Contacts of the helix formed by residues 251 - 268 (chain C) in PDB entry 1EZF
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 ASN 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C VAL* 4.0 14.0 - - + +
245C ASP* 3.0 48.4 + - - +
246C PHE* 4.6 3.1 - - - -
248C LYS* 2.8 16.3 + - - +
250C GLU* 1.3 93.6 - - - +
252C ILE* 1.3 64.0 + - - +
253C ASP 3.4 2.7 - - - -
254C LEU* 3.3 21.8 + - + +
255C ALA* 2.9 21.3 + - - +
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Residues in contact with ILE 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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246C PHE 5.3 2.5 - - - +
248C LYS 3.9 1.6 + - - -
249C PRO* 3.0 23.5 + - + +
250C GLU 3.6 3.5 - - - +
251C ASN* 1.3 73.0 - - - +
253C ASP* 1.3 78.0 + - - +
255C ALA* 2.9 5.9 + - - +
256C VAL* 2.7 39.5 + - - +
307C GLN* 3.9 51.8 - - + +
310C PHE* 4.6 15.9 - - + -
311C LYS* 5.2 11.0 - - - -
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Residues in contact with ASP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C GLU 5.4 0.6 + - - -
251C ASN 3.4 0.6 - - - -
252C ILE* 1.3 94.8 - - - +
254C LEU* 1.3 65.0 + - + +
256C VAL* 3.2 8.2 + - - +
257C GLN* 3.1 32.2 + - - +
307C GLN* 5.0 5.5 - - - +
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C TYR* 3.6 53.3 - - + +
240C VAL* 4.3 6.5 - - + -
246C PHE* 4.2 4.7 - - + -
250C GLU 5.7 0.2 - - - +
251C ASN* 3.3 29.2 + - + +
252C ILE 3.2 0.4 - - - -
253C ASP* 1.3 78.2 - - + +
255C ALA* 1.3 62.4 + - - +
257C GLN* 3.2 15.2 + - - +
258C CYS* 3.0 20.3 + - - +
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C PHE* 3.6 29.1 - - + +
251C ASN 2.9 14.5 + - - +
252C ILE* 2.9 12.5 + - - +
254C LEU* 1.3 77.3 - - - +
256C VAL* 1.3 56.7 + - - +
258C CYS* 3.3 4.0 + - - +
259C LEU 2.9 22.9 + - - -
310C PHE* 3.0 43.0 - - + -
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Residues in contact with VAL 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 ILE* 2.7 24.6 + - + +
253C ASP* 3.7 7.4 - - - +
255C ALA* 1.3 68.9 - - - +
257C GLN* 1.3 61.2 + - + +
259C LEU* 3.3 6.6 - - + +
260C ASN* 2.9 30.5 + - - +
305C ASN* 3.3 44.2 - - - +
306C ASN 4.4 0.7 - - - +
307C GLN* 3.9 39.3 - - + +
310C PHE* 4.0 7.0 - - + -
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Residues in contact with GLN 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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239C TYR* 3.2 29.7 + - + +
253C ASP* 3.1 20.7 + - - +
254C LEU* 3.4 17.1 - - - +
256C VAL* 1.3 77.6 - - + +
258C CYS* 1.3 62.9 + - - +
260C ASN* 3.2 4.7 + - - +
261C GLU* 3.0 22.2 + - - +
352C SER 4.6 8.9 + - - -
353C ASP* 4.2 13.5 - - - +
354C PRO* 3.8 27.1 - - + +
355C SER* 4.5 2.3 + - - -
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Residues in contact with CYS 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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231C TRP* 3.9 2.0 - - + -
235C VAL* 3.8 17.0 - - - -
236C TRP* 3.8 12.1 - - - -
239C TYR* 3.6 17.4 - - + -
246C PHE* 3.5 42.0 - - + -
254C LEU 3.0 6.2 + - - +
255C ALA 3.5 5.2 - - - +
257C GLN* 1.3 74.3 - - - +
259C LEU* 1.3 59.2 + - - +
261C GLU* 3.1 5.0 + - - +
262C LEU* 2.9 52.2 + - - +
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Residues in contact with LEU 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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217C ILE* 3.7 29.4 - - + -
231C TRP* 4.3 11.4 - - + -
255C ALA 2.9 13.6 + - - +
256C VAL* 3.3 10.3 - - - +
257C GLN 3.2 0.2 - - - -
258C CYS* 1.3 75.6 - - - +
260C ASN* 1.3 61.0 + - - +
262C LEU* 3.1 5.0 + - - +
263C ILE* 2.9 42.9 + - + +
303C CYS* 3.3 22.4 - - + +
305C ASN 4.0 4.0 - - - +
306C ASN 3.5 27.4 - - - +
309C VAL* 4.1 21.8 - - + -
310C PHE* 3.7 14.8 - - + -
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Residues in contact with ASN 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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256C VAL* 2.9 20.4 + - - +
257C GLN 3.2 4.9 + - - +
259C LEU* 1.3 76.4 - - - +
261C GLU* 1.3 56.5 + - - +
