Contacts of the helix formed by residues 251 - 268 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A VAL* 4.2 14.7 - - + +
245A ASP* 3.2 43.3 + - - +
246A PHE* 4.6 1.2 - - + -
248A LYS* 3.0 13.8 + - - +
250A GLU* 1.3 98.6 + - - +
252A ILE* 1.3 62.7 + - - +
253A ASP 3.4 2.9 + - - -
254A LEU* 3.4 18.8 + - + +
255A ALA* 3.0 23.2 + - - +
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PHE 5.3 2.0 - - - +
248A LYS 4.0 0.6 + - - -
249A PRO* 3.1 18.8 + - + +
250A GLU 3.4 3.5 - - - +
251A ASN* 1.3 77.2 - - - +
253A ASP* 1.3 76.8 + - - +
255A ALA* 3.1 4.1 + - + +
256A VAL* 2.9 22.5 + - + +
307A GLN* 3.6 59.7 - - + +
310A PHE* 3.8 24.0 - - + -
311A LYS* 5.0 12.3 - - + -
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Residues in contact with ASP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLU 5.1 1.6 + - - +
251A ASN 3.4 1.0 - - - -
252A ILE* 1.3 93.2 - - - +
254A LEU* 1.3 64.3 + - + +
256A VAL* 3.4 6.3 + - - +
257A GLN* 3.2 33.7 + - - +
307A GLN* 4.2 10.6 + - - -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TYR* 3.2 47.2 - - + +
240A VAL* 4.9 5.2 - - + -
246A PHE* 3.8 6.0 - - + -
251A ASN* 3.4 23.8 + - + +
252A ILE 3.3 0.4 - - - -
253A ASP* 1.3 76.6 - - + +
255A ALA* 1.3 64.2 + - - +
257A GLN* 3.5 22.6 + - - +
258A CYS* 3.1 21.3 + - - +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PHE* 3.4 31.8 - - + +
251A ASN 3.0 15.1 + - - +
252A ILE* 3.2 13.2 - - - +
254A LEU* 1.3 78.0 - - - +
256A VAL* 1.3 56.5 + - - +
258A CYS* 3.3 3.3 + - - +
259A LEU 2.9 24.8 + - - -
310A PHE* 3.2 37.4 - - + -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ILE* 2.9 20.1 + - + +
253A ASP* 3.8 5.2 - - - +
255A ALA* 1.3 73.9 - - - +
257A GLN* 1.3 61.2 + - + +
259A LEU* 3.1 8.4 + - + +
260A ASN* 2.8 33.8 + - - +
305A ASN* 3.3 40.4 - - - +
306A ASN 4.4 1.3 - - - -
307A GLN* 3.6 43.5 - - + +
310A PHE* 4.0 7.0 - - + -
353A ASP* 5.4 0.2 - - - +
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Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A TYR* 3.3 32.3 + - + -
253A ASP* 3.2 21.9 + - - +
254A LEU* 3.7 18.4 - - - +
255A ALA 3.4 0.4 - - - -
256A VAL* 1.3 77.6 - - + +
258A CYS* 1.3 62.1 + - - +
260A ASN* 3.2 4.2 + - - +
261A GLU* 3.0 22.0 + - - +
352A SER 5.4 1.8 + - - -
353A ASP* 3.7 15.1 - - - +
354A PRO* 3.8 34.0 - - + +
355A SER* 4.9 0.5 + - - -
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Residues in contact with CYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A TRP* 3.9 13.7 - - - -
235A VAL* 3.8 24.0 - - - -
236A TRP* 4.1 7.4 - - - -
239A TYR* 3.5 28.0 - - + -
246A PHE* 3.5 37.5 - - + -
254A LEU 3.1 6.8 + - - +
255A ALA 3.7 1.1 - - - +
257A GLN* 1.3 75.1 - - - +
259A LEU* 1.3 67.8 + - - +
261A GLU* 3.0 4.6 + - - +
262A LEU* 2.9 24.3 + - - +
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 3.4 32.8 - - + -
231A TRP* 4.2 12.7 - - + -
255A ALA 2.9 14.3 + - - +
256A VAL* 3.2 12.3 - - - +
258A CYS* 1.3 76.1 - - - +
260A ASN* 1.3 62.7 + - - +
262A LEU* 3.0 6.3 + - - +
263A ILE* 3.0 37.9 + - + +
303A CYS* 3.3 23.3 - - + +
305A ASN 4.1 3.8 - - - +
306A ASN 3.6 25.1 - - - +
309A VAL* 4.1 18.6 - - + -
310A PHE* 3.7 16.2 - - + -
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Residues in contact with ASN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A VAL* 2.8 21.2 + - - +
257A GLN 3.4 8.3 - - - +
258A CYS 3.2 0.2 - - - -
259A LEU* 1.3 74.3 - - - +
261A GLU* 1.3 60.7 + - - +
263A ILE* 3.5 2.8 + - - +
