Contacts of the helix formed by residues 449 - 468 (chain C) in PDB entry 3DBL
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 GLN 449 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C ARG* 3.7 32.6 + - - +
444C GLY* 3.8 2.5 - - - -
445C VAL* 3.0 17.0 + - - +
446C SER* 2.7 44.5 + - - +
448C TYR* 1.3 108.4 + - + +
450C VAL* 1.3 67.4 + - - +
451C GLU 3.5 0.4 + - - -
452C GLU* 3.5 3.1 + - - +
453C ASP* 2.8 40.9 + - - +
231H TYR* 5.6 2.0 + - - -
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Residues in contact with VAL 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C GLY* 3.9 10.3 - - - +
446C SER 3.8 2.9 - - - +
447C ASN* 3.6 17.0 - - - +
448C TYR 3.4 0.2 - - - -
449C GLN* 1.3 80.6 - - - +
451C GLU* 1.3 70.1 + - - +
453C ASP* 2.9 9.4 + - - +
454C ILE* 3.1 30.8 + - + +
483C CYS* 4.5 13.7 - - + +
484C ARG* 5.0 4.5 - - + +
26D ARG* 3.7 44.9 - - + +
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Residues in contact with GLU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ASN 4.8 2.1 + - - +
448C TYR 4.3 9.1 + - - +
450C VAL* 1.3 81.6 - - - +
452C GLU* 1.3 78.3 + - + +
454C ILE* 3.5 20.5 + - - +
455C GLY 4.4 1.2 + - - -
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Residues in contact with GLU 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C TYR 4.8 3.3 + - - +
449C GLN* 3.5 4.9 + - - +
450C VAL 3.1 0.8 + - - -
451C GLU* 1.3 92.9 - - + +
453C ASP* 1.3 65.1 + - - +
454C ILE 3.0 6.6 + - - -
455C GLY* 3.3 10.8 + - - +
456C LYS* 3.6 33.3 + - - +
239H LYS* 5.0 9.7 + - - -
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Residues in contact with ASP 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C PHE* 3.5 13.6 - - + -
441C ARG* 2.3 32.5 + - - -
443C PRO* 4.6 2.0 - - + -
444C GLY 3.1 23.8 + - - +
449C GLN* 2.8 49.4 + - - +
450C VAL* 3.6 3.4 - - - +
452C GLU* 1.3 72.6 - - - +
454C ILE* 1.3 62.2 + - - +
455C GLY 3.4 0.2 - - - -
456C LYS* 3.5 11.3 + - - +
457C LEU* 3.1 24.9 + - - +
483C CYS* 3.7 6.5 - - - -
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Residues in contact with ILE 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C VAL* 3.1 30.9 + - + +
451C GLU* 3.5 12.8 - - - +
452C GLU 3.0 1.2 - - - -
453C ASP* 1.3 77.7 - - - +
455C GLY* 1.3 64.4 + - - +
457C LEU* 3.5 0.7 + - - +
458C LYS* 3.3 17.1 + - + +
479C VAL* 3.6 20.3 - - + +
480C HIS* 2.9 53.2 - - + +
483C CYS* 3.7 22.9 - - + -
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Residues in contact with GLY 455 (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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451C GLU 4.4 1.2 + - - -
452C GLU 3.3 7.1 + - - -
454C ILE* 1.3 81.4 - - - +
456C LYS* 1.3 62.2 + - - +
458C LYS* 3.1 17.3 + - - +
459C SER* 3.3 12.1 + - - -
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Residues in contact with LYS 456 (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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435C PHE* 3.9 15.0 - - + -
438C GLN* 5.4 2.5 - - - +
439C GLN* 3.4 28.4 + - - +
441C ARG* 4.4 12.3 - - - +
452C GLU* 3.6 32.1 + - - +
453C ASP* 3.5 15.9 + - - +
454C ILE 3.4 0.4 - - - -
455C GLY* 1.3 75.2 - - - +
457C LEU* 1.3 58.8 + - - +
459C SER* 2.7 25.0 + - - +
460C CYS* 3.1 16.1 - - - -
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C MET* 4.0 19.3 - - + -
431C ALA* 3.9 7.2 - - + +
432C VAL* 3.9 38.1 - - + +
435C PHE* 3.9 22.2 - - + -
443C PRO* 4.0 7.2 - - + -
453C ASP 3.1 17.5 + - - +
454C ILE 3.8 4.3 - - - +
456C LYS* 1.3 71.9 - - - +
458C LYS* 1.3 61.0 + - - +
459C SER 3.1 2.0 - - - -
460C CYS* 3.1 3.7 + - + +
461C LEU* 2.9 28.4 + - + +
479C VAL* 3.8 16.8 - - + +
482C PHE* 4.1 10.8 - - + -
483C CYS* 3.7 21.3 - - - -
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Residues in contact with LYS 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ILE* 3.3 10.3 + - + +
455C GLY* 3.1 12.0 + - - +
457C LEU* 1.3 78.6 - - - +
459C SER* 1.3 57.7 + - - +
461C LEU* 3.8 11.4 - - + +
462C THR* 3.0 38.2 + - - -
474C VAL 5.8 1.8 - - - -
476C ASP* 2.9 40.6 - - - +
479C VAL* 4.0 19.0 - - + +
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Residues in contact with SER 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C GLN* 4.9 5.1 + - - -
