Contacts of the helix formed by residues 486 - 501 (chain A) in PDB entry 6BFN
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 PRO 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A TRP* 4.2 12.8 - - + -
484A PRO 3.8 6.7 - - - +
485A CYS* 1.3 88.3 - - - +
487A PRO* 1.3 73.2 - - + +
488A GLU* 3.2 15.5 - - - +
489A LEU* 3.1 13.9 + - + +
490A GLY 3.0 18.7 + - - -
524A VAL* 4.3 14.6 - - + +
525A VAL* 5.9 4.0 - - + -
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Residues in contact with PRO 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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474A TYR* 3.5 27.1 - - + +
485A CYS 3.3 3.1 - - - +
486A PRO* 1.3 83.1 - - + +
488A GLU* 1.3 72.0 + - + +
491A LEU* 2.9 47.8 + - + +
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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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486A PRO* 3.6 13.7 - - - +
487A PRO* 1.3 90.4 - - + +
489A LEU* 1.3 57.7 + - - +
491A LEU* 4.3 2.8 - - - +
492A GLY* 2.9 27.7 + - - -
521A LEU* 3.8 10.3 - - + +
524A VAL* 3.3 28.7 - - + +
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Residues in contact with LEU 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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312A TRP* 3.7 44.6 - - + +
316A LEU* 3.7 29.2 - - + -
485A CYS* 4.4 6.5 - - - -
486A PRO* 3.1 15.5 + - + +
488A GLU* 1.3 80.0 - - - +
490A GLY* 1.3 57.1 + - - +
492A GLY* 3.8 0.2 - - - -
493A LEU* 2.9 59.6 + - + +
521A LEU* 4.4 9.1 - - + +
524A VAL* 3.8 25.8 - - + +
525A VAL* 4.7 7.9 - - + -
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Residues in contact with GLY 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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418A LEU* 4.4 13.8 - - - +
470A ALA 5.5 0.3 - - - +
473A ILE* 6.0 0.7 - - - +
474A TYR* 3.9 21.1 - - - +
478A LEU* 4.9 1.4 - - - +
485A CYS* 3.6 19.4 - - - -
486A PRO 3.0 9.7 + - - -
489A LEU* 1.3 78.8 - - - +
491A LEU* 1.3 56.6 + - - +
493A LEU* 3.9 1.6 - - - +
494A GLY* 2.9 25.6 + - - -
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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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467A ALA 5.3 0.9 - - - +
470A ALA* 4.0 8.4 - - + +
471A MET* 3.7 55.4 - - + +
474A TYR* 3.7 22.2 - - + -
487A PRO* 2.9 32.3 + - + +
488A GLU* 4.3 2.0 - - - +
490A GLY* 1.3 73.0 - - - +
492A GLY* 1.3 61.1 + - - +
494A GLY* 3.8 0.3 - - - -
495A GLN* 2.9 33.7 + - - +
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Residues in contact with GLY 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 2.9 19.6 + - - -
489A LEU 3.8 0.4 - - - -
491A LEU* 1.3 77.7 - - - +
493A LEU* 1.3 55.9 + - - +
495A GLN* 3.8 6.2 - - - +
496A LEU* 2.9 29.6 + - - +
521A LEU* 3.8 19.1 - - - +
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Residues in contact with LEU 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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312A TRP* 5.2 7.2 - - + +
315A ARG* 6.0 1.8 - - + -
316A LEU* 4.4 9.2 - - + +
319A LEU* 4.1 24.7 - - + -
414A VAL* 3.7 6.5 - - + +
417A THR* 6.3 0.7 - - + -
418A LEU* 3.8 30.3 - - + -
489A LEU* 2.9 42.4 + - + +
490A GLY 3.9 1.6 - - - +
492A GLY* 1.3 72.8 - - - +
494A GLY* 1.3 61.6 + - - +
496A LEU* 3.3 8.4 + - + +
497A ALA* 2.9 29.6 + - - +
518A LEU* 3.6 31.6 - - + -
521A LEU* 3.8 9.2 - - + +
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Residues in contact with GLY 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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418A LEU* 3.7 12.9 - - - +
470A ALA* 3.9 14.1 - - - -
473A ILE* 4.5 13.6 - - - +
490A GLY 2.9 17.5 + - - -
491A LEU 3.8 1.1 - - - -
493A LEU* 1.3 76.6 - - - +
495A GLN* 1.3 56.0 + - - +