264A THR* 2.9 28.9 + - - -
304A TYR* 3.4 25.1 + - + +
305A ASN* 2.7 55.1 + - - +
350A PRO* 4.5 0.8 - - - +
353A ASP* 3.0 34.2 + - - +
355A SER* 4.7 1.6 - - - -
359A THR* 5.8 0.2 - - - +
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLU* 4.5 10.3 - - - +
235A VAL* 3.7 17.1 - - + +
238A ARG* 2.5 34.2 + - - -
239A TYR* 2.7 29.6 + - - +
257A GLN 3.0 12.3 + - - +
258A CYS* 3.0 8.9 + - - +
260A ASN* 1.3 78.3 - - - +
262A LEU* 1.3 62.1 + - + +
264A THR* 3.5 4.2 + - - -
265A ASN* 3.1 20.1 + - - +
355A SER* 3.4 22.2 + - - +
358A LYS* 3.9 18.6 + - + +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 5.5 1.8 - - + +
168A TRP* 3.8 25.6 - - + -
217A ILE* 3.8 17.6 - - + +
231A TRP* 3.3 54.7 - - + -
232A PRO* 4.3 7.9 - - + -
235A VAL* 3.6 36.1 - - + -
258A CYS* 2.9 13.4 + - - +
259A LEU* 3.5 6.7 - - - +
261A GLU* 1.3 75.8 - - + +
263A ILE* 1.3 60.4 + - - +
265A ASN* 3.0 10.8 + - + +
266A ALA* 2.9 26.3 + - - +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 4.1 14.8 - - + -
259A LEU* 3.0 36.1 + - + +
260A ASN 3.8 4.5 - - - +
262A LEU* 1.3 77.0 - - - +
264A THR* 1.3 58.1 + - - +
266A ALA* 2.9 19.5 + - - +
267A LEU* 2.9 25.5 + - + +
300A LEU* 4.0 33.9 - - + +
303A CYS* 4.0 5.2 - - + -
304A TYR* 3.5 51.8 - - + +
345A ILE* 4.6 6.7 - - + -
359A THR* 5.9 0.4 - - + -
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Residues in contact with THR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASN 2.9 19.3 + - - -
261A GLU* 3.7 8.3 - - - -
263A ILE* 1.3 76.3 - - - +
265A ASN* 1.3 59.9 + - - +
267A LEU* 3.5 17.5 + - - +
268A HIS* 2.8 30.3 + - + -
355A SER* 4.2 3.3 - - - -
358A LYS* 3.8 20.9 - - + +
359A THR* 2.7 53.3 + - - +
362A ILE* 4.3 4.5 - - + -
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Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.1 36.3 - - - +
168A TRP* 3.5 18.3 - - - -
169A ASP* 5.2 0.7 - - - +
213A LYS* 2.8 32.9 + - - +
261A GLU 3.1 13.3 + - - +
262A LEU* 3.0 17.2 + - + +
263A ILE 3.1 0.2 - - - -
264A THR* 1.3 76.2 - - - +
266A ALA* 1.3 62.4 + - - +
268A HIS* 3.2 26.1 + - - +
269A HIS* 4.3 3.1 + - - -
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 3.4 16.2 - - + -
213A LYS* 4.4 19.7 - - + -
214A THR* 4.9 1.3 - - + -
217A ILE* 4.5 5.4 - - + -
262A LEU 2.9 11.7 + - - +
263A ILE* 2.9 12.4 + - - +
265A ASN* 1.3 79.6 - - - +
267A LEU* 1.3 66.0 + - - +
268A HIS 3.0 1.2 + - - -
269A HIS* 3.1 24.2 + - - -
300A LEU* 4.0 19.7 - - + -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 4.5 1.3 - - + -
263A ILE* 2.9 21.2 + - + +
264A THR* 3.7 9.4 - - - +
265A ASN 3.3 0.6 - - - -
266A ALA* 1.3 76.4 - - - +
268A HIS* 1.3 57.5 + - - +
269A HIS 2.9 6.8 + - - -
270A ILE* 3.0 28.3 + - + +
271A PRO* 4.0 2.1 - - - +
297A ILE* 5.3 1.3 - - + -
300A LEU* 4.1 17.9 - - + -
342A MET* 3.5 36.3 - - + -
345A ILE* 4.1 20.2 - - + -
359A THR* 4.1 20.2 - - + -
362A ILE* 3.8 33.2 - - + +
363A ILE* 4.2 6.7 - - + -
366A ILE* 4.4 0.5 - - - +
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Residues in contact with HIS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A THR* 2.8 36.9 + - + -
265A ASN* 3.4 14.5 + - - +
266A ALA 3.0 1.6 + - - -
267A LEU* 1.3 75.4 - - - +
269A HIS* 1.3 62.4 + - + +
270A ILE 3.4 0.4 - - - -
271A PRO* 3.7 11.2 - - - +
272A ASP* 5.3 1.2 + - - +
358A LYS* 5.2 3.1 - - + -
362A ILE* 3.7 38.9 - - + +
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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