Contacts of the helix formed by residues 233 - 255 (chain P) in PDB entry 1OCR
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 PHE 233 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71P HIS* 6.2 0.9 - - - +
76P GLN* 5.1 12.5 + - + +
79P LEU* 3.3 56.8 - - + -
80P ARG* 3.6 34.5 - - + +
83P MET* 3.9 16.8 - - + -
231P HIS* 4.0 12.9 - - + +
232P HIS* 1.3 75.2 - - - +
234P GLY* 1.3 66.9 + - - +
235P PHE 3.0 0.2 + - - -
236P GLU* 3.0 17.9 + - + +
237P ALA* 2.9 38.2 + - + +
240P TRP* 4.1 13.9 - + - -
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Residues in contact with GLY 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214P PHE* 3.5 21.5 - - - -
218P CYS* 3.6 9.0 - - - -
221P ARG* 4.2 20.5 - - - +
227P PHE* 4.8 0.2 - - - -
232P HIS 3.2 1.2 - - - -
233P PHE* 1.3 79.9 - - - +
235P PHE* 1.3 56.1 + - - +
237P ALA* 3.8 2.6 + - - -
238P GLY 3.1 19.8 + - - -
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Residues in contact with PHE 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P ILE* 4.1 18.4 - - + -
147P ALA* 3.9 10.3 - - + -
148P HIS* 3.4 57.2 - + + -
151P LEU* 4.2 11.7 - - + -
159P MET* 4.0 21.5 - - + -
163P LEU* 4.3 19.7 - - + -
215P LEU* 5.3 2.7 - - + -
218P CYS* 3.9 21.0 - - + -
227P PHE* 4.2 16.4 - - + -
232P HIS* 2.9 16.4 + + + +
234P GLY* 1.3 76.4 - - - +
236P GLU* 1.3 62.2 + - - +
238P GLY* 3.1 1.6 + - - -
239P ALA* 2.8 31.8 + - + +
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Residues in contact with GLU 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P ARG* 2.6 36.5 + - - -
148P HIS* 4.1 20.2 + - + +
152P MET* 6.2 1.1 - - - -
232P HIS* 3.2 27.8 + - + +
233P PHE* 3.0 19.9 + - + +
235P PHE* 1.3 80.3 - - - +
237P ALA* 1.3 57.9 + - - +
239P ALA* 3.1 5.9 + - - +
240P TRP* 2.9 59.6 + - + +
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Residues in contact with ALA 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P MET* 3.7 37.2 - - + +
214P PHE* 3.9 11.2 - - + -
233P PHE* 2.9 29.2 + - + +
234P GLY* 4.0 4.7 - - - +
236P GLU* 1.3 73.1 - - - +
238P GLY* 1.3 67.5 + - - +
240P TRP* 3.8 6.4 - - - +
241P TYR* 2.9 25.8 + - - +
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Residues in contact with GLY 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211P GLY* 5.6 1.6 - - - +
214P PHE* 3.5 26.6 - - - +
215P LEU* 4.2 17.1 - - - +
218P CYS* 4.9 2.0 - - - -
234P GLY 3.1 15.0 + - - -
235P PHE* 3.1 6.0 + - - -
237P ALA* 1.3 76.6 - - - +
239P ALA* 1.3 56.1 + - - +
241P TYR* 3.5 3.3 + - - +
242P TRP* 3.0 27.2 + - - +
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Residues in contact with ALA 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P ILE* 3.8 28.6 - - + +
148P HIS* 6.0 4.5 - - + -
235P PHE* 2.8 24.9 + - + +
236P GLU* 3.5 7.6 - - - +
238P GLY* 1.3 74.8 - - - +
240P TRP* 1.3 67.6 + - + +
242P TRP* 3.1 2.9 + - - +
243P HIS* 3.0 37.1 + - + +
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Residues in contact with TRP 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P ARG* 3.9 30.7 - - + -
83P MET* 3.9 19.7 - - + -
84P ILE* 3.9 30.3 - - + -
87P ILE* 4.0 15.7 - - + +
233P PHE* 4.1 23.1 - + - -
236P GLU* 2.9 46.0 + - + +
237P ALA* 3.8 5.6 - - - +
