Contacts of the helix formed by residues 482 - 496 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A GLU 3.7 2.4 + - - -
481A TRP* 1.3 75.5 - - - +
483A GLU* 1.3 60.3 + - - +
484A ASP* 3.6 9.8 + - - +
485A LYS* 3.2 21.1 + - - +
486A ARG* 2.9 28.7 + - - +
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Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A SER* 1.3 75.0 - - - +
484A ASP* 1.3 64.7 + - - +
486A ARG* 3.5 10.4 + - - +
487A GLN* 2.7 57.2 + - - +
539A ALA* 3.2 27.0 - - + +
540A PRO* 3.5 1.7 - - + +
541A SER* 2.9 38.4 + - - -
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Residues in contact with ASP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A SER* 3.2 9.6 + - - +
483A GLU* 1.3 83.2 + - - +
485A LYS* 1.3 60.0 + - - +
487A GLN* 3.3 9.3 + - - +
488A GLU* 2.9 30.3 + - - +
580A ARG* 4.4 15.8 + - - -
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Residues in contact with LYS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A TRP* 3.7 50.5 - - + +
482A SER* 3.2 18.3 + - - +
484A ASP* 1.3 77.8 - - - +
486A ARG* 1.3 62.3 + - - +
488A GLU* 3.9 9.1 - - - +
489A TRP* 3.1 24.1 + - + +
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A GLU* 4.9 6.5 + - - -
463A THR* 3.9 23.6 + - - +
478A TYR* 3.2 49.9 + - + +
479A ARG* 2.9 35.2 + - - +
481A TRP* 3.2 22.6 + - + +
482A SER 2.9 21.6 + - - +
483A GLU* 3.6 11.9 + - - +
485A LYS* 1.3 76.4 - - - +
487A GLN* 1.3 56.8 + - - +
489A TRP* 3.3 2.1 + - - +
490A LEU* 2.9 36.1 + - - +
541A SER* 3.7 21.2 + - - +
542A ASP* 5.0 5.5 + - - -
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Residues in contact with GLN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A GLU* 2.7 51.7 + - - +
484A ASP* 3.7 8.1 - - - +
486A ARG* 1.3 75.1 - - - +
488A GLU* 1.3 64.5 + - - +
489A TRP 3.1 0.3 + - - -
490A LEU* 4.6 3.1 - - - -
491A LEU* 2.9 40.2 + - + +
540A PRO* 3.6 23.7 - - - +
541A SER* 4.5 8.7 - - - +
544A LEU* 4.8 8.5 - - + -
580A ARG* 3.4 32.7 + - - +
584A VAL* 5.8 2.1 - - - +
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Residues in contact with GLU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A ASP 2.9 17.8 + - - +
485A LYS* 3.9 9.1 - - - +
487A GLN* 1.3 75.3 - - - +
489A TRP* 1.3 61.6 + - - +
491A LEU* 4.1 3.4 - - - +
492A SER* 3.1 24.4 + - - -
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Residues in contact with TRP 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ILE* 3.9 17.7 - - + -
469A ILE* 5.2 1.3 - - + -
470A THR* 3.9 21.3 - - + -
475A ILE* 4.0 27.6 - - + +
478A TYR* 4.3 4.3 - + - -
481A TRP* 3.5 33.0 - + + -
485A LYS* 3.1 19.2 + - + +
486A ARG 3.8 1.6 - - - +
487A GLN 3.1 0.2 - - - -
488A GLU* 1.3 75.3 - - - +
490A LEU* 1.3 93.1 + - + +
492A SER* 3.0 27.2 + - - -
493A GLU* 3.0 30.3 + - + +
500A LEU* 3.8 26.7 - - + -
548A LEU* 4.1 6.7 - - + -
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ILE* 4.0 16.2 - - + -
478A TYR* 3.5 24.2 - - + +
486A ARG 2.9 22.1 + - - +
487A GLN* 3.8 4.5 - - - +
489A TRP* 1.3 90.8 - - + +
491A LEU* 1.3 58.8 + - + +
493A GLU* 3.3 5.2 + - - +
494A LEU* 2.7 40.0 + - + +
541A SER* 3.8 24.2 - - - +
544A LEU* 3.9 13.2 - - + +
545A ALA* 3.8 14.4 - - - +
548A LEU* 3.8 25.9 - - + +
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Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A GLN* 2.9 36.8 + - + +
488A GLU* 4.3 3.4 - - - +
490A LEU* 1.3 80.4 - - + +
492A SER* 1.3 61.8 + - - +
494A LEU* 4.0 12.8 - - + -
495A ARG* 2.8 64.5 + - + +
544A LEU* 3.4 30.7 - - + -
584A VAL* 3.4 41.3 - - + -
586A TRP* 5.5 3.4 - - + -
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Residues in contact with SER 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A GLU* 3.1 21.6 + - - -
489A TRP* 3.0 16.5 + - - -
491A LEU* 1.3 75.9 - - - +
493A GLU* 1.3 66.8 + - - +
495A ARG* 4.0 5.6 - - - +
496A GLY* 3.1 22.7 + - - -
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A ILE* 5.0 1.4 - - - +
489A TRP* 3.0 53.2 + - + +
490A LEU 3.6 7.0 - - - +
492A SER* 1.3 84.6 + - - +
494A LEU* 1.3 62.6 + - - +
496A GLY* 3.2 12.7 + - - +
498A ARG 4.3 5.4 - - - +
500A LEU* 4.1 9.7 - - + +
548A LEU* 3.9 17.9 - - + -
551A ARG* 3.0 19.4 + - - -
498C ARG* 2.8 41.0 + - - -
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Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A LEU* 2.7 31.8 + - + +
491A LEU* 3.4 11.2 + - + +
493A GLU* 1.3 73.7 - - - +
495A ARG* 1.3 61.5 + - - +
496A GLY 3.8 1.0 - - - +
497A LYS* 4.7 3.3 + - - -
544A LEU* 4.1 31.2 - - + +
547A GLU* 4.4 1.6 - - + +
548A LEU* 3.9 35.2 - - + +
551A ARG* 2.9 29.0 + - - +
586A TRP* 3.4 63.2 + - + +
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A LEU* 2.8 56.0 + - - +
492A SER* 4.4 5.0 - - - +
494A LEU* 1.3 74.6 - - - +
496A GLY* 1.3 64.6 + - - +
497A LYS* 3.3 19.8 + - - +
584A VAL* 4.2 3.6 - - - +
585A ASP* 2.9 37.2 + - - +
586A TRP* 4.6 18.2 - - + +
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Residues in contact with GLY 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A SER 3.1 18.4 + - - -
493A GLU* 3.2 14.0 + - - +
494A LEU 3.8 4.3 - - - +
495A ARG* 1.3 82.4 - - - +
497A LYS* 1.3 67.0 + - - +
498A ARG 3.6 2.9 - - - -
551A ARG* 3.9 9.7 + - - -
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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