Contacts of the helix formed by residues 489 - 496 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450I VAL 4.0 7.6 - - - +
451I ASN* 4.4 14.6 + - - +
452I LEU 4.9 2.9 - - - +
453I PRO* 5.5 6.7 - - + -
454I LEU* 4.5 12.3 - - + +
476I LYS* 3.5 1.7 - - - +
478I THR* 6.1 0.6 - - - +
488I GLY* 1.3 90.3 + - - -
490I GLY* 1.3 57.2 + - - +
491I ILE 3.5 0.7 - - - -
492I ASN* 3.9 22.5 + - - +
493I ASN* 2.7 53.2 + - - +
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Residues in contact with GLY 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450I VAL* 3.7 24.3 + - - +
451I ASN* 4.3 4.0 + - - -
475I VAL* 3.7 9.0 - - - -
476I LYS 2.7 23.1 + - - +
489I GLN* 1.3 78.8 - - - +
491I ILE* 1.3 62.3 + - - -
493I ASN* 3.7 2.6 - - - +
494I LEU* 3.1 23.4 + - - +
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Residues in contact with ILE 491 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475I VAL* 3.6 27.8 - - + +
476I LYS 3.0 5.2 + - - -
477I GLY* 3.4 31.2 - - - +
478I THR 5.3 0.2 - - - +
490I GLY* 1.3 69.9 - - - -
492I ASN* 1.3 66.2 + - - +
494I LEU* 3.3 19.9 + - + +
495I ASP* 3.3 11.4 + - - +
528I MET* 3.6 22.2 - - + -
531I TYR* 4.4 3.4 - - + -
532I SER 3.8 16.6 - - - +
533I VAL* 4.7 0.2 - - + -
534I PRO* 3.5 34.5 - - + -
537I LEU* 3.8 7.8 - - + +
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Residues in contact with ASN 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476I LYS 4.9 1.6 + - - -
477I GLY* 5.0 0.8 - - - -
478I THR* 4.4 21.3 + - - +
488I GLY 3.3 24.5 + - - -
489I GLN* 3.4 24.1 + - - +
490I GLY 3.2 0.6 - - - -
491I ILE* 1.3 79.5 - - - +
493I ASN* 1.3 60.2 + - - +
495I ASP* 3.0 18.4 + - - +
496I ASN* 2.7 26.9 + - - +
476J LYS* 4.1 8.9 + - - +
486J PRO* 5.8 3.3 - - - +
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Residues in contact with ASN 493 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450I VAL* 3.7 27.6 + - + -
452I LEU 3.9 6.5 + - - -
454I LEU* 3.2 42.2 - - - +
457I LEU* 3.4 25.2 - - + +
489I GLN* 2.7 38.7 + - - +
490I GLY 3.7 3.4 - - - +
492I ASN* 1.3 72.1 - - - +
494I LEU* 1.3 62.9 + - - +
496I ASN* 3.0 18.7 + - - +
497I LEU* 3.2 22.1 - - + +
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Residues in contact with LEU 494 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450I VAL* 4.6 6.7 - - + -
472I PHE* 4.2 26.5 - - + -
475I VAL* 4.0 16.8 - - + -
490I GLY 3.1 16.2 + - - +
491I ILE* 3.4 17.0 - - + +
493I ASN* 1.3 76.6 - - - +
495I ASP* 1.3 61.5 + - - +
497I LEU* 3.2 15.8 + - + +
501I LEU* 3.3 30.0 - - + +
526I VAL* 3.8 34.5 - - + -
528I MET* 4.9 1.8 - - + -
537I LEU* 3.6 27.8 - - + -
541I PHE* 4.9 2.9 - - + -
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Residues in contact with ASP 495 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491I ILE 3.3 7.0 + - - +
492I ASN* 3.0 10.8 + - - +
494I LEU* 1.3 74.7 - - - +
496I ASN* 1.3 57.5 + - - +
497I LEU 2.9 9.5 + - - -
498I ARG* 2.8 47.7 + - - +
534I PRO* 4.5 7.1 - - + +
536I THR* 2.8 25.5 + - - -
537I LEU* 4.2 11.5 + - + +
451J ASN* 4.4 1.4 + - - -
476J LYS* 3.5 28.6 - - - +
486J PRO* 3.8 14.3 - - + +
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Residues in contact with ASN 496 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454I LEU* 3.8 25.2 - - + +
492I ASN* 2.7 35.9 + - - +
493I ASN* 3.0 14.7 + - - +
495I ASP* 1.3 75.3 - - - +
497I LEU* 1.3 69.4 + - + +
498I ARG 3.8 1.6 - - - -
449J ASN* 3.4 20.3 + - - -
451J ASN* 3.5 29.0 + - + +
452J LEU* 3.9 1.8 - - + +
476J LYS* 3.1 30.1 + - - +
488J GLY* 5.0 3.5 - - - -
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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