Contacts of the helix formed by residues 489 - 496 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450E VAL 4.0 8.1 - - - +
451E ASN* 4.4 14.7 + - - +
452E LEU 4.9 2.0 - - - +
453E PRO* 5.5 6.3 - - + -
454E LEU* 4.5 13.2 - - + +
476E LYS* 3.5 1.7 - - - +
488E GLY* 1.3 89.2 + - - -
490E GLY* 1.3 57.4 + - - +
491E ILE 3.5 0.9 - - - -
492E ASN* 3.9 23.4 + - - +
493E ASN* 2.7 53.1 + - - +
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Residues in contact with GLY 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL* 3.7 23.7 + - - +
451E ASN* 4.3 4.0 + - - -
475E VAL* 3.7 8.7 - - - -
476E LYS 2.7 23.8 + - - +
489E GLN* 1.3 81.0 - - - +
491E ILE* 1.3 62.1 + - - -
493E ASN* 3.7 2.4 - - - +
494E LEU* 3.1 22.7 + - - +
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Residues in contact with ILE 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E VAL* 3.6 27.6 - - + +
476E LYS 3.0 5.5 + - - +
477E GLY* 3.4 32.1 - - - +
490E GLY* 1.3 71.4 - - - -
492E ASN* 1.3 66.7 + - - +
494E LEU* 3.3 18.0 + - + +
495E ASP* 3.4 11.8 + - - +
528E MET* 3.6 22.2 - - + -
531E TYR* 4.4 3.8 - - + -
532E SER 3.8 17.3 - - - +
533E VAL* 4.7 0.2 - - + -
534E PRO* 3.5 34.5 - - + -
537E LEU* 3.8 7.3 - - + +
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Residues in contact with ASN 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E LYS 4.9 1.8 + - - -
477E GLY* 5.0 0.6 - - - -
478E THR* 4.4 20.7 - - - +
488E GLY 3.3 24.9 + - - -
489E GLN* 3.4 24.0 + - - +
490E GLY 3.2 0.8 - - - -
491E ILE* 1.3 78.0 - - - +
493E ASN* 1.3 61.0 + - - +
495E ASP* 3.0 16.7 + - - +
496E ASN* 2.7 28.2 + - - +
476F LYS* 3.9 12.5 + - - +
486F PRO* 5.5 4.7 - - - +
487F SER 5.5 1.0 - - - +
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Residues in contact with ASN 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL* 3.7 27.9 + - + -
452E LEU 3.9 6.1 + - - -
454E LEU* 3.2 42.4 - - - +
457E LEU* 3.3 25.6 - - + +
489E GLN* 2.7 39.5 + - - +
490E GLY 3.7 3.6 - - - +
492E ASN* 1.3 72.5 - - - +
494E LEU* 1.3 62.9 + - - +
496E ASN* 3.0 18.7 + - - +
497E LEU* 3.2 22.3 - - + +
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Residues in contact with LEU 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL* 4.6 6.7 - - + -
472E PHE* 4.2 26.7 - - + -
475E VAL* 4.0 15.9 - - + -
490E GLY 3.1 18.0 + - - +
491E ILE* 3.4 17.5 - - + +
492E ASN 3.1 0.2 - - - -
493E ASN* 1.3 76.7 - - - +
495E ASP* 1.3 60.6 + - - +
497E LEU* 3.2 17.4 + - + +
501E LEU* 3.3 29.3 - - + +
526E VAL* 3.7 34.8 - - + -
528E MET* 4.9 2.0 - - + -
537E LEU* 3.6 27.4 - - + -
541E PHE* 5.0 3.1 - - + -
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Residues in contact with ASP 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E ILE 3.4 7.3 + - - +
492E ASN* 3.0 10.7 + - - +
494E LEU* 1.3 74.7 - - - +
496E ASN* 1.3 58.2 + - - +
497E LEU 2.9 9.7 + - - -
498E ARG* 2.8 46.1 + - - +
534E PRO* 4.5 5.4 - - + +
536E THR* 2.9 26.2 + - - -
537E LEU* 4.2 11.1 + - + +
451F ASN* 4.2 1.6 + - - -
476F LYS* 3.3 29.3 - - - +
486F PRO* 3.8 15.3 - - + +
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Residues in contact with ASN 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E LEU* 3.8 20.5 - - + +
457E LEU* 6.1 0.4 - - + -
492E ASN* 2.7 35.5 + - - +
493E ASN* 3.0 13.7 + - - +
495E ASP* 1.3 75.5 - - - +
497E LEU* 1.3 64.4 + - + +
498E ARG 3.8 1.3 - - - -
449F ASN* 3.2 25.3 + - - -
451F ASN* 3.3 36.0 + - + +
452F LEU* 3.8 2.3 - - + +
476F LYS* 3.0 29.1 + - - +
488F GLY* 4.8 4.2 - - - -
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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