219L GLU* 1.3 58.5 + - - +
221L PHE* 3.2 23.0 - - - +
222L ALA* 2.9 31.0 + - - +
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Residues in contact with GLU 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L GLU 2.9 13.7 + - - +
216L LEU* 3.2 24.8 + - + +
218L ARG* 1.3 78.6 - - - +
220L LYS* 1.3 72.5 + - - +
222L ALA* 3.5 5.6 + - - +
223L GLU* 3.0 29.2 + - - +
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Residues in contact with LYS 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L PHE* 3.6 31.4 - - + -
167L ASP* 2.6 38.9 + - - +
216L LEU* 3.1 17.0 + - + +
219L GLU* 1.3 84.9 - - - +
221L PHE* 1.3 59.7 + - - +
223L GLU* 3.3 29.3 - - - +
224L LEU* 3.3 11.8 + - - +
258L GLN* 3.8 29.1 + - - +
259L PHE* 3.2 35.2 - - + -
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Residues in contact with PHE 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L LEU* 3.7 27.8 - - + -
148L TYR* 3.5 55.2 - + + -
158L LEU* 4.7 5.8 - - + -
161L LEU* 6.4 0.4 - - + -
162L ILE* 3.6 17.3 - - + -
165L PHE* 3.5 25.1 - + - -
217L ALA 3.4 14.1 + - - +
218L ARG* 3.2 25.9 + - - +
219L GLU 3.2 0.4 - - - -
220L LYS* 1.3 77.8 - - - +
222L ALA* 1.3 62.3 + - - +
223L GLU 3.1 0.7 - - - -
224L LEU* 3.1 45.3 + - + +
225L ARG* 3.3 20.1 + - - +
259L PHE* 5.2 1.3 - + - -
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Residues in contact with ALA 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L TYR* 4.6 5.6 + - - +
218L ARG 2.9 18.9 + - - +
219L GLU* 3.8 6.1 - - - +
221L PHE* 1.3 75.2 - - - +
223L GLU* 1.3 61.6 + - - +
224L LEU 3.6 0.2 + - - -
225L ARG* 4.5 4.3 - - - +
226L ALA* 3.6 21.1 + - - +
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Residues in contact with GLU 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219L GLU* 3.0 19.0 + - - +
220L LYS* 3.3 45.3 - - - +
222L ALA* 1.3 77.3 - - - +
224L LEU* 1.3 61.3 + - - +
226L ALA* 4.1 2.8 - - - +
227L GLN* 3.2 23.0 + - + +
255L VAL* 3.3 43.0 - - + +
259L PHE* 3.6 5.5 - - - -
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Residues in contact with LEU 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L ILE* 3.7 26.0 - - + -
144L LEU* 3.7 19.5 - - + -
145L LEU* 3.7 30.5 - - + +
220L LYS 3.3 10.0 + - - +
221L PHE* 3.1 41.1 + - + +
223L GLU* 1.3 80.6 - - - +
225L ARG* 1.3 55.9 + - + +
227L GLN* 3.1 6.8 + - + +
228L TYR* 2.7 37.9 + - + +
252L LEU* 5.7 2.0 - - + -
255L VAL* 5.5 6.5 - - + -
259L PHE* 4.1 14.6 - - + -
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Residues in contact with ARG 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145L LEU* 2.4 49.6 + - + +
146L GLU* 5.1 1.0 + - - -
148L TYR* 3.3 25.4 - - + -
149L ASP* 1.7 55.0 + - - -
221L PHE 3.3 14.8 + - - +
222L ALA* 3.9 4.7 + - - +
223L GLU 3.5 0.2 - - - -
224L LEU* 1.3 79.6 - - + +
226L ALA* 1.3 60.3 + - - +
228L TYR* 3.8 7.0 - - - +
229L VAL* 3.3 31.0 + - + +
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Residues in contact with ALA 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L ALA 3.6 17.7 + - - +
223L GLU* 4.1 3.6 - - - +
224L LEU 3.2 0.4 - - - -
225L ARG* 1.3 76.4 - - - +
227L GLN* 1.3 64.0 + - - +
228L TYR 3.2 0.2 - - - -
229L VAL* 3.3 8.1 - - - +
230L VAL* 3.3 31.5 + - + +
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Residues in contact with GLN 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L GLU* 3.2 18.8 + - + +
224L LEU* 3.1 6.4 + - + +
226L ALA* 1.3 77.3 - - - +
228L TYR* 1.3 59.8 + - - +
230L VAL* 3.3 20.8 - - - +
231L THR* 3.4 22.9 + - - -
248L GLU 3.9 1.4 + - - -
251L LYS* 3.8 24.7 + - - +
252L LEU* 3.7 23.4 - - + +
255L VAL* 3.8 36.8 - - + +
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Residues in contact with TYR 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L PRO* 5.1 6.4 - - + +
141L ILE* 4.0 25.4 - - + -
142L THR* 3.3 26.0 - - + +
145L LEU* 3.6 31.4 - - + -
224L LEU* 2.7 21.4 + - + +
225L ARG* 4.0 9.0 - - - +
226L ALA 3.2 0.2 - - - -
227L GLN* 1.3 76.7 - - - +
229L VAL* 1.3 60.6 + - + +
231L THR* 3.5 1.0 + - - -
232L ARG* 3.0 79.7 + - + +
252L LEU* 3.6 23.8 - - + -
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Residues in contact with VAL 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L ARG* 3.3 20.4 + - + +
226L ALA* 3.3 14.8 - - - +
228L TYR* 1.3 78.5 - - + +
230L VAL* 1.3 64.0 + - + +
231L THR 3.2 5.6 + - - -
232L ARG* 3.4 25.1 - - - +
233L ASP* 3.2 37.4 - - - +
234L THR* 4.6 1.4 + - - +
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Residues in contact with VAL 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L ALA* 3.3 16.8 + - + +
227L GLN* 3.3 33.9 - - - +
229L VAL* 1.3 81.9 - - + +
231L THR* 1.3 56.3 + - - +
234L THR* 3.0 21.3 + - - +
248L GLU* 3.3 15.4 - - - +
251L LYS* 5.1 5.4 - - - +
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Residues in contact with THR 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L GLN* 3.4 23.0 + - - -
228L TYR 3.5 0.4 + - - -
229L VAL 3.2 0.6 - - - -
230L VAL* 1.3 77.6 - - - +
232L ARG* 1.3 68.0 + - + +
233L ASP 3.4 1.1 - - - -
234L THR* 3.5 13.2 + - - +
235L ILE* 3.5 17.6 + - + +
245L ALA 4.3 0.9 - - - +
248L GLU* 2.7 49.4 + - + +
249L ILE* 3.6 20.9 - - + +
252L LEU* 3.8 16.5 - - + +
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Residues in contact with ARG 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L LEU* 5.4 1.4 - - - +
228L TYR* 3.0 64.1 + - + +
229L VAL* 3.4 17.7 - - - +
231L THR* 1.3 76.8 - - + +
233L ASP* 1.3 102.1 + - - +
235L ILE* 3.3 25.2 + - + +
236L LYS* 4.4 4.9 + - - -
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Residues in contact with ASP 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L VAL* 3.2 29.5 + - - +
231L THR 3.4 0.2 - - - -
232L ARG* 1.3 115.3 + - - +
234L THR* 1.3 61.7 + - + +
235L ILE 3.4 1.6 - - - -
236L LYS* 3.0 27.0 + - - +
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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