Contacts of the helix formed by residues 271 - 289 (chain A) in PDB entry 1PZO
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 THR 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A GLN 5.4 1.1 - - - +
270A ALA* 1.3 71.8 - - - +
272A MET* 1.3 65.6 + - - +
273A ASP* 3.7 9.8 + - - +
274A GLU* 2.3 58.3 + - - +
275A ARG* 3.0 23.0 + - - +
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Residues in contact with MET 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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242A GLY* 5.7 1.3 - - - +
244A ARG* 4.1 12.8 - - - +
271A THR* 1.3 73.1 - - - +
273A ASP* 1.3 57.4 + - - +
275A ARG* 2.5 54.2 - - - +
276A ASN* 2.8 41.7 + - - +
300A CBT 6.3 0.7 - - + -
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Residues in contact with ASP 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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271A THR* 3.1 9.7 - - - +
272A MET* 1.3 75.1 - - - +
274A GLU* 1.3 66.7 + - + +
276A ASN* 3.4 9.5 + - - +
277A ARG* 3.0 57.1 + - - +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN 4.7 7.9 - - - +
40A LEU* 4.0 4.9 - - + -
270A ALA* 3.2 19.7 - - + +
271A THR* 2.3 56.7 + - - +
273A ASP* 1.3 77.4 - - + +
275A ARG* 1.3 63.8 + - - +
277A ARG* 3.3 9.2 + - - +
278A GLN* 3.1 30.6 + - + +
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Residues in contact with ARG 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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40A LEU* 3.9 16.9 - - + +
238A GLY 5.8 0.6 + - - -
242A GLY* 4.1 37.3 - - - -
243A SER 5.7 1.2 + - - -
244A ARG* 3.7 29.5 - - - +
265A THR* 6.0 1.8 - - + -
268A SER* 4.3 10.7 + - - +
270A ALA* 2.8 37.4 + - + +
271A THR* 3.0 11.9 + - - +
272A MET* 2.5 73.7 - - - +
274A GLU* 1.3 77.7 - - - +
276A ASN* 1.3 61.2 + - - +
278A GLN* 3.4 4.9 + - - +
279A ILE* 3.1 26.5 + - - +
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Residues in contact with ASN 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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244A ARG* 2.4 40.5 + - - +
272A MET* 2.8 28.5 + - - +
273A ASP* 3.8 9.7 + - - +
275A ARG* 1.3 71.9 - - - +
277A ARG* 1.3 58.5 + - + +
279A ILE* 3.3 1.1 + - - -
280A ALA* 2.9 26.6 + - - +
300A CBT 3.5 23.4 - - - -
301A CBT 3.1 27.6 - - + +
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Residues in contact with ARG 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 ASP* 3.0 44.1 + - - +
274A GLU* 3.7 7.6 - - - +
276A ASN* 1.3 76.3 - - + +
278A GLN* 1.3 64.9 + - - +
280A ALA* 3.3 7.9 + - + +
281A GLU* 3.0 34.0 + - + +
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Residues in contact with GLN 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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32A LYS 4.6 1.4 - - - +
35A ASP* 4.1 3.3 - - - +
36A ALA* 3.4 26.4 + - + +
39A GLN* 3.4 39.8 + - - +
40A LEU* 3.5 33.2 - - + -
274A GLU* 3.1 18.3 + - - +
275A ARG 3.8 4.0 - - - +
277A ARG* 1.3 81.6 - - - +
279A ILE* 1.3 65.2 + - + +
281A GLU* 3.2 13.7 + - - +
282A ILE* 3.1 29.4 + - + +
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Residues in contact with ILE 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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40A LEU* 5.8 4.3 - - + -
44A VAL* 6.4 0.2 - - + -
244A ARG* 4.3 16.8 - - + +
263A ILE* 4.3 21.3 - - + -
265A THR* 5.5 5.2 - - + -
275A ARG 3.1 16.0 + - - +
276A ASN 3.3 0.9 + - - +
278A GLN* 1.3 75.9 - - + +
280A ALA* 1.3 63.9 + - - +
282A ILE* 3.2 13.3 + - + +
283A GLY 3.0 18.7 + - - -
300A CBT 3.6 41.3 - - + -
301A CBT 3.6 45.3 - - + -
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Residues in contact with ALA 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 ASN 2.9 17.1 + - - +
277A ARG* 3.7 9.9 - - + +
278A GLN 3.2 0.2 - - - -
279A ILE* 1.3 77.5 - - - +
281A GLU* 1.3 62.4 + - - +
283A GLY* 3.4 1.0 + - - -
284A ALA* 2.9 30.1 + - - +
301A CBT 3.4 50.4 + - + +
