Contacts of the helix formed by residues 464 - 478 (chain B) in PDB entry 4BGG
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 ASP 464 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B THR* 4.9 2.1 + - - -
418B MET* 3.9 15.9 - - - +
419B VAL 5.2 0.2 - - - +
420B SER* 3.3 29.5 + - - +
421B ASN* 4.7 2.6 - - - +
460B ARG 4.8 0.2 - - - +
461B TRP 2.9 10.3 + - - +
462B PHE 3.3 0.8 - - - -
463B SER* 1.3 79.8 - - - +
465B PRO* 1.4 60.1 - - - +
466B THR* 3.0 12.9 + - - -
467B LEU* 2.9 27.4 + - + +
468B THR* 2.8 41.4 + - - -
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Residues in contact with PRO 465 (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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463B SER 4.1 4.9 - - - +
464B ASP* 1.4 91.8 - - - +
466B THR* 1.3 58.6 + - - +
468B THR* 3.5 8.4 - - + +
469B SER* 3.0 30.1 + - - -
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Residues in contact with THR 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B THR* 3.4 30.3 + - + +
306B LEU* 4.0 29.4 - - + -
418B MET* 4.4 14.4 - - - -
464B ASP* 3.0 9.0 + - - -
465B PRO* 1.3 77.6 - - - +
467B LEU* 1.3 61.9 + - - +
469B SER* 3.0 8.3 + - - +
470B LEU* 2.8 37.9 + - + +
498B ILE* 4.6 14.6 - - + +
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Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ALA* 3.6 39.5 - - + +
418B MET* 4.1 23.8 - - + +
420B SER* 3.9 15.7 - - - +
460B ARG* 3.4 30.1 - - - +
461B TRP* 3.6 44.2 - - + +
464B ASP* 2.9 13.4 + - + +
466B THR* 1.3 76.6 - - - +
468B THR* 1.3 57.3 + - - +
470B LEU* 3.7 7.8 - - + +
471B ALA* 2.8 31.0 + - - +
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Residues in contact with THR 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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461B TRP 3.0 11.5 + - - -
462B PHE* 3.2 37.9 + - + +
464B ASP 2.8 23.9 + - - -
465B PRO* 3.5 9.2 - - + +
467B LEU* 1.3 77.5 - - - +
469B SER* 1.3 63.8 + - - +
471B ALA* 3.3 3.2 + - - +
472B LYS* 3.3 19.8 + - - +
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Residues in contact with SER 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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465B PRO 3.0 17.3 + - - -
466B THR* 3.0 8.9 + - - -
468B THR* 1.3 76.4 - - - +
470B LEU* 1.3 62.7 + - - +
472B LYS* 3.4 9.0 + - - +
473B LEU* 3.2 25.6 + - - +
494B THR* 5.8 4.3 - - - +
498B ILE* 3.8 30.2 - - - +
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Residues in contact with LEU 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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305B CYS* 3.9 28.3 - - - -
306B LEU* 4.5 9.0 - - + -
309B VAL* 4.5 2.7 - - + -
411B LEU* 4.2 20.9 - - + +
415B ALA* 4.3 20.0 - - + -
461B TRP* 5.8 0.2 - - + -
466B THR* 2.8 32.9 + - + +
467B LEU* 3.2 11.6 + - + +
469B SER* 1.3 71.3 - - - +
471B ALA* 1.3 60.6 + - - +
473B LEU* 3.3 10.3 + - + +
474B MET* 2.9 36.3 + - - +
495B LEU* 3.5 32.3 - - + -
498B ILE* 5.1 2.7 - - + -
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Residues in contact with ALA 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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457B ILE* 4.1 23.4 - - + +
461B TRP* 4.3 4.9 - - + -
462B PHE* 3.9 28.0 - - + -
467B LEU 2.8 20.4 + - - +
468B THR 3.3 5.4 + - - +
