Contacts of the helix formed by residues 464 - 478 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302C THR* 6.1 1.0 - - - -
460C ARG 5.0 2.7 - - - +
461C TRP* 3.0 11.7 + - - +
462C PHE 3.3 0.6 - - - -
463C SER* 1.3 79.5 - - - +
465C PRO* 1.4 62.4 - - - +
466C THR* 3.0 13.1 + - - -
467C LEU* 2.9 27.9 + - + +
468C THR* 2.8 40.8 + - - -
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Residues in contact with PRO 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C SER 4.1 4.7 - - - +
464C ASP* 1.4 92.1 - - - +
466C THR* 1.3 57.7 + - - +
468C THR* 3.5 7.7 - - + +
469C SER* 3.0 30.5 + - - -
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Residues in contact with THR 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C THR* 4.9 24.8 - - - +
305C CYS* 5.5 3.4 - - - -
306C LEU* 5.7 7.4 - - + -
464C ASP* 3.0 8.2 + - - -
465C PRO* 1.3 77.1 - - - +
467C LEU* 1.3 59.9 + - - +
469C SER* 3.0 8.8 + - - -
470C LEU* 2.8 47.6 + - + +
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Residues in contact with LEU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C ALA* 5.6 6.3 - - + +
461C TRP* 3.8 44.7 - - + +
464C ASP* 2.9 19.9 + - + +
466C THR* 1.3 73.4 - - - +
468C THR* 1.3 56.6 + - - +
470C LEU* 3.7 12.5 - - + +
471C ALA* 2.8 30.8 + - - +
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Residues in contact with THR 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLY* 4.7 9.0 - - - -
461C TRP 3.1 10.8 + - - -
462C PHE* 3.2 36.8 + - + +
464C ASP 2.8 24.5 + - - -
465C PRO* 3.5 8.5 - - + +
467C LEU* 1.3 77.2 - - - +
469C SER* 1.3 63.9 + - - +
471C ALA* 3.3 2.5 + - - +
472C LYS* 3.2 44.0 + - - +
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Residues in contact with SER 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C PRO 3.0 18.4 + - - -
466C THR* 3.0 11.1 + - - -
468C THR* 1.3 75.6 - - - +
470C LEU* 1.3 65.8 + - - +
472C LYS* 3.4 12.6 + - - +
473C LEU* 3.2 25.9 + - - +
494C THR* 5.8 6.3 - - - +
495C LEU* 6.5 0.2 - - - -
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Residues in contact with LEU 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C CYS* 3.9 28.5 - - - -
306C LEU* 6.3 0.2 - - - -
309C VAL* 4.5 5.4 - - + -
411C LEU* 4.2 23.7 - - + +
415C ALA* 4.3 20.6 - - + -
461C TRP* 5.9 0.2 - - + -
466C THR* 2.8 33.5 + - + +
467C LEU* 3.7 9.0 - - + +
468C THR 3.2 0.4 - - - -
469C SER* 1.3 75.7 - - - +
471C ALA* 1.3 66.7 + - - +
473C LEU* 3.3 8.1 + - + +
474C MET* 2.9 30.1 + - - +
495C LEU* 3.5 32.5 - - + -
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Residues in contact with ALA 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C ILE* 4.1 21.9 - - + +
461C TRP* 4.3 5.3 - - + -
462C PHE* 3.9 29.6 - - + -
467C LEU 2.8 19.4 + - - +
468C THR* 3.3 5.6 + - - +
470C LEU* 1.3 72.0 - - - +
472C LYS* 1.3 62.6 + - - +
474C MET* 3.3 15.1 + - - +
475C LYS* 3.1 23.9 + - - +
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Residues in contact with LYS 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B GLN 4.1 20.6 - - - +
229B GLY* 3.9 17.5 + - - -
230B GLU* 6.3 0.4 - - - -
462C PHE* 5.6 2.0 - - + -
468C THR* 3.2 31.3 + - + +
469C SER* 3.7 10.3 - - - +
470C LEU 3.2 0.2 - - - -
471C ALA* 1.3 79.1 - - + +
473C LEU* 1.3 63.5 + - + +
475C LYS* 3.4 6.2 + - - +
476C GLU* 3.2 35.4 + - - +
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Residues in contact with LEU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C LEU* 4.2 11.4 - - + -
469C SER* 3.2 14.9 + - - +
470C LEU* 3.7 13.9 - - + +
471C ALA 3.3 0.2 - - - -
472C LYS* 1.3 76.3 - - - +
474C MET* 1.3 67.2 + - - +
476C GLU* 3.0 18.3 + - - +
477C CYS* 3.1 17.9 + - - -
486C LEU* 3.6 25.8 - - + +
491C ILE* 4.2 18.2 - - + -
494C THR* 4.1 31.0 - - + +
495C LEU* 3.6 36.6 - - + -
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Residues in contact with MET 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLY* 3.8 16.8 - - - +
411C LEU* 3.9 16.2 - - + +
412C TRP* 3.3 35.0 - - + -
415C ALA* 5.1 0.4 - - - -
457C ILE* 3.8 16.2 - - + -
461C TRP* 3.7 20.2 - - + -
470C LEU* 2.9 24.7 + - - +
471C ALA* 3.5 7.2 - - - +
473C LEU* 1.3 75.1 - - - +
475C LYS* 1.3 57.3 + - - +
477C CYS* 2.9 30.4 + - - +
478C TRP* 3.1 47.5 + - + -
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Residues in contact with LYS 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ILE* 5.3 6.7 - - + -
471C ALA 3.1 13.5 + - - +
472C LYS* 3.8 6.7 - - - +
473C LEU 3.2 0.2 - - - -
474C MET* 1.3 78.3 - - - +
476C GLU* 1.3 61.2 + - + +
478C TRP* 3.1 28.8 + - + +
479C TYR* 3.7 17.5 + - + +
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Residues in contact with GLU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C LYS* 3.2 25.0 + - - +
473C LEU* 3.0 7.3 + - - +
475C LYS* 1.3 77.5 - - + +
477C CYS* 1.3 57.7 + - - +
478C TRP 3.4 0.2 - - - -
479C TYR* 3.5 32.5 + - + +
485C ARG* 3.3 10.4 - - - -
486C LEU* 3.2 59.8 + - + +
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Residues in contact with CYS 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C ILE* 3.5 30.5 - - - +
405C TRP* 3.6 12.5 - - - -
407C PHE* 4.2 5.2 - - - -
408C GLY* 3.9 21.5 - - - -
411C LEU* 5.0 1.3 - - - -
473C LEU 3.1 18.1 + - - -
474C MET* 2.9 10.5 + - - +
476C GLU* 1.3 80.0 - - - +
478C TRP* 1.3 58.0 + - + +
479C TYR 3.6 1.1 - - - -
485C ARG* 3.1 23.4 + - - -
486C LEU* 5.1 1.6 - - - -
491C ILE* 3.8 28.9 - - - -
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Residues in contact with TRP 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C TRP* 3.4 28.7 + + - -
408C GLY* 3.5 36.8 - - - -
409C LEU* 3.6 10.5 - - + +
412C TRP* 4.2 2.7 - + + -
454C ARG* 2.6 62.5 + - + -
455C PRO* 3.7 48.5 - - + -
457C ILE* 4.4 9.9 - - + -
474C MET* 3.1 52.3 - - + -
475C LYS* 3.1 13.4 + - + +
477C CYS* 1.3 86.9 - - + +
479C TYR* 1.3 61.2 + - - +
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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