Contacts of the helix formed by residues 482 - 495 (chain r) in PDB entry 6FF7
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 ASN 482 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481r LEU* 1.3 74.7 - - - +
483r ARG* 1.3 58.5 + - - +
484r ILE 3.2 2.0 - - - +
485r GLN* 3.1 16.3 + - + +
486r SER* 2.6 34.1 + - - -
507r ALA 4.3 15.0 - - - +
508r GLY 5.9 0.4 - - - +
2201r ADP 3.8 31.9 + - + +
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Residues in contact with ARG 483 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461r LEU* 6.0 3.6 - - - +
481r LEU 3.7 1.2 + - - -
482r ASN* 1.3 72.6 - - - +
484r ILE* 1.3 57.8 + - - +
486r SER* 3.5 7.3 - - - -
487r LYS* 2.9 24.7 + - - +
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Residues in contact with ILE 484 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482r ASN* 3.2 1.8 - - + +
483r ARG* 1.3 74.9 - - - +
485r GLN* 1.3 62.4 + - - +
486r SER 3.1 0.9 - - - -
487r LYS* 2.8 25.3 + - + +
488r LEU* 3.0 14.9 + - - +
503r ALA* 5.5 7.4 - - + -
507r ALA* 5.1 19.1 - - + +
680r PHE* 6.1 5.4 - - + -
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Residues in contact with GLN 485 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481r LEU* 4.5 7.0 - - + -
482r ASN* 3.3 28.3 - - + +
484r ILE* 1.3 77.6 - - - +
486r SER* 1.3 57.7 + - - +
488r LEU* 3.4 0.8 + - - -
489r TYR* 3.0 33.9 + - - +
507r ALA 5.7 1.0 + - - +
508r GLY 5.6 4.3 - - - +
511r ASN* 5.5 8.7 - - + +
512r VAL* 5.3 20.0 - - - +
2201r ADP 6.2 0.4 - - - +
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Residues in contact with SER 486 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460r GLN 4.7 4.4 - - - +
461r LEU* 4.4 8.1 - - - -
462r LEU* 3.9 31.1 - - - +
481r LEU* 4.2 9.1 - - - +
482r ASN 2.6 22.9 + - - -
483r ARG* 3.5 8.5 - - - -
485r GLN* 1.3 70.2 - - - +
487r LYS* 1.3 65.6 + - - +
489r TYR* 4.2 9.5 + - - +
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Residues in contact with LYS 487 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483r ARG 2.9 14.0 + - - +
484r ILE* 2.8 16.6 + - - +
486r SER* 1.3 80.7 - - - +
488r LEU* 1.3 60.5 + - + +
489r TYR 3.8 0.3 + - - -
490r ARG* 4.7 7.1 + - - +
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Residues in contact with LEU 488 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484r ILE 3.0 12.2 + - - +
485r GLN 3.8 1.1 - - - +
487r LYS* 1.3 77.4 - - + +
489r TYR* 1.3 64.8 + - - +
490r ARG* 3.1 4.1 + - - -
491r ALA* 3.2 12.0 + - + +
492r ALA* 2.9 20.9 + - - +
512r VAL* 6.3 2.9 - - + -
674r PHE* 5.3 13.0 - - + -
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Residues in contact with TYR 489 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462r LEU* 6.2 3.1 - - + -
485r GLN 3.0 19.0 + - - +
486r SER* 4.2 7.6 + - - +
487r LYS 3.6 2.2 - - - -
488r LEU* 1.3 74.5 - - - +
490r ARG* 1.3 56.5 + - - +
492r ALA* 3.1 10.0 + - - +
493r LEU* 2.9 32.7 + - - +
515r MET* 5.7 5.1 - - + +
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Residues in contact with ARG 490 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486r SER 5.5 0.2 + - - -
487r LYS 4.7 6.8 + - - +
488r LEU 3.1 1.1 + - - -
489r TYR* 1.3 78.3 - - - +
491r ALA* 1.3 59.0 + - - +
493r LEU* 4.9 0.2 - - - +
494r GLU* 2.9 38.0 + - + +
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Residues in contact with ALA 491 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488r LEU* 3.2 14.4 + - + +
490r ARG* 1.3 76.2 - - - +
492r ALA* 1.3 66.2 + - - +
494r GLU* 4.2 0.7 - - - +
495r THR* 3.6 30.3 + - - +
497r GLU 5.2 2.8 - - - +
671r LYS 4.6 15.0 - - - +
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Residues in contact with ALA 492 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488r LEU 2.9 13.5 + - - +
489r TYR* 3.1 15.7 + - - +
491r ALA* 1.3 80.8 - - - +
493r LEU* 1.3 59.6 + - - +
495r THR 3.9 8.7 - - - +
512r VAL* 4.6 8.3 - - + +
515r MET* 4.2 21.3 - - + -
516r CYS* 4.4 17.6 - - + +
519r ARG* 4.3 9.5 - - - +
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Residues in contact with LEU 493 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468r PRO* 6.1 4.7 - - + -
489r TYR 2.9 15.3 + - - +
490r ARG* 4.9 0.4 - - - +
492r ALA* 1.3 74.5 - - + +
494r GLU* 1.3 59.7 + - - +
495r THR 3.6 1.3 + - - -
515r MET* 5.3 6.7 - - + +
519r ARG* 4.3 21.6 - - + +
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Residues in contact with GLU 494 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490r ARG* 2.9 20.7 + - + +
491r ALA* 5.2 0.4 - - - -
493r LEU* 1.3 79.2 - - - +
495r THR* 1.3 59.4 + - - +
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Residues in contact with THR 495 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491r ALA* 3.6 28.0 + - - +
492r ALA 3.9 7.3 - - - +
493r LEU 3.6 2.0 + - - -
494r GLU* 1.3 81.1 - - - +
496r ASP* 1.3 61.0 + - - +
497r GLU* 3.1 24.3 + - - +
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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