Contacts of the helix formed by residues 355 - 364 (chain A) in PDB entry 4ZTZ
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 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A HIS* 4.4 0.4 - - - -
353A VAL* 3.1 21.5 - - - +
354A ASN* 1.3 80.5 - - - +
356A LEU* 1.3 61.0 + - - +
357A ALA* 3.6 12.1 + - - +
358A GLU* 3.9 12.6 + - - +
359A VAL* 2.8 28.6 + - - +
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Residues in contact with LEU 356 (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 HIS* 3.5 37.6 + - + +
294A THR* 5.2 0.7 - - - +
355A SER* 1.3 74.9 + - - +
357A ALA* 1.3 58.3 + - - +
359A VAL* 3.2 12.4 - - + +
360A HIS* 2.9 31.9 + - - +
369A LEU* 4.5 11.2 - - + -
371A LYS* 4.9 7.9 - - - +
399A ASP* 4.0 35.0 - - + +
402A ALA* 4.8 5.8 - - + -
403A THR* 3.6 37.2 - - + +
406A VAL* 4.9 3.1 - - + -
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Residues in contact with ALA 357 (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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355A SER* 3.3 8.5 + - - +
356A LEU* 1.3 79.8 - - - +
358A GLU* 1.3 63.4 + - + +
360A HIS* 3.7 2.1 + - - +
361A ARG* 2.9 28.4 + - - +
369A LEU* 3.7 39.3 + - + +
371A LYS* 6.1 2.9 - - + -
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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
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312A TRP* 3.2 26.2 - - + -
352A SER* 3.2 19.6 + - - +
353A VAL* 3.6 27.1 - - + +
355A SER* 3.3 13.1 + - - +
356A LEU 3.2 0.4 - - - -
357A ALA* 1.3 79.3 - - + +
359A VAL* 1.3 60.6 + - - +
360A HIS 3.2 0.2 - - - -
361A ARG* 3.2 27.3 + - - +
362A LEU* 2.9 27.5 + - - +
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Residues in contact with VAL 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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269A HIS* 4.0 15.3 - - + -
294A THR 5.0 0.9 - - - +
298A HIS* 3.5 35.0 - - + -
352A SER* 4.6 1.3 - - - -
353A VAL 4.1 8.0 + - - +
354A ASN 4.8 0.9 - - - +
355A SER 2.8 20.0 + - - +
356A LEU* 3.2 26.2 - - + +
358A GLU* 1.3 72.9 - - - +
360A HIS* 1.3 60.8 + - - +
362A LEU* 4.2 4.0 - - - -
363A TYR* 2.9 51.2 + - + +
406A VAL* 4.1 10.1 - - + +
410A GLN* 3.6 8.7 - - - +
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Residues in contact with HIS 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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356A LEU 2.9 19.0 + - - +
357A ALA 3.7 4.4 + - - +
359A VAL* 1.3 75.3 - - - +
361A ARG* 1.3 58.4 + - - +
362A LEU 3.0 4.7 - - - -
364A VAL* 2.9 40.7 + - + +
365A GLY 2.9 21.8 + - - -
366A GLY* 4.5 8.0 + - - -
367A PRO* 4.1 21.5 + - + -
368A PRO* 5.9 0.2 - - - +
369A LEU* 3.8 20.8 + - + +
401A TRP* 6.0 0.4 - - - -
402A ALA* 3.6 27.4 - - + +
405A GLU* 2.7 28.2 + - - -
406A VAL* 3.6 11.4 - - + -
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Residues in contact with ARG 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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312A TRP* 4.2 16.8 - - - -
348A LEU 5.9 0.2 + - - -
349A ASP* 5.6 3.8 + - - -
351A SER 5.8 0.6 + - - -
352A SER* 5.4 2.0 + - - -
357A ALA 2.9 18.6 + - - +
358A GLU* 3.2 30.2 + - - +
360A HIS* 1.3 80.0 + - - +
362A LEU* 1.3 60.9 + - - +
365A GLY* 3.2 21.9 - - - +
366A GLY 5.0 10.3 - - - +
368A PRO* 5.8 11.9 - - + -
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Residues in contact with LEU 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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298A HIS* 4.1 8.3 - - + +
302A SER* 4.3 7.2 - - - +
349A ASP 4.1 10.1 - - - +
350A ILE 4.0 16.2 - - - +
351A SER* 3.9 21.8 - - - +
352A SER* 3.7 27.8 - - - +
358A GLU 2.9 15.3 + - - +
359A VAL* 3.6 5.4 - - - +
360A HIS 3.0 0.4 - - - -
361A ARG* 1.3 83.8 - - - +
363A TYR* 1.3 87.1 + - + +
364A VAL 4.8 0.2 - - - -
365A GLY* 4.4 2.4 + - - -
1081A ARG* 5.1 3.4 - - - +
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Residues in contact with TYR 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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298A HIS* 3.2 29.1 + + - -
301A ILE* 3.3 28.9 - - + +
302A SER* 3.4 12.3 + - - -
359A VAL* 2.9 27.8 + - + +
362A LEU* 1.3 90.1 - - + +
364A VAL* 1.3 62.0 + - + +
406A VAL* 4.7 11.2 - - + -
409A GLN* 3.4 35.4 - - + +
410A GLN* 3.2 45.1 - - + -
413A LEU* 3.9 28.7 - - + -
1081A ARG* 5.0 5.4 - - - -
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Residues in contact with VAL 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 HIS* 2.9 41.1 + - + +
362A LEU 4.8 0.2 - - - -
363A TYR* 1.3 80.4 - - - +
365A GLY* 1.3 63.0 + - - +
366A GLY* 3.2 8.8 + - - +
405A GLU* 3.6 42.4 - - + +
406A VAL* 3.9 13.2 - - + +
409A GLN* 5.4 1.8 - - + -
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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