Contacts of the helix formed by residues 226 - 245 (chain P) in PDB entry 5IY8
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 SER 226 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P LEU* 4.6 1.1 - - - -
168P ILE* 3.9 10.5 - - - -
224P ALA* 3.3 2.5 - - - +
225P LYS* 1.3 85.3 - - - +
227P GLU* 1.3 63.3 + - - +
228P GLU* 3.9 6.1 + - - +
229P GLN* 3.2 24.2 + - - +
230P SER* 2.7 35.3 + - - -
318P ARG* 4.8 6.3 - - - -
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Residues in contact with GLU 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P LEU* 4.2 5.2 - - - +
168P ILE* 4.2 8.6 - - + +
226P SER* 1.3 74.6 - - - +
228P GLU* 1.3 67.5 + - + +
230P SER* 3.3 9.3 - - - -
231P ARG* 2.8 27.4 + - - +
253P PHE* 4.6 3.8 - - - -
255P ILE* 4.4 20.7 - - + +
258P MET* 4.8 15.3 - - + +
318P ARG* 2.9 37.7 + - - -
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Residues in contact with GLU 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226P SER* 3.4 5.3 + - - +
227P GLU* 1.3 84.1 - - + +
229P GLN* 1.3 61.5 + - - +
231P ARG* 2.5 49.5 + - - +
232P LEU* 2.8 29.5 + - + +
235P ARG* 5.3 4.2 + - - -
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Residues in contact with GLN 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207P PRO* 3.1 49.9 + - + +
224P ALA* 3.8 5.7 - - - +
225P LYS* 2.9 41.4 + - - +
226P SER* 3.2 20.6 + - - +
228P GLU* 1.3 77.4 - - - +
230P SER* 1.3 55.4 + - - +
232P LEU* 3.3 18.0 - - + +
233P ALA* 2.9 28.6 + - - +
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Residues in contact with SER 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168P ILE* 4.0 11.2 + - - +
170P SER* 3.3 24.3 + - - -
221P CYS* 4.5 7.0 + - - -
222P THR* 6.0 0.3 - - - -
224P ALA* 3.5 20.3 - - - +
226P SER 2.7 20.7 + - - -
227P GLU* 3.3 13.2 - - - -
228P GLU 3.1 0.2 - - - -
229P GLN* 1.3 71.5 - - - +
231P ARG* 1.3 59.2 + - - +
233P ALA* 4.0 4.4 - - - +
234P ALA* 3.0 29.3 + - - +
253P PHE* 3.9 4.8 - - - -
255P ILE* 4.6 0.7 - - - -
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Residues in contact with ARG 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227P GLU 2.8 14.2 + - - +
228P GLU* 2.5 42.8 + - - +
230P SER* 1.3 72.6 - - - +
232P LEU* 1.3 60.0 - - - +
234P ALA* 3.8 1.2 - - - +
235P ARG* 3.0 45.9 + - - +
250P PHE* 3.9 28.1 - - + -
253P PHE* 3.6 25.2 - - + -
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Residues in contact with LEU 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317N GLU* 2.8 32.2 - - - +
206P GLU* 5.5 1.1 - - + -
207P PRO* 4.3 20.2 - - + -
228P GLU* 2.8 13.0 + - + +
229P GLN* 3.3 25.1 - - + +
231P ARG* 1.3 73.4 - - - +
233P ALA* 1.3 63.2 + - - +
235P ARG* 3.2 16.3 + - - +
236P LYS* 2.8 31.5 + - + +
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Residues in contact with ALA 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204P ILE* 4.3 4.0 - - + -
207P PRO* 4.1 5.8 - - + -
209P THR* 3.4 35.2 - - + +
221P CYS* 4.1 9.9 - - - -
229P GLN 2.9 19.4 + - - +
230P SER* 3.5 4.7 + - - +
232P LEU* 1.3 75.3 - - - +
234P ALA* 1.3 59.0 + - - +
236P LYS* 3.1 9.3 + - - +
237P TYR* 2.9 36.7 + - + -
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Residues in contact with ALA 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172P VAL* 4.7 12.9 - - + +
219P MET* 5.1 3.3 - - - +
221P CYS* 4.1 16.6 - - + -
230P SER 3.0 19.8 + - - +
231P ARG 3.8 4.0 - - - +
233P ALA* 1.3 77.0 - - - +
235P ARG* 1.3 57.6 + - - +
237P TYR* 3.7 5.6 + - - +
238P ALA* 3.2 26.7 + - - +
250P PHE* 4.7 7.3 - - + -
253P PHE* 3.5 29.4 - - + -
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Residues in contact with ARG 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313N PRO* 3.3 36.0 - - - +
314N LEU* 3.9 21.7 - - + +
316N SER* 4.4 10.4 + - - -
317N GLU* 2.7 38.0 + - + +
228P GLU* 5.3 3.0 + - - -
231P ARG* 3.0 46.8 + - - +
232P LEU* 3.5 24.9 - - - +
234P ALA* 1.3 73.9 - - - +
236P LYS* 1.3 60.6 + - - +
238P ALA* 3.4 1.4 + - - +
239P ARG* 2.8 30.0 + - - +
250P PHE* 4.6 8.8 - - + -
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Residues in contact with LYS 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317N GLU* 3.2 23.9 - - - +
320N VAL* 3.5 38.9 + - + +
204P ILE* 3.7 33.2 - - + +
206P GLU* 1.8 56.6 + - + +
232P LEU* 2.8 19.9 + - + +