263C ILE* 3.5 2.8 + - - +
264C THR* 2.7 35.5 + - - +
304C TYR* 3.7 27.8 + - + -
305C ASN* 2.7 56.8 + - - +
350C PRO* 4.0 2.8 - - - +
353C ASP* 3.4 24.7 + - - +
355C SER* 3.8 5.4 - - - +
359C THR* 5.8 0.2 - - - +
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Residues in contact with GLU 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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165C GLU* 5.2 3.0 - - - +
235C VAL* 3.6 12.7 - - + +
238C ARG* 2.6 43.0 + - - -
239C TYR* 2.7 34.6 + - - +
257C GLN 3.0 11.9 + - - +
258C CYS* 3.4 9.2 - - - +
260C ASN* 1.3 78.2 - - - +
262C LEU* 1.3 62.8 + - + +
264C THR* 3.3 4.9 + - - -
265C ASN* 3.1 20.3 + - - +
354C PRO* 5.1 3.3 - - - +
355C SER* 3.5 22.4 + - - +
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C GLU* 5.8 0.2 - - - +
168C TRP* 3.9 22.1 - - + -
217C ILE* 3.8 23.0 - - + +
231C TRP* 3.3 45.3 - - + -
232C PRO* 3.8 27.8 - - + -
235C VAL* 3.9 17.3 - - + -
258C CYS* 2.9 29.3 + - - +
259C LEU* 3.1 7.2 + - - +
261C GLU* 1.3 77.0 - - - +
263C ILE* 1.3 62.0 + - - +
265C ASN* 3.1 9.7 + - + +
266C ALA* 3.0 17.7 + - - +
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ILE* 4.0 14.4 - - + -
259C LEU* 2.9 37.3 + - + +
260C ASN 3.8 4.3 - - - +
262C LEU* 1.3 74.8 - - - +
264C THR* 1.3 58.2 + - - +
266C ALA* 3.1 4.8 + - - +
267C LEU* 2.9 39.4 + - + +
300C LEU* 3.8 34.8 - - + +
303C CYS* 3.9 5.6 - - + -
304C TYR* 3.5 51.6 - - + +
345C ILE* 4.4 7.6 - - + -
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Residues in contact with THR 264 (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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260C ASN 2.7 20.9 + - - -
261C GLU* 3.5 10.8 - - - -
262C LEU 3.3 0.2 - - - -
263C ILE* 1.3 75.6 - - - +
265C ASN* 1.3 55.0 + - - +
267C LEU* 3.3 18.7 + - - +
268C HIS* 2.7 36.9 + - + -
304C TYR* 4.9 0.5 - - - -
355C SER* 4.0 5.9 + - - +
358C LYS* 3.7 17.9 - - + +
359C THR* 2.9 52.3 + - - +
362C ILE* 4.2 1.8 - - + -
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Residues in contact with ASN 265 (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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165C GLU* 2.7 33.3 - - - +
168C TRP* 3.7 20.9 - - + -
169C ASP* 5.1 1.0 - - - +
213C LYS* 2.7 35.0 + - - +
261C GLU 3.1 11.7 + - - +
262C LEU* 3.1 13.8 + - + +
264C THR* 1.3 77.0 - - - +
266C ALA* 1.3 62.6 + - - +
268C HIS* 3.1 27.4 + - - +
269C HIS* 4.4 3.1 - - - -
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Residues in contact with ALA 266 (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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210C PHE* 3.2 23.3 - - + -
213C LYS* 4.1 24.2 - - + -
214C THR* 4.9 1.1 - - + -
217C ILE* 4.3 7.0 - - + -
262C LEU 3.0 9.1 + - - +
263C ILE 3.1 8.5 + - - +
265C ASN* 1.3 80.7 - - - +
267C LEU* 1.3 65.4 + - - +
268C HIS 3.1 1.2 + - - -
269C HIS* 3.2 19.2 + - - -
300C LEU* 4.1 17.3 - - + -
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Residues in contact with LEU 267 (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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210C PHE* 4.9 0.7 - - + -
263C ILE* 2.9 23.3 + - + +
264C THR* 3.5 17.7 - - - +
265C ASN 3.2 0.6 - - - -
266C ALA* 1.3 76.8 - - - +
268C HIS* 1.3 60.8 + - - +
269C HIS 3.1 0.9 + - - -
270C ILE* 3.2 30.2 + - + +
271C PRO* 3.8 2.8 - - - +
300C LEU* 4.3 15.3 - - + -
342C MET* 3.4 29.4 - - + -
345C ILE* 4.0 22.2 - - + -
359C THR* 4.4 15.3 - - + -
362C ILE* 3.8 26.7 - - + +
363C ILE* 4.4 11.4 - - + -
366C ILE* 4.1 1.8 - - + +
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Residues in contact with HIS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C THR* 2.7 39.3 + - + -
265C ASN* 3.2 16.1 + - - +
266C ALA 3.1 1.4 + - - -
267C LEU* 1.3 76.9 - - - +
269C HIS* 1.3 63.2 + - + +
270C ILE 3.4 0.4 - - - -
271C PRO* 3.1 18.2 - - - +
272C ASP* 5.0 1.6 + - - +
358C LYS* 4.9 5.0 + - + +
362C ILE* 3.7 40.0 - - + +
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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