455C GLY 3.3 9.2 + - - -
456C LYS* 2.7 25.4 + - - -
458C LYS* 1.3 76.1 - - - +
460C CYS* 1.3 63.8 + - - +
461C LEU 3.3 0.2 - - - -
462C THR* 3.7 5.8 + - - -
463C GLY* 2.9 22.5 + - - -
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Residues in contact with CYS 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ALA* 4.0 19.5 - - - +
434C ARG* 3.5 17.2 - - + +
435C PHE* 3.7 29.8 - - + +
438C GLN* 3.2 33.9 - - - -
456C LYS 3.1 20.6 - - - -
457C LEU 3.1 6.9 + - - +
459C SER* 1.3 78.3 + - - +
461C LEU* 1.3 57.7 + - - +
463C GLY 4.2 0.4 - - - +
464C PHE* 2.7 33.8 + - - +
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Residues in contact with LEU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LEU* 4.1 14.4 - - + +
428C MET* 4.0 13.9 - - - -
431C ALA* 3.7 25.5 - - + +
457C LEU* 2.9 16.3 + - + +
458C LYS* 3.8 12.6 - - + +
460C CYS* 1.3 76.8 - - - +
462C THR* 1.3 65.1 + - - +
464C PHE* 3.0 7.4 + - + +
465C LEU* 2.9 47.4 + - + +
474C VAL* 3.7 40.2 - - + +
479C VAL* 4.6 10.5 - - + -
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Residues in contact with THR 462 (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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458C LYS* 3.0 30.9 + - - -
459C SER* 3.9 6.5 - - - -
461C LEU* 1.3 80.3 - - - +
463C GLY* 1.3 61.0 + - - +
465C LEU* 3.7 8.7 + - - +
466C GLN* 3.1 42.3 + - - +
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Residues in contact with GLY 463 (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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434C ARG* 2.7 35.2 + - - -
459C SER 2.9 17.2 + - - -
460C CYS 3.5 2.0 - - - -
461C LEU 3.0 0.6 - - - -
462C THR* 1.3 74.9 - - - +
464C PHE* 1.3 62.9 + - - +
466C GLN* 3.1 10.1 + - - +
467C GLU 2.9 18.2 + - - -
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Residues in contact with PHE 464 (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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407C ILE* 5.4 3.8 - - + -
412C ILE* 5.9 0.4 - - + -
426C TYR* 5.0 3.6 - + - -
427C LEU* 3.5 38.8 - - + -
430C ARG* 3.3 66.2 - - + +
431C ALA* 4.9 5.2 - - - -
434C ARG* 2.8 20.4 - - - +
460C CYS 2.7 17.2 + - - +
461C LEU* 3.0 11.0 + - + +
463C GLY* 1.3 74.3 - - - +
465C LEU* 1.3 81.6 + - + +
466C GLN 2.9 1.6 + - - -
467C GLU* 3.1 10.3 + - - +
468C TYR* 3.3 32.2 + + - -
470C LEU* 4.6 8.1 - - + -
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Residues in contact with LEU 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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427C LEU* 4.3 8.7 - - + -
461C LEU* 2.9 40.9 + - + +
462C THR* 4.0 8.1 - - + +
464C PHE* 1.3 96.0 - - + +
466C GLN* 1.3 56.5 + - - +
468C TYR 3.6 0.9 + - - -
469C GLY* 2.8 7.3 + - - -
470C LEU* 2.8 51.4 + - + +
472C VAL* 3.8 42.8 - - + +
474C VAL* 4.7 7.9 - - + -
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Residues in contact with GLN 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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462C THR* 3.1 36.4 + - - +
463C GLY* 3.3 8.5 - - - +
464C PHE 3.0 0.6 - - - -
465C LEU* 1.3 74.0 - - - +
467C GLU* 1.3 56.6 + - - +
468C TYR 2.7 6.7 + - - -
469C GLY* 2.6 25.7 + - - +
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Residues in contact with GLU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LEU* 3.8 37.8 - - + +
434C ARG* 3.3 21.0 + - - +
463C GLY 2.9 12.6 + - - +
464C PHE* 3.1 5.3 + - - +
466C GLN* 1.3 78.1 - - - +
468C TYR* 1.3 72.7 + - + +
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Residues in contact with TYR 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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401C GLU 5.0 0.2 - - - -
402C TYR* 2.6 33.6 + - - +
403C GLY 4.0 3.4 - - - -
404C LEU* 3.5 34.1 - - + +
407C ILE* 3.5 38.4 - - + -
409C LYS* 2.9 31.8 + - - +
430C ARG* 3.6 15.7 + - - -
464C PHE* 3.3 46.8 + + - +
465C LEU 4.3 2.2 - - - +
466C GLN 2.7 1.4 + - - -
467C GLU* 1.3 92.1 + - + +
469C GLY* 1.3 61.8 + - - +
470C LEU* 4.3 9.9 - - + +
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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
------------------------------------------------------------
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