Contacts of the helix formed by residues 240 - 259 (chain C) in PDB entry 1EQR
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 THR 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C MET* 1.3 76.5 - - - +
241C ALA* 1.3 65.6 + - - +
242C PRO* 3.5 11.7 - - - +
243C GLN* 2.7 42.2 + - - +
244C VAL* 3.0 24.7 + - - +
488C VAL* 4.9 1.3 - - - -
529C ALA* 5.4 0.2 - - - -
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C THR* 1.3 70.5 - - - +
242C PRO* 1.3 73.8 - - + +
244C VAL* 3.0 10.1 + - - +
245C ARG* 2.9 40.9 + - - +
455C LYS* 6.3 0.2 - - - -
472C ASN* 3.3 27.5 - - - +
474C TYR* 3.9 12.8 - - + -
488C VAL* 3.8 19.4 - - + +
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Residues in contact with PRO 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C THR* 3.5 16.4 - - - +
241C ALA* 1.3 95.6 - - + +
243C GLN* 1.3 56.2 + - + +
245C ARG* 3.6 29.2 - - + +
246C GLU* 2.9 29.5 + - - +
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Residues in contact with GLN 243 (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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238C PHE 4.2 4.0 + - - -
239C MET* 3.3 26.7 - - + +
240C THR* 2.7 53.3 + - - +
242C PRO* 1.3 75.0 - - + +
244C VAL* 1.3 69.0 + - - +
246C GLU* 3.2 16.3 + - - +
247C VAL* 3.1 20.1 + - - +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C VAL* 5.8 1.6 - - + -
236C THR* 3.9 25.1 - - + +
239C MET* 4.3 8.5 - - + -
240C THR 3.2 15.0 - - - +
241C ALA* 3.0 7.1 + - - +
243C GLN* 1.3 72.7 - - - +
245C ARG* 1.3 68.9 + - - +
246C GLU 2.9 1.4 + - - -
247C VAL* 2.9 28.3 - - + +
248C MET* 2.9 21.8 + - + +
474C TYR* 4.1 22.9 - - + +
529C ALA* 4.2 17.5 - - + -
530C GLY* 4.5 14.1 - - - +
531C LEU* 4.8 0.4 - - + -
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Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ALA* 2.9 36.0 + - - +
242C PRO* 3.6 38.0 - - - +
244C VAL* 1.3 73.1 - - - +
246C GLU* 1.3 55.2 + - - +
248C MET 3.1 0.3 + - - -
249C GLU* 2.7 34.6 + - - +
269C VAL* 4.7 7.5 - - - +
429C TRP* 3.2 65.8 - - + +
431C ILE* 3.4 42.9 - - - +
432C ASP* 5.7 0.8 + - - -
455C LYS* 5.7 4.9 - - - +
472C ASN* 4.7 3.2 + - - -
474C TYR* 3.9 16.7 - - + +
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C PRO 2.9 14.7 + - - +
243C GLN* 3.2 18.8 - - - +
244C VAL 2.9 0.6 + - - -
245C ARG* 1.3 76.0 - - - +
247C VAL* 1.3 63.3 + - - +
249C GLU* 3.2 6.6 + - - +
250C ALA* 3.0 24.2 + - + +
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Residues in contact with VAL 247 (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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151C PHE* 3.5 20.1 - - + -
155C HIS* 4.4 14.8 - - + -
157C PHE* 4.2 28.7 - - + -
208C ARG* 5.5 4.7 - - - +
239C MET* 5.6 7.6 - - - -
243C GLN 3.1 6.5 + - - +
244C VAL* 2.9 36.0 + - + +
246C GLU* 1.3 78.2 - - - +
248C MET* 1.3 78.5 + - + +
250C ALA* 3.4 5.5 + - - +
251C LEU* 3.2 17.7 + - - +
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Residues in contact with MET 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C PHE* 5.0 0.2 - - + -
152C MET* 3.7 33.4 - - + -
157C PHE* 4.7 1.1 - - + -
234C VAL* 3.9 20.9 - - + -
244C VAL* 2.9 31.1 + - + +
245C ARG 3.6 3.1 - - - +
247C VAL* 1.3 102.3 - - + +
249C GLU* 1.3 63.4 + - - +
251C LEU* 3.4 8.6 + - + +
252C VAL* 3.2 18.5 + - - +
429C TRP* 4.0 14.8 - - + -
476C MET* 3.7 11.0 - - - +
531C LEU* 3.8 17.5 - - + -
533C PHE* 3.7 27.4 - - + -
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ARG 2.7 20.3 + - - +
246C GLU* 3.6 6.5 - - - +
248C MET* 1.3 69.8 - - - +
250C ALA* 1.3 61.9 + - - +
251C LEU 3.2 0.4 - - - -
252C VAL* 3.5 1.6 + - - +
253C ARG* 3.0 60.1 + - - +
266C ASP* 3.5 6.6 - - - +
267C PHE* 2.9 49.5 + - + +
429C TRP* 2.8 34.6 + - - +
476C MET* 4.5 5.6 - - - -
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C PHE* 3.7 14.8 - - + -
155C HIS* 5.6 2.7 - - - +
246C GLU* 3.0 12.8 + - + +
247C VAL* 3.7 11.7 - - - +
248C MET 3.3 0.2 - - - -
