Contacts of the helix formed by residues 350 - 361 (chain D) in PDB entry 5ZR1
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 350 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ASP* 6.1 1.3 - - - +
49D PHE* 3.4 14.7 - - + -
349D LYS* 1.3 79.4 - - - +
351D PHE* 1.3 59.7 + - - +
352D GLY* 3.9 9.8 - - - +
353D SER* 2.9 28.5 + - - -
354D LEU* 2.9 27.4 + - - +
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Residues in contact with PHE 351 (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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49D PHE* 3.6 28.3 - + + +
52D LEU* 4.4 4.3 - - + -
301D TRP* 3.5 55.2 - + + +
304D GLN* 3.6 35.4 - - + -
305D TRP* 3.9 38.1 - + + -
308D THR* 5.1 0.2 - - - -
350D ASN* 1.3 74.1 - - - +
352D GLY* 1.3 61.6 + - - +
354D LEU* 4.2 7.0 - - + -
355D CYS* 2.9 44.3 + - + +
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Residues in contact with GLY 352 (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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350D ASN* 3.2 10.1 + - - +
351D PHE* 1.3 80.6 - - - +
353D SER* 1.3 51.9 + - - +
355D CYS* 4.4 3.5 - - - +
356D THR* 2.6 31.5 + - - -
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Residues in contact with SER 353 (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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348D SER* 3.8 4.9 - - - -
349D LYS* 3.3 15.0 + - - -
350D ASN* 2.9 34.4 + - - -
352D GLY* 1.3 75.1 - - - +
354D LEU* 1.3 60.7 + - - +
355D CYS 3.4 0.4 - - - -
356D THR* 3.8 5.4 - - - -
357D ALA* 3.0 30.7 + - - +
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Residues in contact with LEU 354 (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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49D PHE* 3.7 13.5 - - + -
52D LEU* 4.1 19.7 - - + -
53D GLN* 5.4 0.7 - - + -
56D LEU* 4.9 3.6 - - + -
305D TRP* 3.5 32.1 - - + -
344D LEU* 4.0 8.7 - - + +
345D VAL* 3.9 33.2 - - + +
348D SER* 3.4 28.5 - - - +
350D ASN 2.9 17.7 + - - +
351D PHE* 3.4 6.3 + - + +
353D SER* 1.3 74.8 + - - +
355D CYS* 1.3 65.1 + - - +
357D ALA* 3.9 1.5 + - - +
358D ILE* 3.9 18.9 + - - +
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Residues in contact with CYS 355 (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 GLN* 5.8 1.3 - - - -
305D TRP* 5.1 2.5 - - + -
308D THR* 3.7 25.7 - - - +
351D PHE* 2.9 37.4 + - + +
352D GLY* 4.4 3.8 - - - +
354D LEU* 1.3 79.8 - - - +
356D THR* 1.3 60.9 + - - +
358D ILE* 3.8 7.3 - - - +
359D LYS* 3.3 46.0 + - - +
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Residues in contact with THR 356 (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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352D GLY 2.6 23.9 + - - -
353D SER* 3.9 6.5 - - - -
354D LEU 3.3 0.4 - - - -
355D CYS* 1.3 78.6 - - - +
357D ALA* 1.3 58.5 + - - +
359D LYS* 3.0 13.3 + - + +
360D SER* 3.0 33.9 + - - +
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Residues in contact with ALA 357 (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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344D LEU* 3.6 33.2 - - + +
348D SER* 5.6 1.8 - - - -
353D SER 3.0 18.9 + - - +
354D LEU* 3.9 4.0 + - - +
355D CYS 3.5 0.6 - - - -
356D THR* 1.3 78.1 - - - +
358D ILE* 1.3 57.9 + - - +
360D SER* 4.0 7.0 - - - -
361D CYS* 3.1 24.6 + - - -
362D SER* 4.4 2.8 + - - +
363D PHE* 5.2 5.6 + - + +
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Residues in contact with ILE 358 (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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292D LEU* 3.9 14.8 - - + -
305D TRP* 3.6 33.0 - - + -
308D THR* 4.5 13.0 - - + -
309D LEU* 3.8 21.5 - - + -
312D GLU* 3.5 15.7 - - + +
320D LEU* 3.8 24.9 - - + +
341D ILE* 5.6 4.0 - - + -
344D LEU* 4.2 17.0 - - + +
345D VAL* 6.2 0.7 - - + -
354D LEU* 3.9 11.0 + - + +
355D CYS 3.8 11.9 - - - +
357D ALA* 1.3 76.9 - - - +
359D LYS* 1.3 66.8 + - - +
361D CYS* 3.4 14.9 - - - -
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Residues in contact with LYS 359 (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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308D THR* 4.3 8.7 - - + -
311D LYS* 6.2 4.0 - - - -
312D GLU* 3.3 33.3 - - + +
319D ASN* 3.3 22.5 + - - +
355D CYS* 3.3 39.8 - - - +
356D THR* 3.0 12.0 + - + +
358D ILE* 1.3 80.4 - - - +
360D SER* 1.3 59.9 + - - +
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Residues in contact with SER 360 (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 ASN* 3.4 22.7 + - - +
322D ARG* 4.8 3.1 + - - -
356D THR* 3.0 21.6 + - - +
357D ALA* 4.0 5.4 - - - -
359D LYS* 1.3 76.3 - - - +
361D CYS* 1.3 70.7 + - - +
362D SER* 3.4 23.8 + - - -
365D ASP* 5.6 0.2 - - - +
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Residues in contact with CYS 361 (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 ASN* 4.2 2.2 - - + -
320D LEU* 3.7 38.4 - - - -
323D HIS* 3.6 30.1 + - + -
344D LEU* 4.6 5.2 - - - -
357D ALA 3.1 16.1 + - - -
358D ILE* 3.4 26.0 - - - -
360D SER* 1.3 81.4 + - - +
362D SER* 1.3 62.8 + - - +
363D PHE 3.2 3.4 - - - +
364D LEU* 3.4 21.5 + - + -
365D ASP* 3.8 6.6 + - - +
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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