Contacts of the helix formed by residues 464 - 472 (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 LEU 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A ILE* 4.1 11.7 - - + -
400A GLY 2.9 21.4 + - - +
401A TYR* 3.7 16.2 - - + -
462A LEU* 3.5 20.0 - - + +
463A ASP* 1.3 71.9 - - - +
465A LEU* 1.3 56.8 + - - +
467A PHE* 3.7 24.2 - - + +
468A ILE* 2.9 34.2 + - + +
524A PRO* 3.6 25.8 - - + +
527A LEU* 4.1 13.5 - - + -
528A MET* 3.9 31.0 - - + +
531A LEU* 4.8 4.0 - - + -
533A ALA* 4.3 6.5 - - + -
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Residues in contact with LEU 465 (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* 3.5 35.2 - - + +
402A ASN* 3.6 40.4 - - + +
405A ASN* 6.2 0.7 - - - +
463A ASP* 2.9 13.7 + - - +
464A LEU* 1.3 78.6 - - - +
466A GLN* 1.3 63.1 + - - +
468A ILE* 4.0 0.6 - - - -
469A GLN* 3.0 62.1 + - + +
477A TYR* 3.6 19.1 - - + +
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Residues in contact with GLN 466 (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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402A ASN* 5.2 1.6 - - - +
404A THR* 4.2 12.6 - - + +
405A ASN* 3.5 26.7 + - - +
449A ARG* 6.2 2.6 - - - +
463A ASP* 2.9 34.6 + - + +
465A LEU* 1.3 80.9 - - - +
467A PHE* 1.3 65.2 + - - +
469A GLN* 3.7 19.2 + - - +
470A ARG* 3.1 29.1 + - + +
552A LEU* 4.2 20.6 + - + +
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Residues in contact with PHE 467 (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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462A LEU* 3.8 20.2 - - + -
463A ASP 3.1 5.9 + - - -
464A LEU* 3.7 13.0 - - + +
466A GLN* 1.3 77.3 - - - +
468A ILE* 1.3 74.9 + - + +
470A ARG* 3.1 3.6 + - - -
471A GLU* 2.9 41.9 + - + +
472A TYR* 4.4 6.3 - + - -
531A LEU* 4.1 24.7 - - + -
532A MET 5.0 0.2 - - - -
533A ALA* 3.5 42.4 - - + -
536A ASN* 5.6 4.9 - - + -
537A TYR* 3.6 46.0 - + - -
552A LEU* 4.0 9.2 - - + +
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Residues in contact with ILE 468 (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* 3.9 20.6 - - + +
464A LEU* 2.9 28.1 + - + +
465A LEU 4.2 2.0 - - - +
467A PHE* 1.3 78.0 - - + +
469A GLN* 1.3 57.6 + - - +
472A TYR* 2.8 39.8 + - + +
474A LEU* 3.8 28.9 - - + -
477A TYR* 3.8 9.6 - - + -
482A VAL* 4.0 20.0 - - + -
486A PHE* 4.1 8.7 - - + -
527A LEU* 4.2 8.5 - - + -
531A LEU* 3.8 31.2 - - + -
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Residues in contact with GLN 469 (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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465A LEU* 3.0 42.1 + - + +
466A GLN* 3.7 23.7 + - - +
468A ILE* 1.3 78.2 - - - +
470A ARG* 1.3 62.1 + - + +
472A TYR 3.5 9.9 - - - +
477A TYR* 3.6 39.1 + - + +
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Residues in contact with ARG 470 (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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441A PHE* 4.0 12.5 - - - -
446A TYR* 3.4 65.8 + - + +
466A GLN* 3.1 16.1 + - + +
467A PHE 3.1 8.7 + - - +
469A GLN* 1.3 78.6 - - + +
471A GLU* 1.3 66.2 + - + +
472A TYR 3.5 0.6 + - - -
537A TYR* 4.2 14.6 - - - +
551A LEU 2.7 26.5 + - - -
552A LEU* 3.2 31.9 + - + +
554A ARG 2.9 27.7 + - - -
555A GLY* 4.6 2.0 - - - -
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Residues in contact with GLU 471 (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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467A PHE* 2.9 36.9 + - + +
470A ARG* 1.3 85.4 - - - +
472A TYR* 1.3 86.4 + - + +
537A TYR* 2.7 37.5 + - - +
695A GLY* 4.3 17.1 - - - +
699A ALA* 3.8 24.9 - - - +
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Residues in contact with TYR 472 (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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467A PHE* 4.4 14.1 - + - -
468A ILE* 2.8 27.6 + - + +
469A GLN 3.5 7.5 - - - +
470A ARG 3.5 0.8 - - - -
471A GLU* 1.3 100.7 - - + +
473A LYS* 1.3 53.7 + - - +
474A LEU* 4.0 20.6 - - + -
477A TYR* 2.5 23.6 + - - -
485A HIS* 5.9 0.2 - - - -
486A PHE* 3.8 34.7 - + - -
531A LEU* 3.9 19.3 + - + +
691A ASP* 4.1 21.1 - - - -
692A VAL* 3.8 28.1 + - - +
695A GLY* 5.4 7.6 - - - -
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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