470B LEU* 1.3 72.0 - - - +
472B LYS* 1.3 63.0 + - - +
474B MET* 3.3 14.1 + - - +
475B LYS* 3.1 23.4 + - - +
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Residues in contact with LYS 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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468B THR 3.3 8.9 + - - +
469B SER* 3.6 11.7 - - - +
470B LEU 3.2 0.6 - - - -
471B ALA* 1.3 80.1 - - - +
473B LEU* 1.3 61.4 + - - +
475B LYS* 3.4 5.6 + - - +
476B GLU* 3.2 53.0 + - + +
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 4.2 11.9 - - + -
469B SER 3.2 10.3 + - - +
470B LEU* 3.7 17.5 - - + +
471B ALA 3.3 0.2 - - - -
472B LYS* 1.3 76.2 - - - +
474B MET* 1.3 68.7 + - - +
476B GLU* 3.0 18.5 + - - +
477B CYS* 3.1 17.2 + - - -
486B LEU* 3.6 26.3 - - + +
491B ILE* 4.2 17.5 - - + -
494B THR* 4.1 31.6 - - + +
495B LEU* 3.6 36.1 - - + -
498B ILE* 5.9 1.6 - - + -
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Residues in contact with MET 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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408B GLY* 3.8 16.8 - - - +
411B LEU* 4.0 16.8 - - + +
412B TRP* 3.3 35.0 - - + -
415B ALA* 5.1 0.4 - - - -
457B ILE* 3.9 16.8 - - + -
461B TRP* 3.7 20.6 - - + -
470B LEU* 2.9 25.5 + - - +
471B ALA* 3.3 6.9 + - - +
473B LEU* 1.3 73.9 - - - +
475B LYS* 1.3 64.4 + - - +
477B CYS* 2.9 22.6 + - - +
478B TRP* 3.1 46.2 + - + -
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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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457B ILE* 5.4 6.7 - - + -
471B ALA 3.1 12.5 + - - +
472B LYS* 3.9 6.3 - - - +
473B LEU 3.2 0.4 - - - -
474B MET* 1.3 79.3 - - - +
476B GLU* 1.3 61.4 + - + +
477B CYS 3.2 0.2 - - - -
478B TRP* 3.1 29.9 + - + +
479B TYR* 3.8 19.5 + - + -
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Residues in contact with GLU 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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472B LYS* 3.2 46.0 + - + +
473B LEU* 3.0 9.4 + - - +
475B LYS* 1.3 78.5 - - + +
477B CYS* 1.3 59.4 + - - +
478B TRP 3.5 0.4 - - - -
479B TYR* 3.4 32.2 + - + +
485B ARG* 3.3 10.2 - - - -
486B LEU* 3.2 57.7 + - + +
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Residues in contact with CYS 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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404B ILE* 3.5 29.8 - - - +
405B TRP* 3.6 12.8 - - - -
407B PHE* 4.2 4.7 - - - -
408B GLY* 3.8 21.1 - - - -
411B LEU* 5.0 1.3 - - - -
473B LEU 3.1 18.7 + - - -
474B MET* 2.9 10.1 + - - +
476B GLU* 1.3 78.8 - - - +
478B TRP* 1.3 57.7 + - + +
479B TYR 3.6 1.3 - - - -
485B ARG* 3.1 22.9 + - - -
486B LEU* 5.0 1.3 - - - -
491B ILE* 3.8 29.4 - - - -
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Residues in contact with TRP 478 (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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405B TRP* 3.4 29.6 + + - -
408B GLY* 3.5 36.9 - - - -
409B LEU* 3.6 8.7 - - + +
412B TRP* 4.2 2.7 - + + -
454B ARG* 2.6 64.9 + - + -
455B PRO* 3.7 46.0 - - + -
457B ILE* 4.4 10.1 - - + -
474B MET* 3.1 50.3 - - + -
475B LYS* 3.1 13.6 + - + +
477B CYS* 1.3 86.1 - - + +
479B TYR* 1.3 59.6 + - - +
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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