Contacts of the helix formed by residues 486 - 501 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B TRP* 5.0 4.3 - - + -
313B PRO* 6.3 0.7 - - + -
484B PRO 4.4 2.5 - - - +
485B CYS* 1.3 89.7 - - + +
487B PRO* 1.3 71.9 - - + +
488B GLU* 3.3 17.7 - - - +
489B LEU* 3.0 35.2 + - + +
490B GLY 3.2 9.7 + - - -
525B VAL* 5.4 9.0 - - + -
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Residues in contact with PRO 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B TYR* 3.5 23.7 - - + +
485B CYS 3.4 2.9 - - - +
486B PRO* 1.3 84.1 - - + +
488B GLU* 1.3 71.2 + - - +
490B GLY 3.5 0.2 + - - -
491B LEU* 2.9 46.3 + - + +
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Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B PRO* 3.3 14.0 - - + +
487B PRO* 1.3 94.8 - - - +
489B LEU* 1.3 60.5 + - + +
491B LEU* 4.2 8.3 - - - -
492B GLY* 2.9 25.5 + - - -
521B LEU* 3.6 11.3 - - + +
524B VAL* 3.9 29.2 - - + +
525B VAL* 5.7 4.0 - - + -
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 4.0 50.9 - - + +
313B PRO* 4.7 1.3 - - + -
316B LEU* 4.5 10.1 - - + -
485B CYS* 4.7 2.2 - - + -
486B PRO* 3.0 25.6 + - + +
488B GLU* 1.3 80.7 - - - +
490B GLY* 1.3 62.2 + - - +
492B GLY* 3.8 0.2 - - - -
493B LEU* 2.9 59.2 + - + +
521B LEU* 4.7 9.1 - - + +
525B VAL* 3.6 39.0 - - + -
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Residues in contact with GLY 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 4.4 15.4 - - - +
470B ALA 5.2 1.6 - - - +
474B TYR* 3.9 21.2 - - - +
478B LEU* 5.3 1.3 - - - +
485B CYS* 4.0 12.3 - - - -
486B PRO 3.2 6.9 + - - -
489B LEU* 1.3 79.4 - - - +
491B LEU* 1.3 65.1 + - - +
493B LEU* 3.4 1.6 + - - +
494B GLY* 2.9 21.3 + - - -
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ALA 5.9 0.4 - - - +
470B ALA* 3.9 12.4 - - + +
471B MET* 4.1 31.0 - - + -
474B TYR* 3.7 31.4 - - + -
487B PRO* 2.9 32.4 + - + +
488B GLU* 4.1 6.1 - - - +
490B GLY* 1.3 74.0 - - - +
492B GLY* 1.3 64.0 + - - +
494B GLY* 3.0 3.1 + - - -
495B GLN* 2.9 40.9 + - - +
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Residues in contact with GLY 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B GLU 2.9 23.5 + - - -
489B LEU 3.8 0.4 - - - -
491B LEU* 1.3 73.1 - - - +
493B LEU* 1.3 56.0 + - - +
495B GLN* 3.3 13.7 + - - +
496B LEU* 2.9 30.0 + - - +
521B LEU* 4.0 20.1 - - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 5.2 3.6 - - + -
315B ARG* 5.7 2.9 - - + -
316B LEU* 4.1 16.8 - - + +
319B LEU* 3.9 25.4 - - + -
414B VAL* 3.7 10.2 - - + +
417B THR* 6.1 1.1 - - + -
418B LEU* 3.8 30.1 - - + -
489B LEU* 2.9 43.4 + - + +
490B GLY 3.9 1.3 - - - +
492B GLY* 1.3 74.7 - - - +
494B GLY* 1.3 56.5 + - - +
496B LEU* 3.5 4.1 + - + +
497B ALA* 2.9 29.8 + - - +
518B LEU* 3.7 30.3 - - + -
521B LEU* 4.2 6.2 - - + +
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Residues in contact with GLY 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 3.7 13.4 - - - +
470B ALA* 4.0 17.3 - - - -
473B ILE* 5.0 7.0 - - - -
490B GLY 2.9 15.2 + - - -
491B LEU 3.4 3.4 - - - -
493B LEU* 1.3 77.9 - - - +
495B GLN* 1.3 56.3 + - - +
497B ALA* 3.3 5.9 + - - +
498B CYS* 2.9 33.4 + - - -