497A ALA* 3.2 6.3 + - - +
498A CYS* 2.9 31.4 + - - -
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Residues in contact with GLN 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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463A ASP* 3.1 34.0 + - + +
464A ALA* 4.6 2.4 - - - +
466A ALA* 4.2 12.6 - - + -
467A ALA* 4.4 16.4 - - - +
470A ALA* 3.6 11.2 - - + +
491A LEU* 2.9 19.2 + - - +
492A GLY* 3.8 5.7 - - - +
494A GLY* 1.3 73.1 - - - +
496A LEU* 1.3 66.0 + - - +
498A CYS* 3.1 7.5 + - - +
499A CYS* 2.9 30.4 + - - -
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Residues in contact with LEU 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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410A PHE* 4.6 7.0 - - + -
414A VAL* 4.6 8.5 - - + -
492A GLY 2.9 19.3 + - - +
493A LEU* 3.6 8.5 - - + +
495A GLN* 1.3 75.5 - - - +
497A ALA* 1.3 57.8 + - - +
499A CYS* 3.3 6.4 + - - +
500A CYS* 2.9 35.2 + - - -
514A VAL* 4.1 36.3 - - + -
517A ARG* 4.0 33.2 - - + +
518A LEU* 3.7 38.8 - - + +
521A LEU* 5.7 1.8 - - + -
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Residues in contact with ALA 497 (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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411A GLY* 4.2 7.2 - - - +
414A VAL* 3.8 19.0 - - + +
415A LEU* 4.1 28.5 - - + -
418A LEU* 5.0 0.2 - - + -
438A VAL* 5.1 0.9 - - + -
473A ILE* 5.6 0.7 - - + -
493A LEU 2.9 14.5 + - - +
494A GLY* 3.2 10.1 + - - +
496A LEU* 1.3 74.3 - - - +
498A CYS* 1.3 65.2 + - - +
500A CYS* 3.3 5.5 + - - -
501A LEU* 2.9 31.0 + - - +
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Residues in contact with CYS 498 (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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438A VAL* 4.2 22.2 - - + +
465A TRP* 3.8 18.2 - - + -
466A ALA* 3.6 24.0 - - + -
469A ILE* 3.7 35.0 - - - -
470A ALA 4.3 1.6 - - - -
473A ILE* 4.3 5.8 - - - -
494A GLY 2.9 21.8 + - - -
495A GLN 3.1 7.8 + - - +
497A ALA* 1.3 76.8 - - - +
499A CYS* 1.3 62.5 + - - +
501A LEU* 3.2 10.9 + - - +
502A HIS* 3.2 9.5 + - - -
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Residues in contact with CYS 499 (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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463A ASP* 3.5 41.1 - - - -
465A TRP* 4.5 9.6 - - - -
466A ALA* 4.8 5.4 - - - -
495A GLN* 2.9 24.3 + - - +
496A LEU 3.6 6.7 - - - +
498A CYS* 1.3 77.4 - - - +
500A CYS* 1.3 62.4 + - - +
501A LEU 3.4 0.2 + - - -
502A HIS* 3.4 15.8 - - - +
507A ARG 4.4 1.5 - - - +
508A ARG* 3.9 2.4 - - - -
509A PRO* 3.5 22.4 - - + +
517A ARG* 3.7 21.8 - - - +
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Residues in contact with CYS 500 (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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407A THR* 3.6 31.6 - - + +
408A PHE* 3.5 12.1 + - - -
410A PHE* 4.6 9.0 - - - -
411A GLY* 3.7 18.6 - - - -
414A VAL* 5.9 0.2 - - - -
496A LEU* 2.9 30.2 + - - +
497A ALA 3.8 0.4 - - - +
498A CYS 3.3 0.2 - - - -
499A CYS* 1.3 77.2 - - - +
501A LEU* 1.3 60.7 + - - +
502A HIS 3.2 1.3 + - - -
508A ARG* 3.5 20.4 - - - -
509A PRO* 4.3 4.5 - - - -
514A VAL* 3.8 28.7 - - - -
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Residues in contact with LEU 501 (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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408A PHE* 3.4 57.1 - - + +
411A GLY 3.9 8.7 - - - +
412A VAL* 3.7 17.9 - - + +
415A LEU* 3.6 35.7 - - + -
435A LYS* 4.4 12.8 - - + +
438A VAL* 3.7 23.2 - - + +
497A ALA 2.9 19.0 + - - +
498A CYS 3.2 4.4 + - - +
500A CYS* 1.3 74.9 - - - +
502A HIS* 1.3 66.7 + - - +
503A ARG* 3.3 2.8 + - - -
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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