233P ALA* 3.3 11.2 - - - +
235P ARG* 1.3 73.6 - - - +
237P TYR* 1.3 57.4 + - - +
239P ARG* 3.4 6.8 - - - +
240P VAL* 3.0 33.8 + - + +
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Residues in contact with TYR 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P LEU* 5.6 0.2 - - - -
202P MET* 3.2 50.6 + - + +
203P ARG 4.2 0.2 - - - -
204P ILE* 3.1 46.9 + - + +
209P THR* 3.3 24.1 + - - -
210P THR* 3.4 3.2 - - - -
211P ALA* 3.5 30.7 - - + -
213P ILE* 5.2 3.6 - - + -
219P MET* 4.3 15.0 - - + -
221P CYS* 4.4 7.0 - - - -
233P ALA 2.9 30.1 + - - +
234P ALA* 3.9 5.6 - - - +
236P LYS* 1.3 73.1 - - - +
238P ALA* 1.3 59.6 + - - +
240P VAL* 3.1 10.6 + - + +
241P VAL* 2.9 32.5 + - + +
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Residues in contact with ALA 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314N LEU* 3.6 30.4 - - + +
172P VAL* 6.1 1.8 - - + -
174P LEU* 3.8 29.5 - - + +
219P MET* 5.4 0.2 - - - -
234P ALA 3.2 16.7 + - - +
235P ARG 3.8 0.2 - - - +
237P TYR* 1.3 78.0 - - - +
239P ARG* 1.3 57.6 + - - +
241P VAL* 3.4 2.0 + - - -
242P GLN* 2.9 24.3 + - - +
248P ALA* 3.3 11.0 - - + +
249P LYS 5.0 2.5 - - - +
250P PHE* 5.1 4.3 - - + -
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Residues in contact with ARG 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314N LEU* 3.1 22.1 - - - +
315N ASN* 3.1 26.5 - - - +
317N GLU* 3.8 21.3 - - + +
318N ASP* 2.3 44.1 + - - +
319N ASP 4.8 0.6 - - - +
320N VAL* 4.2 9.9 - - + -
235P ARG 2.8 18.5 + - - +
236P LYS* 3.4 9.4 - - - +
238P ALA* 1.3 73.8 - - - +
240P VAL* 1.3 56.0 + - - +
242P GLN* 2.4 40.0 + - - +
243P LYS* 2.7 40.9 + - + +
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Residues in contact with VAL 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320N VAL* 4.7 15.5 - - + +
187P ALA* 5.9 1.6 - - + -
202P MET* 4.0 28.9 - - + -
204P ILE* 5.9 4.9 - - + -
236P LYS* 3.0 24.3 + - + +
237P TYR* 3.1 13.7 + - + +
239P ARG* 1.3 74.5 - - - +
241P VAL* 1.3 59.9 + - + +
243P LYS* 3.1 15.3 + - + +
244P LEU* 3.0 36.5 + - + +
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Residues in contact with VAL 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P LEU* 4.0 22.4 - - + -
176P CYS* 5.6 0.4 - - - -
178P LEU* 4.2 19.5 - - + -
202P MET* 5.8 5.6 - - - -
213P ILE* 5.6 8.5 - - + -
219P MET* 5.9 0.7 - - - -
237P TYR* 2.9 21.9 + - + +
238P ALA* 3.6 9.0 - - - +
239P ARG 3.2 0.2 - - - -
240P VAL* 1.3 74.4 - - + +
242P GLN* 1.3 65.6 + - - +
244P LEU* 3.0 29.0 + - + +
245P GLY 3.5 3.6 + - - -
246P PHE* 3.5 25.8 + - + -
247P PRO 5.6 0.2 - - - -
248P ALA* 3.7 16.6 - - + -
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Residues in contact with GLN 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312N GLU* 4.4 13.9 + - - +
314N LEU* 3.8 24.8 - - - +
315N ASN* 3.2 16.1 + - - +
238P ALA 2.9 14.6 + - - +
239P ARG* 2.4 51.5 + - - +
241P VAL* 1.3 75.9 - - - +
243P LYS* 1.3 53.7 + - - +
245P GLY* 2.9 21.8 + - - -
246P PHE 3.9 6.2 - - - +
248P ALA* 3.3 20.0 + - + +
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Residues in contact with LYS 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320N VAL* 6.5 0.4 - - + -
321N SER* 3.2 34.2 - - - +
324N GLU* 5.3 6.5 + - - -
186P ARG* 4.1 6.1 + - - -
188P ARG* 5.4 7.1 - - - +
239P ARG* 2.7 25.7 + - + +
240P VAL* 3.1 18.6 + - + +
242P GLN* 1.3 70.6 - - - +
244P LEU* 1.3 61.3 + - - +
245P GLY* 3.2 1.1 + - - -
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Residues in contact with LEU 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P ILE* 4.5 20.4 - - + -
186P ARG* 2.7 64.2 + - + +
187P ALA* 5.0 13.2 - - + +
202P MET* 6.2 2.0 - - - -
240P VAL* 3.0 22.7 + - + +
241P VAL* 3.0 27.1 + - + +
243P LYS* 1.3 78.5 - - - +
245P GLY* 1.3 56.4 + - - +
246P PHE* 3.2 32.8 + - + -
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Residues in contact with GLY 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242P GLN 2.9 13.2 + - - -
243P LYS 3.2 1.5 - - - -
244P LEU* 1.3 79.3 - - - +
246P PHE* 1.3 68.0 + - - +
247P PRO* 3.8 3.3 - - - +
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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
------------------------------------------------------------
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