239P ALA* 1.3 80.6 - - + +
241P TYR* 1.3 64.8 + - - +
243P HIS* 3.1 11.2 + - - +
244P PHE* 3.0 22.0 + - - +
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Residues in contact with TYR 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P MET* 4.1 20.2 - - + -
86P PHE* 3.9 12.8 - + - -
87P ILE* 4.1 12.5 - - + +
90P GLU* 3.0 28.5 + - + -
207P HIS* 3.1 27.8 + + - -
210P ILE* 3.7 34.0 - - + +
211P GLY* 3.8 24.0 - - - -
214P PHE* 4.6 12.1 - + + -
237P ALA 2.9 18.1 + - - +
238P GLY 3.6 4.9 - - - +
240P TRP* 1.3 77.7 - - - +
242P TRP* 1.3 61.9 + - - +
244P PHE* 3.1 16.8 + + - +
245P VAL* 3.0 29.0 + - + +
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Residues in contact with TRP 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU* 4.5 12.0 + - + +
140P SER* 2.9 47.9 + - - -
141P GLY* 4.8 3.8 - - - -
144P ILE* 4.1 25.4 - - + -
166P THR* 3.9 10.6 - - + +
167P ILE* 6.3 0.2 - - - -
170P GLY* 3.8 30.7 - - - -
208P VAL* 3.8 32.8 - - + -
211P GLY* 4.0 13.9 - - - -
212P SER* 3.8 15.5 - - - -
215P LEU* 4.0 15.3 - - + -
238P GLY 3.0 15.3 + - - +
239P ALA 3.1 8.9 + - - +
241P TYR* 1.3 77.1 - - - +
243P HIS* 1.3 63.5 + + - +
245P VAL* 3.2 13.8 + - + +
246P ASP* 3.0 24.9 + - + +
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Residues in contact with HIS 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P GLY* 3.6 32.7 + - - -
144P ILE* 3.8 19.3 - - + +
145P THR* 4.1 9.1 + - - -
239P ALA* 3.0 24.5 + - + -
240P TRP* 3.1 11.9 + - - +
242P TRP* 1.3 74.2 - + - +
244P PHE* 1.3 60.8 + - - +
246P ASP* 3.1 12.5 - - + +
247P VAL* 2.8 36.6 + - + +
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Residues in contact with PHE 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P ILE* 4.1 25.1 - - + -
90P GLU* 3.5 27.6 - - + -
91P VAL* 3.7 29.6 - - + -
94P PHE* 4.1 14.4 - + - -
207P HIS* 3.9 23.8 - + + -
240P TRP 3.0 12.7 + - - +
241P TYR* 3.3 25.1 - + - +
243P HIS* 1.3 75.4 - - - +
245P VAL* 1.3 78.8 + - + +
247P VAL* 3.0 8.5 + - + +
248P VAL* 2.9 47.7 + - + +
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Residues in contact with VAL 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU* 4.8 5.6 - - + -
204P HIS* 2.8 30.3 + - + +
207P HIS* 3.7 35.9 - - + +
208P VAL* 3.4 33.9 - - + -
241P TYR* 3.0 23.3 + - + +
242P TRP* 3.5 23.3 - - + +
244P PHE* 1.3 84.7 - - + +
246P ASP* 1.3 63.8 + - - +
248P VAL* 4.6 3.6 - - - -
249P TRP* 3.2 6.4 + - - +
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Residues in contact with ASP 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU* 3.7 34.3 - - + +
138P LEU* 4.0 32.0 + - - +
141P GLY* 4.0 13.2 - - - -
242P TRP* 3.0 16.3 + - + +
243P HIS* 3.1 19.0 - - + +
245P VAL* 1.3 78.7 - - - +
247P VAL* 1.3 64.2 + - + +
249P TRP* 3.2 7.4 + - - +
250P LEU* 3.2 23.7 + - - +
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Residues in contact with VAL 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243P HIS* 2.8 22.7 + - + +
244P PHE* 3.0 6.9 + - + +
246P ASP* 1.3 76.1 - - + +
248P VAL* 1.3 68.4 + - + +
250P LEU* 3.0 26.0 + - + +
251P PHE* 3.2 34.6 + - + -
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Residues in contact with VAL 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P VAL* 6.0 0.4 - - + -
