Contacts of the helix formed by residues 482 - 496 (chain E) in PDB entry 6V3O
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 SER 482 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480E GLU 3.7 2.4 + - - -
481E TRP* 1.3 75.9 - - - +
483E GLU* 1.3 70.6 + - - +
484E ASP* 3.2 20.4 + - - +
485E LYS* 3.9 11.7 + - - +
486E ARG* 2.9 27.8 + - - +
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Residues in contact with GLU 483 (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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482E SER* 1.3 77.2 + - - +
484E ASP* 1.3 63.9 + - - +
486E ARG* 3.3 10.5 + - - +
487E GLN* 2.9 53.3 + - - +
539E ALA* 3.2 25.5 - - + +
540E PRO* 3.6 1.7 - - + -
541E SER* 2.5 42.2 + - - -
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Residues in contact with ASP 484 (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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482E SER* 3.2 12.8 + - - +
483E GLU* 1.3 81.3 - - - +
485E LYS* 1.3 65.3 + - - +
487E GLN* 3.7 11.4 + - - +
488E GLU* 3.0 25.6 + - - +
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Residues in contact with LYS 485 (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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481E TRP* 3.6 50.0 - - + +
482E SER* 3.3 18.0 + - - +
484E ASP* 1.3 78.9 - - - +
486E ARG* 1.3 61.4 + - - +
488E GLU* 4.1 7.7 - - - +
489E TRP* 3.2 23.3 + - + +
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Residues in contact with ARG 486 (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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460E GLU* 5.3 4.6 + - - -
463E THR* 3.9 27.0 + - - +
478E TYR* 3.3 52.9 + - + +
479E ARG* 2.8 35.9 + - - +
481E TRP* 3.2 21.9 + - + +
482E SER 2.9 20.7 + - - +
483E GLU* 3.5 11.3 + - - +
485E LYS* 1.3 74.7 - - - +
487E GLN* 1.3 59.3 + - - +
489E TRP* 3.3 1.7 + - - +
490E LEU* 2.9 36.5 + - - +
541E SER* 4.0 16.4 + - - -
542E ASP* 5.2 4.4 + - - -
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Residues in contact with GLN 487 (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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483E GLU* 2.9 49.6 + - - +
484E ASP* 3.7 9.3 + - - +
486E ARG* 1.3 76.0 - - - +
488E GLU* 1.3 57.5 + - - +
490E LEU* 3.3 6.4 + - - -
491E LEU* 2.8 42.7 + - + +
540E PRO* 3.5 25.9 - - - +
541E SER* 4.4 10.1 - - - +
544E LEU* 4.7 8.1 - - + -
580E ARG* 2.7 44.2 + - - +
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Residues in contact with GLU 488 (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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484E ASP 3.0 17.2 + - - +
485E LYS* 4.1 6.7 - - - +
486E ARG 3.3 0.2 - - - -
487E GLN* 1.3 76.0 - - - +
489E TRP* 1.3 61.6 + - - +
491E LEU* 4.2 5.8 - - - +
492E SER* 3.1 23.2 + - - -
580E ARG* 5.9 1.1 - - - +
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Residues in contact with TRP 489 (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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466E ILE* 3.9 17.5 - - + -
469E ILE* 5.2 2.5 - - + -
470E THR* 3.9 20.0 - - + -
475E ILE* 4.1 28.3 - - + +
478E TYR* 4.3 3.8 - + - -
481E TRP* 3.6 30.5 - + + -
485E LYS* 3.2 19.0 + - + +
486E ARG 3.8 1.6 - - - +
488E GLU* 1.3 76.0 - - - +
490E LEU* 1.3 101.0 + - + +
492E SER* 3.0 11.8 + - - -
493E GLU* 3.0 51.1 + - + +
500E LEU* 4.1 20.4 - - + -
548E LEU* 4.1 7.4 - - + -
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Residues in contact with LEU 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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466E ILE* 4.0 16.6 - - + -
478E TYR* 3.3 24.9 - - + +
486E ARG 2.9 21.3 + - - +
487E GLN* 3.8 4.3 - - - +
489E TRP* 1.3 89.6 - - + +
491E LEU* 1.3 58.7 + - - +
493E GLU* 3.1 5.8 + - - +
494E LEU* 2.7 36.4 + - + +
541E SER* 3.7 25.6 - - - +
544E LEU* 3.9 18.6 - - + +
545E ALA* 3.9 12.8 - - - +
548E LEU* 3.7 25.1 - - + +
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Residues in contact with LEU 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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487E GLN* 2.8 28.4 + - + +
488E GLU* 4.2 5.6 - - - +
490E LEU* 1.3 75.3 - - - +
492E SER* 1.3 58.2 + - - +
494E LEU* 4.2 12.8 - - + -
495E ARG* 2.9 60.7 + - - +
544E LEU* 3.8 28.3 - - + -
580E ARG* 4.4 17.3 - - - +
584E VAL* 3.6 34.3 - - + -
586E TRP* 4.8 10.1 - - + -
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Residues in contact with SER 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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488E GLU 3.1 15.0 + - - -
489E TRP* 3.0 17.1 + - - -
491E LEU* 1.3 77.0 - - - +
493E GLU* 1.3 62.2 + - - +
495E ARG* 3.9 4.4 - - - +
496E GLY* 3.0 25.1 + - - -
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Residues in contact with GLU 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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475E ILE* 5.1 1.7 - - - +
489E TRP* 3.0 54.4 + - + +
490E LEU 3.6 6.5 - - - +
492E SER* 1.3 81.7 + - - +
494E LEU* 1.3 61.7 + - - +
496E GLY* 3.2 11.9 + - - +
498E ARG 4.2 11.6 - - - +
500E LEU* 4.1 9.7 - - + +
548E LEU* 4.0 19.1 - - + -
551E ARG* 2.9 19.4 + - - -
498H ARG* 2.8 34.3 + - - -
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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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490E LEU* 2.7 30.3 + - + +
491E LEU* 3.9 9.6 - - + +
493E GLU* 1.3 74.5 - - - +
495E ARG* 1.3 59.8 + - - +
496E GLY 3.4 1.9 + - - +
544E LEU* 4.1 39.3 - - + +
547E GLU 4.4 1.6 - - - +
548E LEU* 3.8 36.1 - - + +
551E ARG* 2.8 29.5 + - - +
586E TRP* 3.5 51.7 + - + -
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Residues in contact with ARG 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 LEU* 2.9 46.3 + - - +
492E SER* 4.3 4.6 - - - +
494E LEU* 1.3 74.8 - - - +
496E GLY* 1.3 63.3 + - - +
497E LYS* 4.7 5.9 - - - +
584E VAL* 3.7 18.2 - - - +
585E ASP* 2.8 38.2 + - - +
586E TRP* 4.4 18.5 - - + +
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Residues in contact with GLY 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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492E SER 3.0 18.3 + - - -
493E GLU* 3.2 9.6 + - - +
494E LEU 3.2 9.5 - - - +
495E ARG* 1.3 84.1 - - - +
497E LYS* 1.3 62.2 + - - +
498E ARG 3.5 3.8 + - - -
551E ARG* 4.0 8.5 + - - -
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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