Contacts of the helix formed by residues 489 - 496 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450F VAL 4.0 8.3 - - - +
451F ASN* 4.4 15.2 + - - +
452F LEU 4.9 2.2 - - - +
453F PRO* 5.5 6.3 - - + -
454F LEU* 4.5 13.0 - - + +
476F LYS* 3.5 1.7 - - - +
478F THR* 6.1 0.6 - - - +
488F GLY* 1.3 89.3 + - - -
490F GLY* 1.3 57.0 + - - +
491F ILE 3.5 0.4 - - - -
492F ASN* 3.9 23.4 + - - +
493F ASN* 2.7 53.5 + - - +
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Residues in contact with GLY 490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F VAL* 3.7 23.4 + - - +
451F ASN* 4.3 4.4 + - - -
475F VAL* 3.7 9.2 - - - -
476F LYS 2.7 23.7 + - - +
489F GLN* 1.3 80.5 - - - +
491F ILE* 1.3 61.8 + - - -
493F ASN* 3.7 2.4 - - - +
494F LEU* 3.1 22.9 + - - +
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Residues in contact with ILE 491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F VAL* 3.5 28.4 - - + +
476F LYS 3.0 5.9 + - - -
477F GLY* 3.4 31.4 - - - +
478F THR 5.3 0.2 - - - +
490F GLY* 1.3 70.2 - - - -
492F ASN* 1.3 65.3 + - - +
494F LEU* 3.3 19.0 + - + +
495F ASP* 3.4 11.4 + - - +
528F MET* 3.6 22.4 - - + -
531F TYR* 4.4 3.8 - - + -
532F SER 3.8 17.5 - - - +
533F VAL* 4.7 0.2 - - + -
534F PRO* 3.5 34.3 - - + -
537F LEU* 3.8 6.1 - - + +
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Residues in contact with ASN 492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A LYS* 4.2 5.6 + - - +
476F LYS 4.9 1.8 + - - -
477F GLY* 5.0 0.6 - - - -
478F THR* 4.4 21.3 - - - +
488F GLY 3.3 24.7 + - - -
489F GLN* 3.7 23.6 + - - +
490F GLY 3.2 0.4 - - - -
491F ILE* 1.3 80.2 - - - +
493F ASN* 1.3 59.7 + - - +
495F ASP* 3.0 17.8 + - - +
496F ASN* 2.7 28.5 + - - +
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Residues in contact with ASN 493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F VAL* 3.7 27.9 + - + -
452F LEU 4.0 6.3 + - - -
454F LEU* 3.2 41.8 - - - +
457F LEU* 3.3 25.8 - - + +
489F GLN* 2.7 40.0 + - - +
490F GLY 3.7 3.6 - - - +
492F ASN* 1.3 73.6 - - - +
494F LEU* 1.3 62.2 + - - +
496F ASN* 3.0 18.5 + - - +
497F LEU* 3.2 22.7 - - + +
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Residues in contact with LEU 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F VAL* 4.6 7.2 - - + -
472F PHE* 4.2 26.0 - - + -
475F VAL* 4.0 17.0 - - + -
490F GLY 3.1 16.8 + - - +
491F ILE* 3.4 16.8 - - + +
492F ASN 3.1 0.2 - - - -
493F ASN* 1.3 76.7 - - - +
495F ASP* 1.3 61.6 + - - +
497F LEU* 3.2 16.8 + - + +
501F LEU* 3.3 30.0 - - + +
526F VAL* 3.8 34.1 - - + -
528F MET* 4.9 2.5 - - + -
537F LEU* 3.6 27.4 - - + -
541F PHE* 5.0 2.7 - - + -
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Residues in contact with ASP 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A ASN* 4.5 0.9 + - - -
476A LYS* 3.1 29.9 - - - +
486A PRO* 3.5 12.7 - - + +
491F ILE 3.4 7.2 + - - +
492F ASN* 3.0 10.6 + - - +
494F LEU* 1.3 75.3 - - - +
496F ASN* 1.3 57.7 + - - +
497F LEU 2.9 9.8 + - - -
498F ARG* 2.8 46.6 + - - +
534F PRO* 4.5 6.9 - - + +
536F THR* 2.9 25.5 + - - -
537F LEU* 4.2 11.4 + - + +
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Residues in contact with ASN 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ASN* 3.5 8.5 + - - -
451A ASN* 3.5 39.4 + - + +
452A LEU* 3.6 2.7 - - + +
476A LYS* 3.2 24.1 + - - +
488A GLY* 4.9 5.0 - - - -
454F LEU* 3.8 26.8 - - + +
457F LEU* 6.1 0.4 - - + -
492F ASN* 2.7 36.5 + - - +
493F ASN* 3.0 13.4 + - - +
495F ASP* 1.3 75.6 - - - +
497F LEU* 1.3 69.2 + - + +
498F ARG 3.8 1.1 - - - -
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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