Contacts of the helix formed by residues 482 - 496 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480F GLU 3.7 1.6 + - - -
481F TRP* 1.3 76.2 - - - +
483F GLU* 1.3 58.7 + - - +
484F ASP* 3.2 12.8 + - - +
485F LYS* 3.1 24.0 + - - +
486F ARG* 2.8 28.3 + - - +
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Residues in contact with GLU 483 (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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481F TRP 4.0 0.2 + - - -
482F SER* 1.3 75.0 - - - +
484F ASP* 1.3 63.4 + - - +
486F ARG* 3.3 9.7 + - - +
487F GLN* 2.9 51.1 + - - +
539F ALA* 3.3 24.5 - - + +
540F PRO* 5.0 0.7 - - + -
541F SER* 2.4 47.6 + - - -
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Residues in contact with ASP 484 (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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482F SER* 3.1 9.6 + - - +
483F GLU* 1.3 80.6 - - - +
485F LYS* 1.3 64.5 + - - +
487F GLN* 3.5 14.4 + - - +
488F GLU* 3.1 26.0 + - - +
580F ARG* 5.8 2.8 + - - -
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Residues in contact with LYS 485 (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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481F TRP* 3.7 51.0 - - + +
482F SER* 3.1 21.4 + - - +
484F ASP* 1.3 74.3 - - - +
486F ARG* 1.3 65.0 + - - +
488F GLU* 3.0 35.8 - - - +
489F TRP* 3.1 12.5 + - + +
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Residues in contact with ARG 486 (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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460F GLU* 3.9 19.8 + - - -
463F THR* 4.0 7.7 - - - +
478F TYR* 3.3 60.0 + - + +
479F ARG* 3.0 37.4 + - - +
481F TRP* 3.3 21.4 + - + +
482F SER 2.8 22.7 + - - +
483F GLU* 3.5 11.1 + - - +
485F LYS* 1.3 72.8 - - - +
487F GLN* 1.3 57.7 + - - +
489F TRP* 3.2 2.1 + - - +
490F LEU* 2.8 36.1 + - - +
541F SER* 4.0 18.4 + - - -
542F ASP* 5.0 4.8 + - - -
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Residues in contact with GLN 487 (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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483F GLU* 2.9 48.1 + - - +
484F ASP* 3.8 12.9 + - - +
486F ARG* 1.3 75.1 - - - +
488F GLU* 1.3 63.9 + - - +
490F LEU* 3.9 7.1 - - - +
491F LEU* 2.9 37.8 + - + +
540F PRO* 3.6 28.1 - - + +
541F SER* 4.6 7.4 - - - +
544F LEU* 4.8 10.8 - - + -
580F ARG* 3.5 28.2 - - - +
584F VAL* 5.9 1.6 - - - +
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Residues in contact with GLU 488 (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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484F ASP 3.1 14.7 + - - +
485F LYS* 3.0 38.3 - - - +
487F GLN* 1.3 76.0 - - - +
489F TRP* 1.3 63.8 + - - +
491F LEU* 4.0 5.3 - - - +
492F SER* 3.0 22.3 + - - -
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Residues in contact with TRP 489 (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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466F ILE* 3.9 17.3 - - + -
469F ILE* 5.3 1.1 - - + -
470F THR* 3.9 11.7 - - + -
475F ILE* 3.6 34.4 - - + +
478F TYR* 4.3 3.6 - + - -
481F TRP* 3.5 30.8 - + + -
485F LYS* 3.1 19.0 + - + +
486F ARG 3.7 2.0 - - - +
488F GLU* 1.3 79.8 - - + +
490F LEU* 1.3 92.4 + - + +
492F SER* 3.0 13.1 + - - -
493F GLU* 2.9 45.0 + - + +
500F LEU* 3.7 26.0 - - + -
548F LEU* 4.1 8.1 - - + -
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Residues in contact with LEU 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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466F ILE* 4.0 16.4 - - + -
478F TYR* 3.4 25.4 - - + +
486F ARG 2.8 24.1 + - - +
487F GLN* 3.9 3.6 - - - +
489F TRP* 1.3 87.8 - - + +
491F LEU* 1.3 58.6 + - - +
493F GLU* 3.2 4.6 + - - +
494F LEU* 2.8 36.0 + - + +
541F SER* 3.7 29.6 - - - +
544F LEU* 4.0 21.3 - - + +
545F ALA* 4.0 7.6 - - - +
548F LEU* 3.8 26.1 - - + +
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Residues in contact with LEU 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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487F GLN* 2.9 28.5 + - + +
488F GLU* 4.2 4.7 - - - +
490F LEU* 1.3 72.8 - - - +
492F SER* 1.3 66.2 + - - +
494F LEU* 4.2 15.0 - - + -
495F ARG* 2.9 57.6 + - - +
544F LEU* 4.0 24.9 - - + -
584F VAL* 3.6 43.7 - - + -
586F TRP* 4.8 8.3 - - + -
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Residues in contact with SER 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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488F GLU 3.0 16.1 + - - -
489F TRP* 3.0 18.4 + - - -
491F LEU* 1.3 76.6 - - - +
493F GLU* 1.3 65.6 + - - +
495F ARG* 3.9 3.1 - - - +
496F GLY* 3.0 24.1 + - - -
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Residues in contact with GLU 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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475F ILE* 5.4 0.3 - - - +
489F TRP* 2.9 58.3 + - + +
490F LEU 3.7 5.8 - - - +
492F SER* 1.3 78.0 + - - +
494F LEU* 1.3 64.7 + - - +
496F GLY* 3.3 12.6 + - - +
498F ARG 4.3 4.0 - - - +
500F LEU* 4.1 8.9 - - + +
548F LEU* 4.0 18.6 - - + -
551F ARG* 2.9 20.3 + - - +
498G ARG* 2.8 43.5 + - - -
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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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490F LEU* 2.8 28.6 + - + +
491F LEU* 4.0 10.1 - - + +
492F SER 3.4 0.2 - - - -
493F GLU* 1.3 74.5 - - - +
495F ARG* 1.3 61.0 + - - +
496F GLY 3.4 2.3 - - - +
544F LEU* 4.1 41.7 - - + +
547F GLU 4.3 1.8 - - - +
548F LEU* 3.7 36.6 - - + +
551F ARG* 2.9 27.3 + - - +
586F TRP* 3.5 53.8 + - + +
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Residues in contact with ARG 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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491F LEU* 2.9 48.2 + - + +
492F SER* 4.3 3.1 - - - +
494F LEU* 1.3 72.4 - - - +
496F GLY* 1.3 64.8 + - - +
497F LYS* 4.5 9.2 + - - +
584F VAL* 3.8 17.1 - - - +
585F ASP* 2.9 37.1 + - - +
586F TRP* 4.5 20.3 - - + +
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Residues in contact with GLY 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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492F SER 3.0 17.3 + - - -
493F GLU* 3.3 10.2 + - - +
494F LEU 3.2 10.2 - - - +
495F ARG* 1.3 82.5 - - - +
497F LYS* 1.3 63.7 + - - +
498F ARG* 3.5 3.8 - - - -
551F ARG* 4.1 8.7 + - - -
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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