Contacts of the helix formed by residues 247 - 261 (chain C) in PDB entry 4EOZ
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 GLU 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245C ASP 5.9 0.4 - - - +
246C VAL* 1.3 74.3 - - - +
248C PRO* 1.3 66.6 - - + +
249C GLU* 3.7 13.7 - - - +
250C VAL* 2.7 25.4 + - + +
251C PHE* 2.6 32.3 + - - -
272C ASP* 5.3 7.2 - - - +
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Residues in contact with PRO 248 (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 VAL* 4.1 19.7 - - + +
207C ALA* 4.5 11.4 - - + -
209C GLN* 3.6 35.4 - - - +
211C PHE* 4.4 11.7 - - + -
246C VAL 3.9 3.8 - - - +
247C GLU* 1.3 94.7 - - + +
249C GLU* 1.3 59.7 + - - +
251C PHE* 3.5 9.8 - - + +
252C LYS* 2.7 43.4 + - - +
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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
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247C GLU* 3.7 22.2 - - - +
248C PRO* 1.3 80.3 - - - +
250C VAL* 1.3 59.2 + - + +
252C LYS* 3.5 17.0 + - - +
253C GLU* 3.1 25.8 + - - +
268C LYS* 6.2 1.1 - - - +
269C MET* 3.9 16.4 - - + +
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Residues in contact with VAL 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C VAL* 3.7 16.4 - - + -
247C GLU* 2.7 31.5 + - + +
249C GLU* 1.3 72.5 - - + +
251C PHE* 1.3 63.6 + - - +
253C GLU* 3.2 1.9 + - - -
254C MET* 3.0 20.6 + - - +
269C MET* 3.7 26.0 - - + -
272C ASP* 3.9 26.7 - - + +
273C LEU* 3.8 30.1 - - + +
276C ALA* 4.1 8.3 - - + -
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Residues in contact with PHE 251 (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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194C TRP* 4.2 2.2 - + - -
204C LEU* 4.0 18.8 - - + -
206C VAL* 3.7 29.4 - - + -
211C PHE* 3.5 39.7 - + + -
225C PHE* 5.2 0.4 - + - -
243C ILE* 4.0 20.4 - - + -
246C VAL* 3.7 16.4 - - + +
247C GLU 2.6 14.8 + - - +
248C PRO* 3.5 10.5 - - + +
250C VAL* 1.3 73.1 - - - +
252C LYS* 1.3 59.0 + - - +
254C MET* 3.0 26.1 + - + +
255C MET* 2.9 63.3 + - + +
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Residues in contact with LYS 252 (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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194C TRP* 4.2 16.4 + - + +
209C GLN* 5.4 3.4 + - - -
211C PHE* 3.9 33.3 - - + -
248C PRO* 2.7 25.7 + - - +
249C GLU* 3.6 18.0 - - - +
250C VAL 3.2 0.2 - - - -
251C PHE* 1.3 76.9 - - + +
253C GLU* 1.3 59.9 + - - +
255C MET* 3.5 5.9 + - - +
256C CYS* 3.1 25.8 + - - +
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Residues in contact with GLU 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 3.1 9.3 + - - +
250C VAL 3.2 2.2 + - - +
251C PHE 3.2 0.4 - - - -
252C LYS* 1.3 76.6 - - - +
254C MET* 1.3 66.9 + - - +
256C CYS* 3.3 10.1 + - - +
257C PHE* 3.0 21.5 + - - +
263C ALA* 3.2 17.4 - - + +
264C PRO* 3.2 18.2 - - - +
265C ASN* 2.7 50.7 + - - +
266C LEU 4.4 4.3 - - - +
269C MET* 3.6 27.6 - - - +
273C LEU* 4.1 15.4 - - + +
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Residues in contact with MET 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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225C PHE* 4.0 24.2 - - + -
246C VAL* 5.7 2.0 - - + -
250C VAL 3.0 12.6 + - - +
251C PHE* 3.0 35.3 + - + +
253C GLU* 1.3 77.0 - - - +
255C MET* 1.3 57.2 + - - +
257C PHE* 3.2 8.7 + - - +
258C ILE* 2.9 32.3 + - + +
273C LEU* 3.8 10.9 - - + +
276C ALA* 4.0 22.7 - - + +
280C TYR* 3.6 36.8 - - + -
282C LEU* 3.4 23.8 - - + -
285C LEU* 4.5 6.5 - - + -
