Contacts of the helix formed by residues 355 - 364 (chain A) in PDB entry 1HDZ
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 ILE 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ALA* 4.0 23.8 - - + -
21A PHE* 4.3 7.9 - - + -
23A ILE* 4.0 23.1 - - + -
45A ILE* 4.0 0.2 - - - +
146A PHE* 3.6 42.4 - - + -
351A PRO 4.1 0.4 + - - -
352A PHE* 3.0 20.9 + - + +
354A LYS* 1.3 74.7 - - - +
356A ASN* 1.3 72.0 + - - +
358A GLY* 2.9 12.3 + - - -
359A PHE* 3.1 26.5 + - + -
372A LEU* 3.7 27.4 - - + -
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Residues in contact with ASN 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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20A PRO* 3.3 15.7 - - - +
21A PHE* 2.9 55.7 + - - +
23A ILE* 4.6 6.9 - - - +
353A GLU 4.9 0.8 + - - -
354A LYS 3.2 1.0 + - - -
355A ILE* 1.3 85.9 - - - +
357A GLU* 1.3 62.6 + - - +
359A PHE* 3.1 11.6 + - - +
360A ASP* 2.8 29.8 + - - +
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Residues in contact with GLU 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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350A LEU* 3.9 19.1 - - + +
354A LYS* 2.8 41.8 + - + +
356A ASN* 1.3 78.1 - - - +
358A GLY* 1.3 59.3 + - - +
360A ASP* 3.1 15.5 + - + +
361A LEU* 3.0 43.5 + - - +
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Residues in contact with GLY 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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45A ILE* 3.7 21.4 - - - +
350A LEU* 3.6 15.6 - - - +
354A LYS 3.2 6.6 + - - -
355A ILE* 2.9 9.3 + - - -
357A GLU* 1.3 77.0 - - - +
359A PHE* 1.3 60.2 + - - +
361A LEU* 3.2 6.7 + - - +
362A LEU* 3.2 19.6 + - - +
370A THR* 4.1 12.2 + - - -
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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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21A PHE* 3.9 24.7 - + + -
45A ILE* 3.5 40.8 - - + -
49A ASP* 4.0 4.9 - - + -
50A ASP* 3.0 44.4 - - + +
53A VAL* 4.2 7.6 - - + -
146A PHE* 3.6 23.8 - + - -
355A ILE* 3.1 31.3 + - + -
356A ASN* 3.1 11.5 + - - +
358A GLY* 1.3 77.5 - - - +
360A ASP* 1.3 57.6 + - - +
362A LEU* 3.6 5.0 + - - +
363A HIS* 2.9 43.0 + + + -
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Residues in contact with ASP 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 ASN* 2.8 20.9 + - - +
357A GLU* 3.1 19.1 + - + +
359A PHE* 1.3 74.7 - - - +
361A LEU* 1.3 66.4 + - + +
363A HIS* 3.4 13.0 + - - +
364A SER* 2.8 31.5 + - - +
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Residues in contact with LEU 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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348A HIS* 3.5 46.0 - - + +
350A LEU* 4.5 11.9 - - + -
357A GLU* 3.0 31.9 + - - +
358A GLY* 3.2 11.2 + - - +
360A ASP* 1.3 74.5 - - + +
362A LEU* 1.3 68.4 + - - +
364A SER* 3.2 10.0 + - - -
366A LYS* 3.3 31.2 + - + +
367A SER* 3.0 17.6 + - - +
370A THR* 3.8 9.0 - - - +
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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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45A ILE* 3.8 32.8 - - + +
46A CYS 4.9 3.8 - - - +
47A GLY* 4.9 4.7 - - - +
50A ASP* 3.8 32.5 - - + +
358A GLY 3.2 9.1 + - - +
359A PHE* 3.7 7.4 - - + +
361A LEU* 1.3 74.3 - - - +
363A HIS* 1.3 57.0 + - + +
364A SER 2.7 13.5 + - - -
365A GLY* 2.9 12.3 + - - -
367A SER* 3.0 18.5 + - - +
368A ILE 4.2 15.7 - - - +
369A ARG* 5.4 1.6 - - - +
377A NAD 3.6 36.1 - - - +
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Residues in contact with HIS 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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50A ASP* 2.7 39.5 + - - -
53A VAL* 5.5 8.5 - - + -
359A PHE* 2.9 31.7 + + + +
360A ASP* 3.6 15.1 + - - +
362A LEU* 1.3 80.9 - - + +
364A SER* 1.3 58.5 + - - +
365A GLY 3.6 0.4 - - - -
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Residues in contact with SER 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 ASP* 2.8 18.7 + - - +
361A LEU* 3.2 1.3 + - - -
362A LEU 2.7 5.7 + - - -
363A HIS* 1.3 75.9 - - - +
365A GLY* 1.3 57.1 + - - +
366A LYS* 2.9 43.0 + - - -
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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