Contacts of the helix formed by residues 478 - 488 (chain A) in PDB entry 3IAY
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 THR 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A TYR* 4.1 0.7 - - - -
476A SER* 3.5 11.1 + - - +
477A TYR* 1.3 81.0 - - - +
479A LEU* 1.3 67.0 + - - +
480A ASN* 3.9 7.8 + - - +
481A ALA* 3.0 26.9 + - - +
482A VAL* 3.0 21.5 + - - +
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Residues in contact with LEU 479 (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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321A ASP* 6.0 0.9 - - - +
401A TYR* 3.6 49.8 - - + -
478A THR* 1.3 72.0 - - - +
480A ASN* 1.3 56.9 + - - +
482A VAL* 3.4 2.1 + - - +
483A SER* 2.7 55.6 + - - +
520A ASP* 3.6 46.9 - - + +
523A LEU* 4.1 18.6 - - + -
524A PRO* 4.9 1.6 - - + -
527A LEU* 4.1 8.5 - - + -
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Residues in contact with ASN 480 (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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478A THR* 3.2 7.3 - - - +
479A LEU* 1.3 80.7 - - - +
481A ALA* 1.3 63.3 + - - +
483A SER* 3.8 4.9 - - - -
484A ALA* 3.0 25.8 + - - +
489A GLU* 5.3 0.7 - - - +
490A GLN 5.5 4.8 - - - -
523A LEU* 6.4 0.4 - - - -
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Residues in contact with ALA 481 (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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476A SER* 3.5 31.2 - - - +
478A THR* 3.0 25.4 + - - +
480A ASN* 1.3 77.8 - - - +
482A VAL* 1.3 58.4 + - - +
484A ALA* 3.4 5.4 + - - +
485A HIS* 3.0 28.2 + - - +
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Residues in contact with VAL 482 (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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401A TYR* 3.4 35.4 - - + +
468A ILE* 4.0 13.0 - - + -
474A LEU* 3.8 16.4 - - + -
476A SER 3.8 7.2 - - - +
477A TYR* 3.8 16.6 - - - -
478A THR 3.0 12.4 + - - +
479A LEU* 3.4 9.9 - - - +
481A ALA* 1.3 72.6 - - - +
483A SER* 1.3 64.1 - - - +
485A HIS* 4.1 6.1 - - - -
486A PHE* 2.8 38.8 + - + +
527A LEU* 3.9 21.2 - - + +
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Residues in contact with SER 483 (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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479A LEU* 2.7 39.1 + - - +
480A ASN* 3.8 5.2 - - - -
482A VAL* 1.3 76.1 - - - +
484A ALA* 1.3 60.4 + - - +
487A LEU* 2.8 41.6 + - - +
488A GLY 3.0 2.8 + - - -
489A GLU* 3.2 20.1 + - - -
523A LEU* 3.7 23.2 - - - +
527A LEU* 4.5 3.8 - - - +
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Residues in contact with ALA 484 (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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480A ASN 3.0 18.2 + - - +
481A ALA* 3.7 5.8 - - - +
483A SER* 1.3 76.0 - - - +
485A HIS* 1.3 62.4 + - - +
488A GLY* 3.2 18.9 + - - -
489A GLU* 2.9 29.7 - - - +
490A GLN 4.5 7.9 - - - +
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Residues in contact with HIS 485 (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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472A TYR* 5.9 0.4 - - - -
474A LEU* 3.8 24.2 - - + +
481A ALA 3.0 17.6 + - - +
482A VAL* 3.8 6.7 - - - +
483A SER 3.3 0.2 - - - -
484A ALA* 1.3 79.9 - - - +
486A PHE* 1.3 101.2 + + - +
488A GLY 4.7 0.5 + - - -
688A PHE* 5.4 1.7 - - - -
691A ASP* 5.8 2.4 + - - -
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Residues in contact with PHE 486 (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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468A ILE* 4.1 17.3 - - + -
472A TYR* 3.8 43.5 - + - -
474A LEU* 4.0 18.6 - - + -
482A VAL* 2.8 30.9 + - + +
485A HIS* 1.3 102.6 - + - +
487A LEU* 1.3 66.5 + - + +
488A GLY 3.6 0.4 - - - -
527A LEU* 4.1 14.8 - - + -
531A LEU* 3.8 27.4 - - + -
688A PHE* 3.0 39.0 - + + -
691A ASP* 5.3 6.5 - - + -
692A VAL* 6.2 0.4 - - + -
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Residues in contact with LEU 487 (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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483A SER* 2.8 21.4 + - - +
486A PHE* 1.3 82.8 - - + +
488A GLY* 1.3 62.2 + - - +
489A GLU* 3.2 13.7 - - - +
523A LEU* 3.8 28.0 - - + -
526A ARG* 3.8 44.6 + - + +
527A LEU* 3.7 32.3 - - + -
530A LYS* 4.3 22.0 - - + -
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Residues in contact with GLY 488 (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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483A SER 3.0 2.2 + - - -
484A ALA 3.2 14.1 + - - -
485A HIS 4.6 0.6 + - - -
486A PHE 3.6 1.2 - - - -
487A LEU* 1.3 79.6 - - - +
489A GLU* 1.3 67.4 + - - +
490A GLN 4.0 0.3 + - - -
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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