94P PHE* 4.1 35.0 - - + -
98P PHE* 4.3 6.5 - - + -
204P HIS* 3.4 25.6 - - + -
244P PHE* 2.9 49.7 + - + +
245P VAL* 3.8 1.1 - - - +
247P VAL* 1.3 76.5 - - + +
249P TRP* 1.3 63.1 + - - +
251P PHE* 3.1 10.6 + - - +
252P LEU* 3.1 26.2 + - + +
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Residues in contact with TRP 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P PRO* 3.9 11.7 - - + -
133P ASN* 3.7 24.2 - - + -
134P THR* 2.9 37.7 + - + +
137P LEU* 3.7 18.6 - - + -
173P PHE* 3.8 18.6 - + - -
177P GLN* 3.5 24.0 - - - -
201P THR* 4.9 0.9 - - + -
204P HIS* 3.3 29.5 + + + +
245P VAL 3.2 3.8 + - - -
246P ASP* 3.4 9.9 - - - +
247P VAL 3.1 0.6 - - - -
248P VAL* 1.3 78.9 - - - +
250P LEU* 1.3 69.4 + - + +
252P LEU* 3.0 16.3 + - + +
253P TYR* 2.8 34.1 + + + +
257P TYR* 3.6 34.3 - + - -
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Residues in contact with LEU 250 (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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134P THR* 4.1 26.2 - - + -
138P LEU* 4.2 25.6 - - + -
246P ASP* 3.2 16.5 + - - +
247P VAL* 3.0 20.8 + - + +
249P TRP* 1.3 83.3 - - + +
251P PHE* 1.3 64.6 + - + +
253P TYR* 3.5 6.2 + - + +
254P VAL* 3.1 33.3 + - + +
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Residues in contact with PHE 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P PHE* 3.6 23.1 - + + -
247P VAL* 3.2 42.5 + - + -
248P VAL* 3.1 10.1 + - - +
250P LEU* 1.3 79.3 - - + +
252P LEU* 1.3 62.1 + - - +
254P VAL* 4.6 3.4 - - + +
255P SER* 2.7 41.6 + - - -
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Residues in contact with LEU 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P PHE* 5.7 1.1 - - + -
98P PHE* 3.5 24.7 - - + -
200P ALA* 4.1 26.0 - - + +
201P THR* 3.9 20.9 - - + -
204P HIS* 3.7 35.7 - - + -
248P VAL* 3.1 18.2 + - + +
249P TRP* 3.0 19.6 + - + +
251P PHE* 1.3 74.6 - - - +
253P TYR* 1.3 66.9 + - - +
256P ILE* 2.8 36.9 + - + +
257P TYR* 3.3 13.2 + - + -
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Residues in contact with TYR 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P PRO* 2.7 42.5 + - + +
127P LEU* 4.3 6.6 - - - +
130P PRO* 3.5 29.6 - - + -
131P LEU* 3.8 19.9 - - + +
134P THR* 3.5 24.7 - - + +
249P TRP* 2.8 30.2 + + + +
250P LEU* 3.7 9.0 - - + +
252P LEU* 1.3 78.4 - - - +
254P VAL* 1.3 68.8 + - + +
257P TYR* 3.2 14.8 + - + +
258P TRP* 2.8 48.6 + + - +
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Residues in contact with VAL 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P TYR* 5.7 1.1 - - - +
250P LEU* 3.1 20.3 + - + +
251P PHE* 4.2 4.5 - - + +
253P TYR* 1.3 83.0 - - + +
255P SER* 1.3 61.1 + - - +
258P TRP* 3.4 30.2 - - + +
259P TRP* 2.9 34.1 + - + +
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Residues in contact with SER 255 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P PHE* 3.8 13.7 - - - -
101P PHE* 3.5 11.0 - - - -
102P TYR* 2.7 42.1 + - - -
251P PHE* 2.7 31.8 + - - +
254P VAL* 1.3 75.0 - - - +
256P ILE* 1.3 56.0 + - - +
259P TRP* 3.6 4.3 - - - -
260P GLY* 2.6 35.2 + - - -
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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