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Residues in contact with GLN 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ALA* 5.4 5.4 - - - +
466B ALA* 4.0 13.3 - - + +
467B ALA* 4.1 23.9 + - - +
470B ALA* 3.6 16.1 - - + +
491B LEU* 2.9 36.6 + - - +
492B GLY* 3.7 10.8 - - - +
494B GLY* 1.3 71.5 - - - +
496B LEU* 1.3 66.5 + - - +
498B CYS* 3.2 2.8 + - - +
499B CYS* 2.9 32.6 + - - -
517B ARG* 5.5 0.7 - - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B PHE* 4.8 4.7 - - + -
414B VAL* 5.3 4.7 - - + -
492B GLY 2.9 17.6 + - - +
493B LEU* 3.7 8.5 - - + +
495B GLN* 1.3 75.5 - - - +
497B ALA* 1.3 57.0 + - - +
499B CYS* 3.3 3.4 + - - +
500B CYS* 2.9 40.3 + - - -
509B PRO* 5.1 1.6 - - + -
514B VAL* 3.7 37.2 - - + +
517B ARG* 3.8 38.8 - - + +
518B LEU* 3.7 39.0 - - + -
521B LEU* 5.6 2.7 - - + -
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Residues in contact with ALA 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLY* 4.3 5.8 - - - +
414B VAL* 3.9 20.1 - - + +
415B LEU* 3.9 30.1 - - + -
438B VAL* 5.2 0.2 - - - -
493B LEU 2.9 19.0 + - - +
494B GLY* 3.3 6.7 - - - +
495B GLN 3.2 0.2 - - - -
496B LEU* 1.3 77.3 - - - +
498B CYS* 1.3 63.8 + - - +
500B CYS* 3.2 6.7 + - - +
501B LEU* 3.0 30.8 + - + +
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Residues in contact with CYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B VAL* 4.1 24.1 - - + +
465B TRP* 3.6 16.5 - - + -
466B ALA* 3.6 28.7 - - + -
469B ILE* 3.7 37.2 - - + -
470B ALA 4.5 0.9 - - - -
473B ILE* 4.4 7.2 - - - -
494B GLY 2.9 18.3 + - - -
495B GLN 3.2 1.8 + - - +
497B ALA* 1.3 75.0 - - - +
499B CYS* 1.3 63.8 + - - +
501B LEU* 3.1 10.9 + - - +
502B HIS 3.2 9.7 + - - -
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Residues in contact with CYS 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B TRP* 4.5 14.6 - - - +
466B ALA* 4.3 13.2 - - - -
495B GLN* 2.9 29.0 + - - +
496B LEU 3.7 3.6 - - - +
498B CYS* 1.3 76.9 - - - +
500B CYS* 1.3 62.5 + - - +
501B LEU 3.4 0.5 + - - -
502B HIS* 3.5 14.6 + - - +
507B ARG 4.5 2.7 - - - +
508B ARG* 3.9 3.1 - - - +
509B PRO* 3.5 23.8 - - + +
517B ARG* 3.9 26.7 - - - +
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Residues in contact with CYS 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B THR* 3.6 31.8 - - - +
408B PHE* 3.6 11.3 + - - -
410B PHE* 4.4 10.5 - - - -
411B GLY* 3.6 21.5 - - - -
414B VAL* 5.9 0.2 - - - -
496B LEU* 2.9 29.5 + - - +
497B ALA* 3.6 4.9 - - - +
499B CYS* 1.3 78.0 - - - +
501B LEU* 1.3 59.2 + - - +
502B HIS 3.3 0.7 - - - -
508B ARG* 3.4 23.9 - - - -
509B PRO* 4.4 2.9 - - - -
514B VAL* 4.1 20.9 - - - -
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Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PHE* 3.4 57.3 - - + +
411B GLY* 3.8 7.4 - - - +
412B VAL* 3.6 17.5 - - + +
415B LEU* 3.6 35.2 - - + -
435B LYS* 4.3 12.8 - - + +
438B VAL* 3.7 24.0 - - + +
439B GLU* 5.4 4.3 - - - +
465B TRP* 5.5 0.7 - - - -
497B ALA 3.0 18.4 + - - +
498B CYS 3.1 6.2 + - - +
500B CYS* 1.3 75.7 - - - +
502B HIS* 1.3 67.9 + - - +
503B ARG* 3.4 2.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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