Contacts of the helix formed by residues 356 - 367 (chain A) in PDB entry 1Z3S
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 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A TYR 3.7 4.3 - - - -
343A LYS 3.6 10.3 - - - -
344A VAL 3.9 0.7 - - - -
345A GLY 3.6 10.8 - - - -
354A TRP* 2.6 18.8 + - - -
355A LEU* 1.3 75.3 - - - +
357A ASN* 1.3 63.2 + - - -
358A GLU 3.4 2.2 - - - -
359A PHE* 3.7 5.7 + - - +
360A VAL* 3.3 28.6 + - - +
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Residues in contact with ASN 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A TRP* 5.6 1.0 + - - -
342A TYR* 2.8 28.2 + - - +
343A LYS* 3.0 2.5 + - - +
354A TRP* 3.2 23.3 - - - +
356A GLY* 1.3 70.9 - - - -
358A GLU* 1.3 65.5 + - - +
360A VAL* 4.2 3.7 - - - +
361A SER* 3.0 26.9 + - - -
392A LEU* 4.1 13.5 - - + +
399A TYR* 3.5 37.3 - - + -
423A PHE* 3.6 39.0 - - - -
446A TRP* 4.8 0.5 - - - -
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PHE* 3.9 18.8 - - + -
343A LYS* 3.0 32.5 + - + +
344A VAL* 5.5 1.8 - - + -
357A ASN* 1.3 78.1 - - - +
359A PHE* 1.3 64.3 + - - +
361A SER* 3.7 1.9 - - - -
362A GLN* 3.0 51.9 + - - +
394A SER* 5.9 0.2 - - - -
395A GLU* 4.5 5.5 + - - +
399A TYR* 2.6 38.5 + - - +
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Residues in contact with PHE 359 (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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282A ARG 3.5 22.4 - - - -
300A LEU* 3.8 23.3 - - + -
301A THR 3.8 21.1 - - - -
302A PHE* 3.6 44.6 - + + -
303A PRO* 4.3 3.6 - - + -
309A ILE* 3.9 24.9 - - + -
323A THR* 5.0 1.6 - - + -
343A LYS 4.6 0.6 + - - -
355A LEU* 4.2 24.2 - - + +
356A GLY* 3.7 10.2 + - - +
357A ASN 3.4 0.4 - - - -
358A GLU* 1.3 78.9 - - - +
360A VAL* 1.3 66.3 + - + +
362A GLN* 3.0 4.4 + - - +
363A LEU* 2.9 45.5 + - + +
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Residues in contact with VAL 360 (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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325A ILE* 3.7 33.9 - - + -
354A TRP* 5.6 0.4 - - + +
355A LEU* 4.2 11.7 - - + -
356A GLY 3.3 19.7 + - - +
357A ASN* 4.2 1.1 - - - +
359A PHE* 1.3 79.3 - - + +
361A SER* 1.3 51.7 + - - +
363A LEU* 3.3 4.4 + - - -
364A THR* 2.7 55.6 + - + +
390A PHE* 3.9 13.2 - - + -
392A LEU* 3.5 26.9 - - + -
491A ILE* 4.8 5.6 - - + -
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Residues in contact with SER 361 (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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357A ASN 3.0 20.4 + - - -
358A GLU* 3.7 4.5 - - - -
360A VAL* 1.3 77.3 - - - +
362A GLN* 1.3 64.6 + - - +
364A THR* 3.4 5.6 + - - -
365A ASN* 2.8 32.2 + - - +
392A LEU* 3.1 15.3 + - - +
393A SER 2.9 29.7 + - - -
394A SER* 3.7 7.0 + - - -
399A TYR* 3.9 11.0 - - - -
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Residues in contact with GLN 362 (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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302A PHE* 3.6 19.3 - - - -
303A PRO* 2.7 56.2 + - + +
304A ASN* 4.9 2.7 + - - +
305A SER* 5.1 2.3 - - - -
358A GLU* 3.0 39.8 + - - +
359A PHE 3.0 7.9 + - - +
361A SER* 1.3 75.2 - - - +
363A LEU* 1.3 67.2 + - - +
365A ASN* 3.4 5.2 + - - +
366A GLN* 3.4 18.2 + - - +
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Residues in contact with LEU 363 (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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282A ARG* 3.4 31.0 - - + +
283A ASP* 3.7 10.3 - - + -
303A PRO* 4.3 4.9 - - + +
323A THR* 5.1 2.7 - - + -
359A PHE* 2.9 44.3 + - + +
360A VAL* 3.6 5.4 - - - +
362A GLN* 1.3 77.3 - - - +
364A THR* 1.3 59.6 + - + +
366A GLN* 2.9 46.8 + - - +
367A GLN 3.5 0.2 + - - -
369A TYR* 3.1 47.9 - - + +
491A ILE* 4.3 10.8 - - + -
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Residues in contact with THR 364 (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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360A VAL* 2.7 32.4 + - + +
361A SER* 3.4 6.6 + - - -
363A LEU* 1.3 72.8 - - - +
365A ASN* 1.3 57.1 + - - +
366A GLN 3.4 0.2 - - - -
367A GLN 3.2 12.7 - - - +
369A TYR* 3.6 22.0 - - + -
389A HIS* 4.8 3.3 - - - -
390A PHE* 3.7 36.9 - - + +
391A TYR* 3.3 25.6 - - - +
392A LEU 3.2 20.4 + - - -
491A ILE* 4.2 7.0 - - + -
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Residues in contact with ASN 365 (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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361A SER* 2.8 21.8 + - - +
362A GLN* 4.0 4.5 - - - +
363A LEU 3.0 1.4 - - - -
364A THR* 1.3 77.8 + - - +
366A GLN* 1.3 63.0 + - - +
367A GLN 3.4 0.9 - - - -
391A TYR* 3.8 22.3 - - - -
392A LEU 2.7 25.9 + - - +
393A SER* 4.6 3.4 - - - +
394A SER 5.0 1.2 + - - -
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Residues in contact with GLN 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 4.4 22.7 + - - +
303A PRO* 3.7 28.7 - - + +
362A GLN 3.4 8.7 + - - +
363A LEU* 2.9 28.4 + - - +
365A ASN* 1.3 81.5 - - - +
367A GLN* 1.3 65.9 + - + +
369A TYR* 5.2 0.6 + - - -
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 3.9 25.5 - - - +
283A ASP* 4.2 3.8 + - - -
363A LEU 3.5 1.2 + - - +
364A THR 3.2 14.2 - - - +
365A ASN 3.4 0.8 - - - -
366A GLN* 1.3 87.6 - - + +
368A ARG* 1.3 61.8 + - - +
369A TYR* 3.1 49.9 + - + -
389A HIS* 5.0 0.2 - - - -
493A PRO* 3.6 24.2 - - - +
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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