Contacts of the helix formed by residues 265 - 280 (chain A) in PDB entry 1ZHH
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 SER 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A PHE* 3.4 31.6 - - - -
215A ARG* 4.0 11.2 - - - +
239A ALA* 5.0 1.2 + - - -
263A ALA* 3.4 2.1 + - - +
264A CYS* 1.3 80.8 - - - +
266A THR* 1.3 64.5 - - - +
267A ASP* 4.4 1.4 + - - +
268A VAL* 3.2 29.4 + - - +
269A ALA* 3.0 24.9 + - - +
289A TRP* 4.2 7.8 - - - +
295A GLU* 4.8 0.2 - - - -
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Residues in contact with THR 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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215A ARG* 5.3 0.2 - - - +
265A SER* 1.3 73.0 - - - +
267A ASP* 1.3 73.1 + - - +
269A ALA* 3.1 4.9 + - - +
270A LEU* 3.0 38.2 + - + +
289A TRP 3.2 12.7 + - - -
290A GLY* 5.2 0.3 - - - -
292A GLY 5.6 0.9 + - - -
294A ALA* 5.0 7.2 - - + -
295A GLU* 2.7 44.9 + - + +
310A ARG* 5.9 0.3 + - - -
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Residues in contact with ASP 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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239A ALA 4.4 11.0 - - - +
240A THR* 4.1 4.0 - - - -
241A LYS* 3.3 37.0 + - + +
265A SER* 3.5 2.5 + - - +
266A THR* 1.3 91.5 - - - +
268A VAL* 1.3 62.5 + - - +
270A LEU* 3.4 10.1 + - - +
271A GLY 3.0 18.0 + - - -
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Residues in contact with VAL 268 (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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204A LEU* 3.7 34.5 - - + +
205A TYR 4.2 4.9 - - - +
206A PHE* 5.2 0.7 - - + -
237A THR* 3.5 26.9 - - + +
239A ALA* 4.1 11.7 - - - -
240A THR 3.9 17.0 - - - +
244A GLY* 3.8 14.9 - - - -
263A ALA* 4.3 4.9 - - + -
265A SER* 3.2 25.6 + - - +
266A THR 3.2 0.2 - - - -
267A ASP* 1.3 77.4 - - - +
269A ALA* 1.3 63.0 + - - +
271A GLY* 3.3 2.6 + - - -
272A ALA* 3.0 20.1 + - - +
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Residues in contact with ALA 269 (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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263A ALA* 3.7 11.9 - - + -
265A SER 3.0 17.9 + - - +
266A THR 3.1 4.9 + - - +
268A VAL* 1.3 78.0 - - - +
270A LEU* 1.3 58.0 + - + +
272A ALA* 3.1 7.8 + - - +
273A VAL* 2.9 31.6 + - - +
286A ILE* 4.0 3.0 - - + +
287A ASN 3.2 26.9 - - - +
288A GLY* 4.2 7.2 - - - -
295A GLU* 5.3 0.2 - - - +
304A LEU* 4.2 10.8 - - + -
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Residues in contact with LEU 270 (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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241A LYS* 3.8 25.0 - - + +
266A THR* 3.0 37.0 + - + +
267A ASP* 4.0 11.7 - - - +
269A ALA* 1.3 73.2 - - + +
271A GLY* 1.3 63.7 + - - +
273A VAL* 3.4 12.4 + - + +
274A ASP* 3.3 18.2 + - - +
294A ALA* 4.1 22.9 - - + +
295A GLU* 5.1 1.3 - - + -
298A ALA* 4.0 26.0 - - + -
304A LEU* 4.2 17.7 - - + -
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Residues in contact with GLY 271 (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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241A LYS* 3.5 36.2 - - - +
245A TYR* 3.5 20.0 - - - +
267A ASP 3.0 10.5 + - - -
268A VAL 3.3 3.1 + - - -
270A LEU* 1.3 73.8 - - - +
272A ALA* 1.3 63.0 + - - +
274A ASP* 3.3 5.7 + - - +
275A ALA 3.2 15.6 + - - -
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Residues in contact with ALA 272 (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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204A LEU* 3.8 21.1 - - + -
244A GLY 4.0 1.6 - - - -
248A ALA* 3.8 17.4 - - + +
261A ILE* 5.3 2.0 - - + -
268A VAL 3.0 12.7 + - - +
