Contacts of the helix formed by residues 352 - 361 (chain A) in PDB entry 1Y8G
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 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU* 3.5 16.1 - - - +
118A VAL 4.9 1.8 - - - -
345A SER* 3.0 27.6 + - - -
350A ARG* 4.0 24.5 - - + +
351A TYR* 1.3 75.0 - - - +
353A GLU* 1.3 64.9 + - + +
354A VAL* 3.9 10.5 - - - +
355A MSE 3.1 18.4 + - - +
356A ALA 2.9 23.9 + - - -
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Residues in contact with GLU 353 (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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52A ASN* 3.8 22.4 + - + +
72A HIS* 5.1 0.9 + - - -
117A GLU* 3.6 21.3 + - - +
337A TYR* 4.3 15.8 + - - +
341A GLU* 4.9 3.5 - - - +
352A ASN* 1.3 78.2 - - + +
354A VAL* 1.3 76.1 + - + +
356A ALA* 3.1 2.9 + - - +
357A THR* 3.0 27.0 + - - -
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Residues in contact with VAL 354 (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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332A MSE 3.4 23.9 - - + +
337A TYR* 3.8 20.4 - - + -
341A GLU* 3.4 27.4 - - + +
342A ILE* 3.7 31.0 - - + +
345A SER* 3.5 21.3 - - - +
346A LEU* 5.9 0.9 - - + -
352A ASN* 3.7 8.3 - - - +
353A GLU* 1.3 86.5 - - - +
355A MSE 1.3 63.0 + - - +
357A THR 3.4 0.2 + - - -
358A TYR* 3.2 18.6 + - + +
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Residues in contact with MSE 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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114A LYS* 4.7 1.6 - - - +
116A PHE 5.1 0.4 - - - +
345A SER* 3.7 18.4 - - - +
346A LEU* 3.8 19.3 - - + -
349A GLN* 3.5 32.1 - - - +
350A ARG 3.8 2.7 - - - -
351A TYR* 3.4 61.0 - - + +
352A ASN* 3.1 20.7 + - - +
354A VAL* 1.3 80.7 - - - +
356A ALA* 1.3 58.4 + - - +
358A TYR* 3.3 5.1 + - - +
359A LEU* 2.9 49.7 + - + +
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Residues in contact with ALA 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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52A ASN* 5.4 0.2 - - - +
53A TYR* 3.5 13.2 - - - +
72A HIS* 4.9 2.7 - - - +
116A PHE* 3.3 27.1 + - + +
117A GLU* 3.5 24.5 - - + +
352A ASN 2.9 9.2 + - - +
353A GLU 3.1 6.9 + - - +
355A MSE 1.3 76.9 - - - +
357A THR* 1.3 57.7 + - - +
359A LEU* 3.7 2.8 - - - +
360A LEU* 2.8 39.5 + - + +
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Residues in contact with THR 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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72A HIS* 3.3 26.2 + - + -
74A LEU* 4.0 1.7 - - + +
75A THR* 4.1 10.1 - - + -
332A MSE 4.0 4.9 - - + -
335A MSE 4.0 11.2 - - - -
337A TYR* 2.7 41.6 + - + -
353A GLU 3.0 6.6 + - - -
354A VAL 3.8 6.5 - - - -
355A MSE 3.3 0.2 - - - -
356A ALA* 1.3 73.4 - - - +
358A TYR* 1.3 61.0 + - - +
360A LEU* 3.1 2.1 + - - +
361A LEU* 2.8 48.4 + - + +
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Residues in contact with TYR 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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322A ASP 2.8 28.5 + - - -
323A TYR* 3.2 11.2 - + - -
325A ASP* 3.0 26.8 + - - +
328A ARG* 2.9 59.5 + - + -
329A THR* 4.2 12.6 - - - -
332A MSE 3.6 27.5 - - + -
342A ILE* 4.5 4.5 - - + -
346A LEU* 3.6 41.3 - - + -
354A VAL* 3.2 10.3 + - + +
355A MSE 3.6 7.0 - - - +
357A THR* 1.3 80.8 - - - +
359A LEU* 1.3 72.3 + - + +
361A LEU* 3.4 7.5 + - - -
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Residues in contact with LEU 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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114A LYS* 3.9 16.4 - - + +
115A LEU 3.5 24.5 - - - +
116A PHE* 3.9 28.0 - - + +
323A TYR* 6.6 0.2 - - + -
328A ARG* 4.2 4.5 + - - +
346A LEU* 5.3 2.5 - - + -
355A MSE 2.9 47.0 + - + +
356A ALA 3.7 3.4 - - - +
358A TYR* 1.3 85.7 - - + +
360A LEU* 1.3 58.5 + - - +
362A GLY* 2.9 22.9 + - - -
363A TYR* 3.8 11.8 - - + -
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Residues in contact with LEU 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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53A TYR* 4.4 7.0 - - - +
72A HIS* 3.4 41.1 - - + +
75A THR* 3.9 16.3 - - + +
77A LYS* 3.9 30.9 - - + +
79A VAL* 3.7 26.7 - - + -
116A PHE* 3.7 28.9 - - + -
356A ALA* 2.8 27.9 + - + +
357A THR 3.7 2.9 - - - +
359A LEU* 1.3 68.0 - - - +
361A LEU* 1.3 56.4 + - - +
362A GLY 3.0 9.8 + - - -
363A TYR* 3.6 16.8 + - + +
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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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75A THR* 3.9 23.1 - - + +
327A ARG* 3.7 22.5 + - - +
328A ARG* 3.4 28.9 - - + +
331A LEU* 3.6 31.4 - - + -
332A MSE 3.5 36.1 - - + -
335A MSE 3.9 8.3 - - + -
357A THR* 2.8 26.1 + - + +
359A LEU 3.3 0.4 - - - -
360A LEU* 1.3 71.3 - - - +
362A GLY* 1.3 57.8 + - - +
363A TYR 3.4 2.8 + - - -
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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