Contacts of the helix formed by residues 251 - 268 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B VAL* 4.2 19.7 - - + +
245B ASP* 3.1 36.9 + - - +
246B PHE* 4.3 1.7 - - - -
248B LYS* 2.8 27.9 + - - +
250B GLU* 1.3 83.4 - - - +
252B ILE* 1.3 58.2 + - - +
253B ASP* 3.2 3.8 + - - -
254B LEU* 3.3 13.5 + - + +
255B ALA* 2.9 27.0 + - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PHE 4.4 8.5 - - - +
247B ALA 5.9 0.2 - - - -
248B LYS 3.7 2.7 + - - +
249B PRO* 3.3 34.5 - - + +
250B GLU 3.5 1.5 - - - +
251B ASN* 1.3 77.2 - - - +
253B ASP* 1.3 73.8 + - - +
255B ALA* 3.2 8.2 - - - +
256B VAL* 2.9 28.5 + - + +
307B GLN* 5.4 13.2 - - + +
310B PHE* 5.0 10.3 - - + +
311B LYS* 3.8 32.1 - - + +
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Residues in contact with ASP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B GLU 5.0 4.2 + - - +
251B ASN 3.2 1.2 - - - -
252B ILE* 1.3 89.1 - - - +
254B LEU* 1.3 66.3 + - + +
256B VAL* 3.4 5.9 + - - +
257B GLN* 3.4 23.8 + - - +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TYR* 3.3 44.4 - - + +
240B VAL* 4.9 4.0 - - + -
246B PHE* 3.9 4.0 - - + -
251B ASN* 3.3 15.6 + - + +
253B ASP* 1.3 80.3 - - + +
255B ALA* 1.3 64.9 + - - +
257B GLN* 3.1 30.8 + - - +
258B CYS* 3.1 19.6 + - - +
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PHE* 3.3 32.9 - - + +
251B ASN 2.9 14.6 + - - +
252B ILE* 3.2 15.9 - - - +
254B LEU* 1.3 76.7 - - - +
256B VAL* 1.3 57.4 + - - +
258B CYS* 3.1 5.5 + - - +
259B LEU 2.9 23.6 + - - -
310B PHE* 3.3 32.2 - - + -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ILE 2.9 20.0 + - - +
253B ASP* 3.9 6.1 - - - +
254B LEU 3.3 0.2 - - - -
255B ALA* 1.3 75.4 - - - +
257B GLN* 1.3 61.4 + - + +
259B LEU* 3.4 8.0 - - + +
260B ASN* 3.0 23.1 + - - +
305B ASN* 3.6 42.0 - - - +
306B ASN 4.1 5.4 - - - +
307B GLN* 3.6 42.8 - - + +
310B PHE* 4.1 6.3 - - + -
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Residues in contact with GLN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TYR* 3.4 19.3 + - + -
253B ASP 3.4 15.5 + - - +
254B LEU* 3.1 31.5 + - - +
255B ALA 3.1 0.6 - - - -
256B VAL* 1.3 77.9 - - + +
258B CYS* 1.3 62.3 + - - +
260B ASN* 3.2 6.1 + - - +
261B GLU* 3.2 16.1 + - - +
352B SER* 4.3 8.7 + - - -
353B ASP* 4.1 12.2 - - - +
354B PRO* 3.3 37.5 - - + +
355B SER* 4.8 1.7 + - - -
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Residues in contact with CYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B TRP* 4.1 1.3 - - + -
235B VAL* 3.7 17.7 - - - -
236B TRP* 3.7 32.5 - - - -
239B TYR* 3.5 17.0 - - + -
246B PHE* 3.5 26.5 - - + -
254B LEU 3.1 7.0 + - - +
255B ALA 3.4 8.5 - - - +
257B GLN* 1.3 71.8 - - - +
259B LEU* 1.3 69.5 + - - +
261B GLU* 2.8 14.8 + - - +
262B LEU* 2.9 28.5 + - - +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ILE* 3.5 31.2 - - + -
231B TRP* 4.2 12.2 - - + -
255B ALA 2.9 13.2 + - - +
256B VAL* 3.4 12.6 - - - +
258B CYS* 1.3 76.9 - - - +
260B ASN* 1.3 65.1 + - - +
262B LEU* 3.0 4.5 + - - +
263B ILE* 2.9 40.5 + - + +
303B CYS* 3.2 21.1 - - + +
305B ASN 4.1 3.8 - - - +
306B ASN 3.4 27.6 - - - +
309B VAL* 3.8 24.2 - - + -
310B PHE* 3.9 11.4 - - + -
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Residues in contact with ASN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 3.0 20.3 + - - +
257B GLN 3.5 7.6 - - - +
258B CYS 3.2 0.2 - - - -
259B LEU* 1.3 76.7 - - - +
261B GLU* 1.3 58.1 + - - +
263B ILE* 3.5 3.9 + - - +
264B THR* 2.8 32.0 + - - -
304B TYR* 3.3 26.0 - - + -