269A ALA* 3.1 3.3 + - - +
271A GLY* 1.3 75.4 - - - +
273A VAL* 1.3 57.1 + - - +
275A ALA* 3.1 3.2 + - - +
276A LEU* 2.9 33.4 + - - +
286A ILE* 3.4 27.6 - - + -
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Residues in contact with VAL 273 (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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269A ALA 2.9 18.5 + - - +
270A LEU* 3.5 18.2 - - + +
271A GLY 3.2 0.4 - - - -
272A ALA* 1.3 75.5 - - - +
274A ASP* 1.3 68.2 + - - +
276A LEU* 3.3 10.7 + - - +
277A ALA* 3.1 22.7 + - + +
282A GLU* 5.9 0.2 - - - +
286A ILE* 4.1 8.1 - - + -
303A ASP* 3.5 48.2 - - + +
304A LEU* 3.9 20.9 - - + -
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Residues in contact with ASP 274 (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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241A LYS* 3.5 25.6 + - - -
245A TYR* 4.2 13.5 - - + -
270A LEU 3.3 10.3 + - - +
271A GLY* 3.3 11.1 + - - +
273A VAL* 1.3 84.0 - - - +
275A ALA* 1.3 57.2 + - - +
277A ALA* 3.3 7.7 + - - +
278A GLU* 3.0 28.9 + - - +
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Residues in contact with ALA 275 (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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245A TYR* 3.8 25.5 - - + +
248A ALA* 3.8 24.9 - - + -
249A LYS* 4.0 12.8 - - + +
252A LEU* 5.5 0.4 - - + -
271A GLY 3.2 10.6 + - - +
272A ALA 3.1 8.6 + - - +
274A ASP* 1.3 76.3 - - - +
276A LEU* 1.3 63.2 + - + +
278A GLU* 3.3 4.1 + - - +
279A LEU* 3.0 32.5 + - + +
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Residues in contact with LEU 276 (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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248A ALA* 5.9 0.4 - - + -
252A LEU* 3.7 26.7 - - + -
261A ILE* 4.4 8.7 - - + -
272A ALA 2.9 19.1 + - - +
273A VAL* 3.6 9.4 - - + +
275A ALA* 1.3 76.2 - - + +
277A ALA* 1.3 56.8 + - - +
279A LEU* 3.3 0.8 + - - -
280A GLY* 3.0 8.5 + - - -
281A ARG* 2.8 54.7 + - + +
282A GLU* 4.0 9.1 + - + +
284A ILE* 3.5 34.5 - - + +
286A ILE* 3.9 28.0 - - + -
303A ASP 5.7 0.9 - - - +
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Residues in contact with ALA 277 (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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273A VAL* 3.1 14.7 + - + +
274A ASP* 3.7 9.9 - - - +
276A LEU* 1.3 74.8 - - - +
278A GLU* 1.3 63.0 + - - +
280A GLY* 3.3 11.1 + - - -
282A GLU* 3.7 23.6 - - + +
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Residues in contact with GLU 278 (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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245A TYR* 2.5 32.7 + - - -
249A LYS* 3.3 26.4 + - - -
274A ASP 3.0 16.3 + - - +
275A ALA 3.6 5.6 - - - +
277A ALA* 1.3 80.1 - - - +
279A LEU* 1.3 67.0 + - + +
280A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 279 (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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249A LYS* 4.3 28.0 - - + +
252A LEU* 3.9 34.8 - - + -
253A ALA 5.8 0.4 - - - +
275A ALA* 3.0 21.3 + - + +
276A LEU 4.1 1.1 - - - +
278A GLU* 1.3 86.5 - - + +
280A GLY* 1.3 63.0 + - - +
281A ARG* 3.5 21.0 + - + +
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Residues in contact with GLY 280 (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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276A LEU 3.0 3.4 + - - -
277A ALA 3.3 6.5 + - - -
278A GLU 3.3 4.8 + - - -
279A LEU* 1.3 79.3 - - - +
281A ARG* 1.3 61.6 - - - +
282A GLU* 3.4 20.1 + - - +
283A ASP* 4.2 3.3 - - - +
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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