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Residues in contact with MET 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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194C TRP* 3.5 38.8 - - + -
204C LEU* 4.7 2.5 - - + -
213C ALA* 3.5 32.3 - - + -
218C LEU* 3.9 28.9 - - + -
225C PHE* 5.2 1.8 - - - -
251C PHE* 2.9 55.2 + - + +
252C LYS 3.8 1.1 - - - +
254C MET* 1.3 74.8 - - + +
256C CYS* 1.3 67.1 + - - +
258C ILE* 3.2 12.3 + - - -
259C TYR* 3.1 36.1 + - + -
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Residues in contact with CYS 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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194C TRP* 4.3 15.5 - - + +
252C LYS 3.1 13.9 + - - +
253C GLU* 3.5 16.8 - - - +
255C MET* 1.3 74.6 - - - +
257C PHE* 1.3 58.1 + - - +
259C TYR* 3.5 1.7 + - - -
260C THR* 2.7 47.6 + - - +
262C LYS* 3.5 13.9 - - - -
264C PRO* 3.9 22.4 - - - -
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Residues in contact with PHE 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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185A ARG* 6.2 0.9 - - + -
221C ARG* 2.8 29.9 + - - -
253C GLU 3.0 12.5 + - - +
254C MET 3.4 7.4 - - - +
256C CYS* 1.3 77.7 - - - +
258C ILE* 1.3 62.1 + - - +
261C GLY* 2.7 40.9 + - - +
262C LYS 3.4 13.0 + - - +
263C ALA* 4.7 1.1 - - + -
282C LEU* 4.0 30.3 - - + -
284C ARG* 3.4 36.1 - - + -
285C LEU* 3.6 56.1 - - + -
288C MET* 4.1 8.1 - - - -
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Residues in contact with ILE 258 (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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186A LEU* 3.6 2.6 - - - +
217C ILE* 4.1 18.3 - - + +
218C LEU* 3.7 28.3 - - + -
221C ARG* 2.6 40.8 + - + +
222C SER* 5.3 0.4 - - - -
225C PHE* 4.0 20.6 - - + -
254C MET* 2.9 20.5 + - + +
255C MET* 3.2 26.9 + - - +
257C PHE* 1.3 76.9 - - - +
259C TYR* 1.3 68.7 + - + +
282C LEU* 3.8 31.4 - - + -
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Residues in contact with TYR 259 (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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186A LEU* 3.6 13.5 - - - +
187C ALA 4.0 0.5 - - - +
190C LEU* 3.4 45.7 - - + +
191C GLY* 4.5 0.7 - - - -
193C LEU* 4.3 1.3 - - + -
194C TRP* 3.7 32.9 - + + -
213C ALA* 3.4 8.7 - - - +
214C HIS* 2.8 51.4 + + - +
217C ILE* 4.0 31.2 - - + -
218C LEU* 4.4 2.4 - - + +
255C MET* 3.1 48.4 + - + +
256C CYS* 4.2 1.8 - - - +
258C ILE* 1.3 89.6 - - + +
260C THR* 1.3 68.0 + - + +
261C GLY 3.8 0.2 - - - -
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Residues in contact with THR 260 (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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184A CYS* 5.2 2.1 - - - -
186A LEU* 3.9 11.3 - - - +
187C ALA* 3.5 37.6 - - - +
188C ASP* 5.3 1.1 - - - +
191C GLY* 3.5 18.4 - - - -
194C TRP* 6.4 0.9 - - + -
256C CYS* 2.7 30.6 + - - +
259C TYR* 1.3 83.6 - - + +
261C GLY* 1.3 61.6 + - - +
262C LYS* 3.1 33.4 + - - +
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Residues in contact with GLY 261 (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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184A CYS* 4.7 10.8 - - - -
186A LEU* 4.4 0.8 - - - +
221C ARG* 3.7 13.7 - - - +
257C PHE* 2.7 35.7 + - - -
259C TYR 3.8 0.2 - - - -
260C THR* 1.3 71.0 - - - +
262C LYS* 1.3 58.7 + - - +
284C ARG* 2.9 31.9 + - - -
288C MET* 4.2 2.8 - - - +
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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
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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