305B ASN* 2.7 53.7 + - - -
350B PRO* 4.5 0.4 - - - +
353B ASP* 3.1 31.7 + - - +
355B SER* 4.6 1.8 - - - -
359B THR* 5.8 0.2 - - - +
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 4.4 14.0 - - - +
235B VAL* 3.6 12.9 - - + +
238B ARG* 2.6 37.7 + - - -
239B TYR* 2.7 30.4 + - - +
257B GLN 3.2 4.0 + - - +
258B CYS 2.8 15.1 + - - +
260B ASN* 1.3 71.1 - - - +
262B LEU* 1.3 64.5 + - + +
264B THR* 3.3 4.4 + - - -
265B ASN* 3.0 21.8 + - - +
355B SER* 3.4 21.0 + - - +
358B LYS* 3.7 21.8 + - + +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 5.7 1.8 - - - +
168B TRP* 4.4 18.1 - - + -
217B ILE* 3.7 24.5 - - + +
231B TRP* 3.3 45.8 - - + -
232B PRO* 4.0 22.0 - - + -
235B VAL* 3.6 26.2 - - + -
258B CYS* 2.9 27.7 + - - +
259B LEU* 3.6 4.7 - - - +
261B GLU* 1.3 76.7 - - + +
263B ILE* 1.3 63.4 + - - +
265B ASN* 3.0 9.9 + - + +
266B ALA* 3.0 18.5 + - - +
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 3.9 18.8 - - + -
259B LEU* 2.9 41.3 + - + +
260B ASN 3.7 5.2 - - - +
261B GLU 3.2 0.2 - - - -
262B LEU* 1.3 75.9 - - - +
264B THR* 1.3 62.7 + - - +
266B ALA* 3.1 4.8 + - - +
267B LEU* 3.0 33.2 + - + +
300B LEU* 4.1 20.4 - - + +
303B CYS* 3.9 4.3 - - + -
304B TYR* 3.4 52.7 - - + +
345B ILE* 4.4 17.0 - - + -
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Residues in contact with THR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ASN 2.8 22.6 + - - -
261B GLU* 3.3 8.3 + - - -
263B ILE* 1.3 76.4 - - - +
265B ASN* 1.3 55.2 + - - +
267B LEU* 3.5 16.4 + - - +
268B HIS* 2.8 35.1 + - + -
304B TYR* 5.0 0.5 - - - -
355B SER* 4.1 4.1 - - - -
358B LYS* 3.7 21.3 - - + +
359B THR* 2.7 51.8 + - - +
362B ILE* 4.1 6.1 - - + -
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Residues in contact with ASN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLU* 3.3 32.2 - - - +
168B TRP* 3.5 14.7 - - + -
169B ASP* 5.4 0.3 - - - +
213B LYS* 2.8 39.9 + - - +
261B GLU 3.0 12.2 + - - +
262B LEU* 3.1 16.1 - - + +
264B THR* 1.3 75.9 - - - +
266B ALA* 1.3 63.8 + - - +
268B HIS* 3.1 26.9 + - - +
269B HIS* 4.5 2.4 + - - -
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B PHE* 3.2 20.7 - - + -
213B LYS* 4.2 27.8 - - + -
214B THR* 5.0 1.6 - - + -
217B ILE* 4.3 6.5 - - + -
262B LEU 3.0 11.9 + - - +
263B ILE 3.1 8.9 + - - +
265B ASN* 1.3 81.7 - - - +
267B LEU* 1.3 62.9 - - - +
268B HIS 3.0 1.6 + - - -
269B HIS* 3.1 15.2 + - - -
300B LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B PHE* 4.3 1.1 - - + -
263B ILE* 3.0 21.5 + - + +
264B THR* 3.7 12.8 - - - +
265B ASN 3.3 0.6 - - - -
266B ALA* 1.3 75.1 - - - +
268B HIS* 1.3 57.7 + - - +
269B HIS 2.9 6.4 + - - -
270B ILE* 3.0 30.6 + - + +
271B PRO* 3.8 2.8 - - - +
297B ILE* 5.9 2.2 - - + -
300B LEU* 3.8 22.7 - - + -
342B MET* 3.4 37.0 - - + -
345B ILE* 4.0 17.0 - - + -
359B THR* 4.4 14.6 - - + -
362B ILE* 3.9 31.8 - - + +
363B ILE* 4.5 3.1 - - + -
366B ILE* 4.4 0.8 - - + +
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Residues in contact with HIS 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 2.8 38.7 + - + -
265B ASN* 3.1 15.6 + - - +
266B ALA 3.0 1.2 + - - -
267B LEU* 1.3 74.8 - - - +
269B HIS* 1.3 61.8 + - + +
270B ILE 3.4 0.4 - - - -
271B PRO* 3.2 16.9 - - - +
272B ASP* 5.2 1.6 + - - +
358B LYS* 5.1 5.3 + - + -
362B ILE* 3.7 37.2 - - + +
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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
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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