Contacts of the helix formed by residues 316 - 327 (chain D) in PDB entry 1PZY
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 GLY 316 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311D TYR* 3.8 7.6 - - - -
315D GLY* 1.3 70.7 - - - -
317D GLU* 1.3 62.9 + - - +
318D ASP 3.2 2.5 - - - -
319D ASP* 3.0 20.6 + - - +
320D ASP* 2.9 20.1 + - - +
359D ARG* 4.4 2.0 - - - -
363D ILE* 3.6 13.8 - - - +
406D NAG 2.9 26.8 + - - -
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Residues in contact with GLU 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ARG* 2.7 45.2 + - - +
229D ALA* 3.8 30.3 - - + +
308D PRO* 4.5 1.4 - - + +
311D TYR* 3.6 34.7 - - + +
313D GLY 5.0 3.1 - - - +
314D ALA* 4.9 0.3 - - - -
315D GLY* 3.3 24.6 + - - +
316D GLY* 1.3 71.9 - - - +
318D ASP* 1.3 75.2 + - - +
320D ASP* 3.2 5.3 + - - +
321D ILE* 3.0 33.3 + - + +
406D NAG 5.1 0.2 + - - -
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Residues in contact with ASP 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D ARG* 4.3 4.3 - - - +
286D TYR* 4.0 1.9 + - - -
289D TYR* 3.6 16.6 - - - -
290D PHE* 3.8 11.4 + - - +
291D GLY* 3.6 24.3 + - - +
316D GLY 3.7 0.3 - - - -
317D GLU* 1.3 98.2 + - - +
319D ASP* 1.3 60.6 + - - +
321D ILE* 3.4 12.0 + - + +
322D TYR* 3.0 24.8 + - - +
406D NAG 2.7 47.2 + - - -
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Residues in contact with ASP 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C MET* 4.3 10.6 - - + +
286D TYR* 2.6 34.5 + - - -
288D GLN* 4.5 3.9 - - - +
289D TYR* 5.1 0.5 - - - -
290D PHE 5.4 0.3 + - - -
316D GLY* 3.0 13.2 + - - +
318D ASP* 1.3 80.3 - - - +
320D ASP* 1.3 59.9 + - - +
322D TYR* 3.0 9.8 + - + +
323D ASN* 2.8 36.0 + - - +
363D ILE* 4.3 15.3 - - + -
406D NAG 2.6 39.2 + - - +
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Residues in contact with ASP 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D PRO* 3.3 12.9 - - + +
311D TYR* 3.0 41.3 + - + +
316D GLY 2.9 6.2 + - - +
317D GLU 3.4 8.7 - - - +
319D ASP* 1.3 76.4 - - - +
321D ILE* 1.3 56.4 + - - +
323D ASN* 3.2 7.2 + - - +
324D ARG* 3.0 59.4 + - - +
362D ARG 4.2 1.4 - - - +
363D ILE* 4.5 2.6 - - + +
366D THR* 2.6 34.5 + - - +
369D THR* 4.5 4.0 + - - -
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Residues in contact with ILE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ARG* 5.2 5.8 - - - +
229D ALA* 5.0 1.6 - - + -
232D LEU* 5.2 0.9 - - + -
290D PHE* 3.7 25.8 - - + +
296D LEU* 5.7 0.2 - - + -
304D ILE* 4.6 5.6 - - + -
307D PHE* 3.5 58.8 - - + -
308D PRO* 4.0 11.0 - - + -
317D GLU* 3.0 27.8 + - + +
318D ASP* 3.5 16.4 - - + +
320D ASP* 1.3 73.8 - - - +
322D TYR* 1.3 66.5 + - - +
324D ARG* 3.0 19.9 + - - +
325D LEU* 3.1 15.0 + - + +
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Residues in contact with TYR 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLU* 6.1 0.4 - - - -
114C LYS* 3.9 20.4 + - - -
287D VAL* 4.5 7.2 + - - +
288D GLN* 3.4 57.7 - - + +
289D TYR 5.5 0.2 - - - -
290D PHE* 4.2 12.6 - + + -
318D ASP 3.0 13.9 + - - +
319D ASP* 3.2 10.1 - - - +
321D ILE* 1.3 76.9 - - - +
323D ASN* 1.3 76.9 + - - +
325D LEU* 3.1 21.4 + - + +
326D ALA* 3.3 19.8 + - + +
332D VAL* 3.6 31.8 - - + +
334D ARG* 5.4 0.2 - - - -
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Residues in contact with ASN 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ASP* 2.8 19.4 + - - +
320D ASP* 3.4 7.4 - - - +
321D ILE 3.2 0.2 - - - -
322D TYR* 1.3 90.5 - - - +
324D ARG* 1.3 63.0 + - - +
326D ALA* 3.2 6.9 + - - +
327D PHE* 2.9 40.6 + - + -
363D ILE* 3.0 36.0 + - - +
366D THR* 3.4 19.2 + - + -
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Residues in contact with ARG 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D ILE* 3.4 31.5 + - + -
305D ASN 3.5 5.9 + - - -
306D GLY 2.8 25.1 + - - -
307D PHE 3.4 6.1 - - - -
308D PRO* 3.0 34.2 - - - +
320D ASP* 3.0 32.1 + - - +
321D ILE* 3.0 12.1 + - - +
323D ASN* 1.3 76.7 - - - +
325D LEU* 1.3 63.5 + - - +
327D PHE* 3.2 3.2 + - - +
328D ARG* 3.1 27.2 + - - +
366D THR* 3.6 9.4 - - + -
369D THR* 4.6 1.4 + - - -
370D MET* 3.5 42.2 + - + +
373D ASP* 2.8 31.6 + - - +
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D PRO* 3.5 41.1 - - + -
290D PHE* 3.8 28.7 - - + -
296D LEU* 4.1 14.4 - - + -
304D ILE* 4.0 15.5 - - + -
321D ILE* 3.1 13.0 + - + +
322D TYR* 3.1 10.0 + - + +
324D ARG* 1.3 77.6 - - - +
326D ALA* 1.3 61.4 + - - +
328D ARG* 3.0 9.4 + - - -
329D GLY 3.2 0.2 + - - -
330D MET* 2.8 51.0 + - + +
331D SER 5.0 0.2 - - - +
332D VAL* 4.4 14.1 - - + -
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D TYR* 3.3 17.7 + - + +
323D ASN* 3.2 10.4 + - - +
325D LEU* 1.3 72.6 - - - +
327D PHE* 1.3 63.4 + - + +
328D ARG 2.8 11.2 + - - -
329D GLY* 2.9 14.3 + - - -
330D MET 3.8 10.5 + - - +
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Residues in contact with PHE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D ASN* 2.9 36.5 + - + +
324D ARG 3.7 4.9 - - - +
326D ALA* 1.3 77.4 - - + +
328D ARG* 1.3 84.9 + - - +
329D GLY 3.5 0.4 - - - -
366D THR* 3.9 15.3 - - + -
367D LYS* 3.2 74.7 + - + +
370D MET* 4.0 3.8 - - - -
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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