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Residues in contact with GLU 281 (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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32A LYS* 3.8 35.0 + - + +
277A ARG* 3.0 22.5 + - + +
278A GLN* 3.2 16.5 + - - +
280A ALA* 1.3 77.3 - - - +
282A ILE* 1.3 67.5 + - - +
284A ALA* 3.4 11.2 + - - +
285A SER* 3.2 15.4 + - - -
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Residues in contact with ILE 282 (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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29A THR* 4.1 6.5 - - + +
32A LYS* 4.1 27.1 - - + +
33A VAL* 4.1 18.8 - - + +
36A ALA* 4.1 18.4 - - + -
44A VAL* 4.8 4.7 - - + -
46A TYR* 3.9 28.0 - - + +
263A ILE* 4.3 20.6 - - + -
278A GLN* 3.1 17.9 + - + +
279A ILE* 3.6 19.7 - - + +
281A GLU* 1.3 77.4 - - + +
283A GLY* 1.3 63.2 + - - +
285A SER* 3.1 5.9 + - - -
286A LEU* 3.1 20.7 + - + +
301A CBT 5.9 0.2 - - + -
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Residues in contact with GLY 283 (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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279A ILE 3.0 10.9 + - - -
280A ALA 3.7 0.2 - - - -
282A ILE* 1.3 77.9 - - - +
284A ALA* 1.3 61.7 + - - +
286A LEU* 3.3 5.8 - - - +
287A ILE* 3.2 29.4 + - - +
301A CBT 3.7 42.8 - - - -
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Residues in contact with ALA 284 (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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280A ALA 2.9 17.1 + - - +
281A GLU* 3.7 16.2 - - - +
282A ILE 3.3 0.6 - - - -
283A GLY* 1.3 76.0 - - - +
285A SER* 1.3 56.6 + - - +
287A ILE* 3.4 4.9 + - - +
288A LYS* 3.0 29.1 + - - +
301A CBT 4.9 3.7 - - - +
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Residues in contact with SER 285 (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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28A GLU* 3.6 3.5 + - - +
29A THR* 2.8 35.1 + - - -
32A LYS* 3.7 31.8 - - - -
281A GLU 3.2 1.4 + - - -
282A ILE 3.1 6.9 + - - -
284A ALA* 1.3 75.6 - - - +
286A LEU* 1.3 67.6 + - - +
288A LYS* 3.1 11.2 + - - +
289A HIS* 2.9 38.5 + - - +
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Residues in contact with LEU 286 (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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29A THR* 3.6 8.8 + - - -
46A TYR* 3.8 20.6 - - - +
48A GLU* 3.9 17.0 - - - -
250A LEU* 4.4 7.6 - - + -
259A ARG* 3.9 6.4 + - - +
261A VAL* 4.1 20.4 - - + -
282A ILE* 3.1 11.9 + - + +
283A GLY* 3.3 8.3 - - - +
285A SER* 1.3 77.4 - - - +
287A ILE* 1.3 64.7 + - + +
289A HIS* 3.7 1.8 - - - +
290A TRP* 3.1 50.9 + - + -
301A CBT 3.9 35.7 - - + -
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Residues in contact with ILE 287 (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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225A LEU* 3.5 31.2 - - + -
226A PRO* 4.8 18.2 - - + -
229A TRP* 3.8 31.2 - - + -
250A LEU* 4.5 1.8 - - + -
283A GLY 3.2 17.6 + - - +
284A ALA* 3.8 4.9 - - - +
285A SER 3.2 0.2 - - - -
286A LEU* 1.3 84.8 - - + +
288A LYS* 1.3 68.7 + - - +
290A TRP* 3.1 28.4 + - + +
301A CBT 5.2 1.1 - - + -
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Residues in contact with LYS 288 (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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28A GLU* 5.6 1.8 - - - +
32A LYS* 5.2 11.7 - - - +
284A ALA 3.0 19.3 + - - +
285A SER* 3.1 12.1 + - - +
287A ILE* 1.3 80.6 - - - +
289A HIS* 1.3 91.8 + - + +
290A TRP* 3.5 0.9 + - - +
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Residues in contact with HIS 289 (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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26A HIS* 3.4 52.6 + + + +
28A GLU* 3.5 23.0 - - + +
29A THR* 4.4 2.2 - - - +
259A ARG* 5.0 2.6 + - - -
285A SER* 2.9 38.8 + - - +
286A LEU* 3.7 3.1 - - - +
288A LYS* 1.3 110.0 + - + +
290A TRP* 1.3 67.5 + - - +
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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