Contacts of the helix formed by residues 489 - 496 (chain J) in PDB entry 4E2I
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 GLN 489 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450J VAL 4.0 7.2 - - - +
451J ASN* 4.4 15.7 + - - +
452J LEU 4.9 2.7 - - - +
453J PRO* 5.5 5.8 - - + -
454J LEU* 4.5 12.4 - - + +
476J LYS* 3.5 1.9 - - - +
478J THR* 6.1 0.4 - - - +
488J GLY* 1.3 89.5 + - - -
490J GLY* 1.3 57.8 + - - +
491J ILE 3.5 0.9 - - - -
492J ASN* 3.9 22.8 + - - +
493J ASN* 2.7 53.1 + - - +
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Residues in contact with GLY 490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450J VAL* 3.7 23.5 + - - +
451J ASN* 4.3 4.0 + - - -
475J VAL* 3.7 9.6 - - - -
476J LYS 2.7 23.2 + - - +
489J GLN* 1.3 80.5 - - - +
491J ILE* 1.3 62.2 + - - -
493J ASN* 3.7 2.3 - - - +
494J LEU* 3.1 23.6 + - - +
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Residues in contact with ILE 491 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475J VAL* 3.6 28.0 - - + +
476J LYS 3.0 5.8 + - - +
477J GLY* 3.4 31.6 - - - +
478J THR 5.3 0.2 - - - +
490J GLY* 1.3 71.0 - - - -
492J ASN* 1.3 66.9 + - - +
494J LEU* 3.3 18.2 + - + +
495J ASP* 3.3 11.4 + - - +
528J MET* 3.6 22.7 - - + -
531J TYR* 4.4 3.8 - - + -
532J SER 3.8 17.9 - - - +
533J VAL* 4.7 0.2 - - + -
534J PRO* 3.5 34.3 - - + -
537J LEU* 3.8 6.4 - - + +
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Residues in contact with ASN 492 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476J LYS 4.9 2.2 + - - -
477J GLY* 5.0 0.4 - - - -
478J THR* 4.4 21.3 + - - +
488J GLY 3.3 24.2 + - - -
489J GLN* 3.4 23.8 + - - +
490J GLY 3.2 0.4 - - - -
491J ILE* 1.3 79.5 - - - +
493J ASN* 1.3 60.3 + - - +
495J ASP* 3.0 17.6 + - - +
496J ASN* 2.7 28.7 + - - +
476K LYS* 4.2 6.0 + - - +
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Residues in contact with ASN 493 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450J VAL* 3.7 28.1 + - + -
452J LEU 3.9 6.1 + - - -
454J LEU* 3.2 41.4 - - - +
457J LEU* 3.3 25.6 - - + +
489J GLN* 2.7 39.2 + - - +
490J GLY 3.7 3.4 - - - +
492J ASN* 1.3 72.5 - - - +
494J LEU* 1.3 63.7 + - - +
496J ASN* 3.0 17.9 + - - +
497J LEU* 3.2 22.4 - - + +
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Residues in contact with LEU 494 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450J VAL* 4.6 7.2 - - + -
472J PHE* 4.2 26.2 - - + -
475J VAL* 4.0 16.2 - - + -
490J GLY 3.1 16.9 + - - +
491J ILE* 3.4 17.7 - - + +
492J ASN 3.1 0.2 - - - -
493J ASN* 1.3 76.0 - - - +
495J ASP* 1.3 59.7 + - - +
497J LEU* 3.2 16.8 + - + +
501J LEU* 3.3 29.2 - - + +
526J VAL* 3.8 35.4 - - + -
528J MET* 4.9 2.0 - - + -
537J LEU* 3.6 27.6 - - + -
541J PHE* 5.0 2.9 - - + -
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Residues in contact with ASP 495 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491J ILE 3.3 7.3 + - - +
492J ASN* 3.0 10.3 + - - +
494J LEU* 1.3 74.9 - - - +
496J ASN* 1.3 57.5 + - - +
497J LEU 2.9 9.8 + - - -
498J ARG* 2.8 46.9 + - - +
534J PRO* 4.5 7.0 - - + +
536J THR* 2.9 25.8 + - - -
537J LEU* 4.2 11.7 + - + +
451K ASN* 4.4 0.7 + - - -
476K LYS* 3.1 30.1 - - - +
486K PRO* 3.5 13.3 - - + +
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Residues in contact with ASN 496 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454J LEU* 3.8 23.8 - - + +
492J ASN* 2.7 36.5 + - - +
493J ASN* 3.0 13.0 + - - +
495J ASP* 1.3 75.6 - - - +
497J LEU* 1.3 70.1 + - + +
498J ARG 3.8 1.1 - - - -
449K ASN* 3.4 8.1 + - - -
451K ASN* 3.4 42.2 - - + +
452K LEU* 3.6 2.7 - - + +
476K LYS* 3.2 26.3 + - - +
488K GLY* 4.8 4.7 - - - -
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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