Contacts of the helix formed by residues 354 - 364 (chain A) in PDB entry 1D1T
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 LYS 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A LEU* 4.0 26.0 - - + +
351A PRO* 2.7 46.8 + - + +
353A LYS* 1.3 77.5 - - + +
355A ILE* 1.3 64.0 + - - -
356A SER* 3.2 3.4 - - - -
357A GLU* 2.8 25.0 + - + +
358A GLY* 3.2 7.8 + - - -
372A LEU* 4.4 2.9 - - - -
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Residues in contact with ILE 355 (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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12A ALA* 3.7 22.2 - - + -
21A PHE* 3.9 25.1 - - + -
23A ILE* 4.6 12.1 - - + -
45A ILE* 4.1 0.3 - - - +
146A PHE* 3.7 30.7 - - + -
352A PHE* 3.2 20.1 + - + +
353A LYS 3.1 7.6 - - - +
354A LYS* 1.3 75.1 - - - +
356A SER* 1.3 72.6 + - - +
358A GLY* 3.0 12.3 + - - -
359A PHE* 3.0 31.3 + - + -
372A LEU* 3.6 28.0 - - + -
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Residues in contact with SER 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* 5.4 7.8 - - - +
21A PHE* 5.7 6.1 - - - -
353A LYS 4.7 1.5 + - - -
354A LYS* 3.1 1.5 + - - -
355A ILE* 1.3 85.6 - - - +
357A GLU* 1.3 62.4 + - - +
359A PHE* 3.3 8.7 + - - +
360A GLU* 3.0 20.6 + - - +
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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 19.5 - - + -
354A LYS* 2.8 25.9 + - + +
356A SER* 1.3 73.1 - - - +
358A GLY* 1.3 57.9 + - - +
360A GLU* 2.7 29.9 + - - +
361A LEU* 2.9 31.4 + - + +
408A ZN 2.0 36.5 - - - -
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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 21.3 - - - +
350A LEU* 4.2 3.7 - - - +
354A LYS 3.2 4.6 + - - -
355A ILE 3.0 8.4 + - - -
357A GLU* 1.3 78.0 - - - +
359A PHE* 1.3 55.5 + - - +
361A LEU* 3.4 6.8 + - - +
362A LEU* 3.1 26.3 + - - +
370A THR* 3.9 23.1 + - - -
372A LEU* 5.4 0.4 - - - -
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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* 3.6 14.4 - + + -
45A ILE* 3.5 32.3 - - + -
49A ASP* 4.1 4.9 - - + -
50A ASP* 3.3 37.9 - - + -
53A ILE* 3.8 24.0 - - + -
146A PHE* 3.5 24.7 - + - -
355A ILE* 3.0 40.1 + - + +
356A SER* 3.8 10.1 - - - +
357A GLU 3.2 0.2 - - - -
358A GLY* 1.3 73.9 - - - +
360A GLU* 1.3 64.7 + - - +
362A LEU* 3.8 5.8 - - + +
363A ASN* 2.8 33.6 + - - +
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Residues in contact with GLU 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 SER 3.0 12.4 + - - +
357A GLU* 2.7 22.6 + - - +
359A PHE* 1.3 73.1 - - - +
361A LEU* 1.3 54.0 + - + +
363A ASN* 3.4 4.7 + - - +
364A SER* 2.7 37.6 + - - +
366A GLN* 5.5 2.3 - - - +
408A ZN 1.9 37.2 - - - -
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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* 3.7 39.9 - - + +
350A LEU* 4.9 3.8 - - + -
357A GLU* 2.9 44.3 + - + +
358A GLY* 3.7 8.5 - - - +
360A GLU* 1.3 75.8 - - - +
362A LEU* 1.3 62.3 + - - +
364A SER* 3.2 5.3 + - - +
365A GLY 3.2 0.2 + - - -
366A GLN* 2.9 58.0 + - + +
367A SER* 3.0 17.9 + - - +
370A THR* 4.9 0.7 - - - +
408A ZN 4.0 7.9 - - - -
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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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45A ILE* 4.0 32.3 - - + +
46A CYS 4.6 0.2 - - - +
47A ARG* 3.4 45.5 + - - +
50A ASP* 4.4 17.9 - - + +
228A LYS* 5.5 1.0 + - - -
358A GLY 3.1 14.4 + - - +
359A PHE* 3.8 5.6 - - + +
361A LEU* 1.3 75.4 - - - +
363A ASN* 1.3 59.6 + - - +
364A SER 3.1 5.4 + - - -
365A GLY* 3.2 12.5 + - - -
367A SER* 3.0 15.8 + - - +
368A ILE 4.4 14.1 - - - +
369A ARG* 5.4 2.0 - - - +
370A THR* 5.7 0.7 - - - +
1377A NAD 3.9 29.6 + - - +
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Residues in contact with ASN 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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47A ARG* 2.8 29.7 + - - +
50A ASP* 2.9 26.3 + - - +
54A LYS* 3.1 23.0 + - - +
359A PHE* 2.8 27.7 + - - +
360A GLU* 3.7 3.8 - - - +
362A LEU* 1.3 80.4 - - - +
364A SER* 1.3 58.1 + - - +
365A GLY 3.5 0.2 - - - -
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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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225A ASN* 5.9 0.2 - - - -
360A GLU* 2.7 27.4 + - - +
361A LEU* 3.2 13.3 + - - +
362A LEU 3.1 0.2 - - - -
363A ASN* 1.3 77.8 - - - +
365A GLY* 1.3 61.2 + - - +
366A GLN* 3.3 27.1 + - - +
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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