249C GLU* 1.3 77.7 - - - +
251C LEU* 1.3 56.3 + - - +
253C ARG* 3.9 8.1 - - - +
254C HIS* 3.0 28.2 + - - +
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LEU 4.6 0.7 - - - +
148C VAL* 4.1 28.5 - - + +
151C PHE* 3.4 50.6 - - + -
152C MET* 4.7 8.5 - - - -
232C ILE* 5.6 2.5 - - + -
247C VAL 3.2 8.5 + - - +
248C MET* 3.5 14.4 - - + +
249C GLU 3.2 0.4 - - - -
250C ALA* 1.3 75.0 - - - +
252C VAL* 1.3 75.7 + - + +
254C HIS* 3.1 19.5 + - + +
255C LEU* 3.1 30.2 + - + +
533C PHE* 4.5 15.0 - - + -
538C LEU* 5.7 0.9 - - + -
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C MET 3.2 5.8 + - - +
249C GLU 3.5 2.9 + - - +
251C LEU* 1.3 83.9 - - + +
253C ARG* 1.3 64.4 + - - +
255C LEU* 3.2 8.9 + - + +
256C TRP* 3.1 48.0 + - + +
264C LEU* 4.1 4.9 - - + -
267C PHE* 3.9 18.6 - - + -
476C MET* 3.5 31.2 - - + -
478C ILE* 4.1 8.3 - - + -
533C PHE* 3.7 18.6 - - + -
538C LEU* 5.2 6.5 - - + -
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Residues in contact with ARG 253 (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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249C GLU* 3.0 43.3 + - - +
250C ALA* 3.9 7.9 - - - +
252C VAL* 1.3 76.2 - - - +
254C HIS* 1.3 64.1 + - - +
256C TRP* 3.3 2.5 + - - +
257C LEU* 3.0 26.7 + - - +
262C VAL 4.8 0.9 - - - +
263C ASP* 4.0 13.3 + - - +
264C LEU* 4.4 15.6 + - + +
265C GLY* 2.9 46.7 + - - +
266C ASP* 3.3 17.2 + - - +
267C PHE* 3.7 16.2 - - + -
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Residues in contact with HIS 254 (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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147C LEU* 4.0 40.4 + - + +
150C ARG* 5.8 2.2 - - - +
151C PHE* 4.1 23.1 + + + +
250C ALA 3.0 14.4 + - - +
251C LEU* 3.1 13.9 - - + +
253C ARG* 1.3 77.7 - - - +
255C LEU* 1.3 57.1 + - + +
257C LEU* 3.2 8.2 + - - +
258C GLU* 2.9 55.7 + - + +
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Residues in contact with LEU 255 (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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144C ILE* 4.0 26.0 - - + +
147C LEU* 3.5 39.0 - - + -
148C VAL* 4.1 15.9 - - + +
251C LEU* 3.1 32.9 + - + +
252C VAL* 3.2 11.4 + - + +
254C HIS* 1.3 78.3 - - + +
256C TRP* 1.3 65.8 + - + +
259C VAL* 2.8 37.4 + - + +
538C LEU* 4.3 18.4 - - + -
542C LEU* 4.5 9.2 - - + -
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Residues in contact with TRP 256 (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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252C VAL* 3.1 42.3 + - + +
253C ARG 3.3 3.1 + - - +
255C LEU* 1.3 82.5 - - + +
257C LEU* 1.3 58.0 + - - +
260C LYS* 3.3 10.0 + - + +
261C GLY 2.9 20.8 + - - -
262C VAL* 2.9 37.6 + - + +
264C LEU* 3.4 32.1 - - + +
425C TRP* 3.4 47.6 - + - -
478C ILE* 3.5 22.0 - - + -
538C LEU* 4.4 17.9 - - + -
541C LEU* 4.2 14.4 - - + -
542C LEU* 3.5 40.2 - - + +
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Residues in contact with LEU 257 (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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253C ARG 3.0 17.9 + - - +
254C HIS* 3.6 7.6 - - - +
256C TRP* 1.3 79.6 - - - +
258C GLU* 1.3 67.5 + - + +
261C GLY* 3.1 24.3 + - - -
262C VAL 3.2 14.3 + - - +
263C ASP* 5.1 10.5 - - + -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LYS* 3.8 17.1 + - - -
147C LEU* 3.4 27.9 - - + +
254C HIS* 2.9 43.1 + - + +
257C LEU* 1.3 87.2 - - + +
259C VAL* 1.3 64.1 + - - +
261C GLY 4.6 0.7 + - - -
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Residues in contact with VAL 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C THR* 4.1 22.4 - - + -
143C LYS* 4.4 15.7 + - + +
144C ILE* 4.0 20.4 - - + -
147C LEU* 3.8 20.9 - - + -
255C LEU* 2.8 26.4 + - + +
258C GLU* 1.3 75.7 - - - +
260C LYS* 1.3 76.6 + - + +
542C LEU* 4.3 18.2 - - + +
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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