Contacts of the helix formed by residues 465 - 477 (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 TRP 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438B VAL* 4.4 14.1 - - + -
439B GLU* 4.8 8.1 - - - -
442B ALA* 5.6 3.1 - - + -
447B VAL* 4.2 28.8 - - + +
448B ALA* 4.6 15.9 - - + -
464B ALA* 1.3 82.5 - - - +
466B ALA* 1.3 72.7 + - + +
468B PRO* 3.3 14.1 - - - +
469B ILE* 4.2 27.1 - - + +
498B CYS* 3.6 30.1 - - + -
499B CYS* 4.5 11.7 - - - +
502B HIS* 3.3 39.8 - + + -
503B ARG* 5.5 0.9 - - - -
507B ARG* 4.2 22.1 - - - +
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Residues in contact with ALA 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ALA* 3.0 3.8 - - - -
465B TRP* 1.3 89.4 - - + +
467B ALA* 1.3 65.7 - - - +
469B ILE* 2.8 19.8 + - - +
470B ALA* 2.9 10.9 + - - +
495B GLN* 4.0 21.3 - - + +
498B CYS* 3.6 29.9 - - + -
499B CYS* 4.3 13.0 - - - -
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Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ALA* 3.3 16.3 + - + +
466B ALA* 1.3 78.0 - - - +
468B PRO* 1.4 68.9 - - + +
470B ALA* 3.2 10.1 + - - +
471B MET* 2.9 30.4 + - + +
491B LEU* 5.9 0.3 - - - +
495B GLN* 4.1 20.5 + - - +
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Residues in contact with PRO 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B ALA* 5.4 7.2 - - + -
447B VAL* 5.2 13.7 - - + -
464B ALA 3.7 6.7 - - - +
465B TRP* 3.3 18.2 - - - +
466B ALA 3.4 0.2 - - - -
467B ALA* 1.4 93.9 - - + +
469B ILE* 1.3 59.0 + - + +
471B MET* 3.0 10.9 + - + +
472B GLN* 2.9 30.9 + - - +
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Residues in contact with ILE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B VAL* 3.9 33.9 - - + +
441B GLU* 3.8 31.6 - - + +
442B ALA* 4.1 15.7 - - + -
445B ALA* 5.6 1.1 - - + -
447B VAL* 5.2 7.2 - - + -
465B TRP* 4.2 28.0 - - + +
466B ALA* 2.8 12.2 + - - +
468B PRO* 1.3 73.8 - - + +
470B ALA* 1.3 57.4 + - - +
472B GLN* 3.2 8.9 + - - +
473B ILE* 2.9 43.5 + - + +
498B CYS* 3.7 19.3 - - - -
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Residues in contact with ALA 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B ALA 2.9 9.2 + - - +
467B ALA* 3.3 9.9 - - - +
469B ILE* 1.3 77.1 - - - +
471B MET* 1.3 56.3 + - - +
473B ILE* 3.5 10.2 + - - +
474B TYR* 2.9 29.0 + - - +
490B GLY 5.2 1.2 - - - +
491B LEU* 3.9 16.1 - - + +
494B GLY* 4.0 5.9 - - - -
495B GLN* 3.6 41.1 - - + +
498B CYS* 4.5 0.8 - - - -
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Residues in contact with MET 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B ALA* 2.9 18.0 + - + +
468B PRO* 3.3 11.2 - - + +
470B ALA* 1.3 73.3 - - - +
472B GLN* 1.3 59.2 + - - +
474B TYR* 3.1 11.8 + - + +
475B LYS* 2.9 56.9 + - + +
491B LEU* 4.1 30.2 - - + +
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Residues in contact with GLN 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B GLU* 2.9 54.9 + - + +
444B GLU* 4.1 8.1 - - - +
445B ALA* 3.7 20.8 - - - +
468B PRO* 2.9 15.7 + - - +
469B ILE* 3.2 11.9 + - - +
471B MET* 1.3 76.5 - - + +
473B ILE* 1.3 56.5 + - - +
475B LYS* 4.9 4.5 - - - -
476B LYS* 2.9 63.6 + - - +
477B HIS* 4.8 0.2 - - - -
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Residues in contact with ILE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B LEU* 4.2 29.4 - - + -
418B LEU* 4.7 16.8 - - + -
419B ALA* 5.9 2.0 - - + +
437B LEU* 4.5 8.7 - - + -
438B VAL* 5.1 4.7 - - + -
441B GLU* 4.9 2.9 - - + -
469B ILE* 2.9 40.5 + - + +
470B ALA* 3.8 6.5 - - - +
472B GLN* 1.3 72.4 - - - +
474B TYR* 1.3 65.0 + - - +
477B HIS* 2.8 56.1 + - + -
478B LEU* 3.2 14.2 + - + +
494B GLY* 4.9 6.7 - - - +
498B CYS* 4.4 11.0 - - - -
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Residues in contact with TYR 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B ALA 2.9 19.0 + - - +
471B MET* 3.1 11.0 + - - +
473B ILE* 1.3 76.7 - - - +
475B LYS* 1.3 72.7 + - + +
478B LEU* 3.2 40.4 - - + +
485B CYS* 3.1 36.1 + - - -
487B PRO* 3.5 35.6 - - + +
490B GLY* 3.9 13.7 - - - +
491B LEU* 3.7 24.9 - - + +
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Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B MET* 2.9 41.4 + - + +
472B GLN* 4.0 3.4 - - - +
474B TYR* 1.3 91.4 - - + +
476B LYS* 1.3 70.8 + - + +
478B LEU* 4.6 3.1 + - - +
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Residues in contact with LYS 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B GLU* 4.0 10.6 + - - +
444B GLU* 3.1 22.4 + - - -
472B GLN* 2.9 49.3 + - - +
475B LYS* 1.3 81.8 - - + +
477B HIS* 1.3 80.4 + - + +
478B LEU 3.7 2.8 + - - +
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Residues in contact with HIS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ALA* 3.1 27.7 - - + +
421B GLN* 4.7 10.4 + - - +
437B LEU* 3.5 39.3 - - + +
441B GLU* 3.4 29.9 + - - -
473B ILE* 2.8 43.7 + - + +
476B LYS* 1.3 92.3 + - + +
478B LEU* 1.3 64.6 + - - +
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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