Contacts of the helix formed by residues 456 - 462 (chain L) 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 ARG 456 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456G ARG* 3.7 11.6 - - - +
454K LEU 4.3 6.1 - - - +
455K ASP* 3.1 32.8 + - - +
456K ARG* 3.3 26.3 - - - +
458K ASN* 3.4 39.1 + - - +
459K PHE* 3.4 26.6 - - - -
510K GLU* 5.4 1.3 - - - -
452L LEU* 4.9 8.5 - - + -
453L PRO* 3.6 6.4 + - + +
455L ASP* 1.3 99.1 - - + +
457L LEU* 1.3 63.6 + - - +
458L ASN 3.1 2.5 - - - -
459L PHE* 3.0 36.1 + - + +
460L GLU* 3.1 15.8 + - - +
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Residues in contact with LEU 457 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452G LEU* 4.5 11.0 - - + -
449L ASN 4.4 7.6 - - - +
450L VAL* 3.8 31.0 - - + -
452L LEU* 5.3 1.6 - - - +
453L PRO 3.5 6.5 + - - +
454L LEU* 3.6 30.7 - - + +
455L ASP 3.1 0.8 - - - -
456L ARG* 1.3 78.2 - - - +
458L ASN* 1.3 52.4 + - - +
460L GLU* 3.2 4.8 + - + -
461L LEU* 2.8 67.3 + - + +
493L ASN* 3.4 24.5 - - - +
497L LEU* 4.3 17.5 - - + -
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Residues in contact with ASN 458 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452G LEU* 3.5 26.8 - - - +
456G ARG* 3.3 46.7 + - + +
459G PHE* 5.5 1.6 - - - +
460G GLU* 4.5 9.1 + - - +
454L LEU 3.6 7.4 - - - +
455L ASP 3.9 0.4 - - - +
456L ARG 3.1 0.4 - - - -
457L LEU* 1.3 79.3 - - - +
459L PHE* 1.3 62.8 + - + +
460L GLU 3.1 0.7 + - - -
461L LEU* 4.3 6.6 - - - +
462L GLY* 3.5 15.4 + - - -
500L TYR* 5.7 1.4 + - - -
510L GLU* 3.5 38.6 + - + +
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Residues in contact with PHE 459 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456G ARG* 3.5 33.0 - - - -
459G PHE* 6.2 4.0 - + - -
458K ASN* 5.5 1.1 - - - +
459K PHE* 6.0 6.1 - + - -
508K ASN* 6.1 0.2 - - - +
510K GLU* 4.3 22.2 - - - +
515K ASN* 5.1 9.9 + - - +
455L ASP 4.0 11.0 - - - -
456L ARG* 3.0 26.9 + - + +
458L ASN* 1.3 75.9 - - - +
460L GLU* 1.3 58.0 + - - +
462L GLY* 4.4 3.2 + - - -
463L VAL* 4.6 6.4 - - - +
510L GLU* 3.7 24.8 - - + +
513L HIS* 5.6 13.2 - + - -
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Residues in contact with GLU 460 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458K ASN* 4.2 16.5 + - - +
500K TYR* 4.0 15.2 + - - -
508K ASN* 3.7 26.3 - - + +
448L LEU* 3.2 19.0 - - + +
449L ASN* 2.7 53.1 + - - +
452L LEU* 4.4 10.3 - - - +
456L ARG 3.1 13.7 + - - +
457L LEU* 3.9 5.6 - - + +
459L PHE* 1.3 80.2 - - - +
461L LEU* 1.3 59.0 + - + +
462L GLY 3.0 4.9 - - - -
463L VAL* 3.0 24.9 - - - +
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Residues in contact with LEU 461 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452G LEU* 5.5 3.6 - - + -
448L LEU* 3.9 14.8 - - + -
449L ASN 6.0 0.4 - - - +
450L VAL* 5.1 0.2 - - + -
457L LEU* 2.8 57.5 + - + +
458L ASN* 4.5 5.6 - - - +
460L GLU* 1.3 72.2 - - + +
462L GLY* 1.3 56.7 + - - +
463L VAL 3.0 10.6 + - - -
464L ALA* 3.5 8.8 + - - +
472L PHE* 4.4 13.5 - - + -
497L LEU* 3.9 21.1 - - + -
500L TYR* 4.0 19.1 - - + +
509L LEU* 3.3 21.4 - - + +
521L PHE* 3.7 31.2 - - + -
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Residues in contact with GLY 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458L ASN 3.5 9.3 + - - -
459L PHE 5.1 2.7 - - - -
460L GLU* 3.0 3.0 - - - +
461L LEU* 1.3 77.3 - - - +
463L VAL* 1.3 59.2 + - - +
464L ALA 3.4 0.4 - - - -
465L ILE* 3.0 34.1 - - - +
509L LEU* 4.3 6.1 - - - -
510L GLU 3.7 23.3 - - - +
511L LYS* 4.5 8.0 - - - +
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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