Contacts of the helix formed by residues 449 - 464 (chain C) in PDB entry 3LLK
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 CYS 449 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C PRO* 6.2 2.2 - - + -
447C PHE* 3.1 18.9 + - + -
448C GLY* 1.3 75.7 - - - +
450C ARG* 1.3 57.3 + - - +
451C ASP* 3.8 9.4 - - - -
452C CYS* 2.0 55.7 - - + +
453C ALA* 3.0 24.4 + - - +
550C FAD 4.6 3.1 - - - -
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Residues in contact with ARG 450 (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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450B ARG* 6.1 7.9 - - + -
318C ARG* 5.0 6.2 - - - +
443C VAL 2.7 26.5 + - - -
444C HIS* 2.9 29.8 + - - +
445C TYR 4.5 1.0 - - - -
446C PHE 4.4 2.6 - - - +
447C PHE 3.0 24.4 + - - +
448C GLY 3.4 7.1 + - - +
449C CYS* 1.3 69.8 - - - +
451C ASP* 1.3 62.0 - - - +
453C ALA* 3.2 18.1 + - - +
454C SER* 2.8 30.7 + - - -
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Residues in contact with ASP 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ARG* 5.7 5.2 - - - -
449C CYS* 3.4 8.0 - - - -
450C ARG* 1.3 77.8 - - - +
452C CYS* 1.3 63.0 - - - +
454C SER* 3.3 8.1 + - - -
455C HIS* 2.9 29.7 + - + -
550C FAD 3.4 19.7 - - + +
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Residues in contact with CYS 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C PRO* 6.3 0.4 - - - -
447C PHE* 3.3 13.9 - - + -
449C CYS* 2.0 48.9 - - - +
451C ASP* 1.3 80.9 - - - +
453C ALA* 1.3 56.1 + - - +
455C HIS 3.3 1.0 + - - -
456C PHE* 2.9 25.5 + - - +
550C FAD 2.8 75.4 + - + -
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Residues in contact with ALA 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C VAL* 3.4 31.5 - - + +
444C HIS* 4.8 2.2 - - - -
447C PHE* 4.5 1.1 - - + +
449C CYS 3.0 7.1 + - - +
450C ARG* 3.2 43.0 + - - +
452C CYS* 1.3 77.9 - - - +
454C SER* 1.3 58.0 + - - +
456C PHE* 3.4 1.4 + - - +
457C GLU* 2.9 32.6 + - - +
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Residues in contact with SER 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C ARG 2.8 18.0 + - - -
451C ASP* 3.4 8.5 - - - -
453C ALA* 1.3 78.5 - - - +
455C HIS* 1.3 59.1 + - - +
457C GLU* 3.5 5.4 + - - +
458C GLN* 3.0 47.9 + - - +
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Residues in contact with HIS 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ASP* 2.9 18.3 + - + +
452C CYS 3.9 1.6 - - - +
454C SER* 1.3 75.5 - - - +
456C PHE* 1.3 67.2 + - - +
458C GLN* 3.3 37.2 + - - +
459C MET* 3.3 19.2 + - + +
484C VAL* 5.3 8.2 - - + +
487C ARG* 3.3 46.6 + - - -
488C LEU* 5.3 0.4 - - + +
550C FAD 2.4 37.9 + + - +
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Residues in contact with PHE 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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408C TRP* 4.4 5.6 - + - -
411C PHE* 5.7 0.4 - + - -
436C LEU* 6.3 0.7 - - + -
439C ILE* 4.3 18.4 - - + -
440C ARG* 3.8 32.3 - - + -
443C VAL* 4.1 17.0 - - + -
452C CYS 2.9 12.9 + - - +
453C ALA 3.8 3.8 - - - +
455C HIS* 1.3 76.0 - - - +
457C GLU* 1.3 62.8 + - - +
459C MET* 3.1 24.9 + - + +
460C ALA* 2.9 24.4 + - + -
464C MET* 4.2 9.2 - - + -
476C TRP* 4.1 22.0 - + - -
477C LEU* 3.9 23.1 - - + -
550C FAD 3.0 37.4 - - + -
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Residues in contact with GLU 457 (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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440C ARG* 2.6 57.0 + - - +
444C HIS* 4.9 23.6 - - + +
453C ALA 2.9 18.6 + - - +
454C SER* 3.7 6.3 - - - +
456C PHE* 1.3 80.6 - - + +
458C GLN* 1.3 61.9 + - - +
460C ALA* 4.2 1.1 - - - -
461C ALA* 3.0 29.4 + - + +
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Residues in contact with GLN 458 (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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454C SER* 3.0 37.3 + - - +
455C HIS* 3.4 32.1 - - - +
456C PHE 3.2 0.4 - - - -
457C GLU* 1.3 76.5 - - + +
459C MET* 1.3 62.5 + - + +
461C ALA* 4.2 3.9 - - - +
462C ALA* 3.3 22.7 + - - +
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Residues in contact with MET 459 (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 TRP* 5.3 0.4 - - + -
455C HIS* 3.3 8.0 + - + +
456C PHE* 3.1 34.5 + - + +
458C GLN* 1.3 74.9 - - + +
460C ALA* 1.3 67.7 + - - +
462C ALA* 3.3 6.3 + - - +
463C SER* 3.1 21.5 + - - +
476C TRP* 3.6 16.7 - - + -
480C SER* 3.5 40.2 - - - +
483C ARG* 3.9 29.4 - - - +
484C VAL* 3.6 27.4 - - + -
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Residues in contact with ALA 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ARG* 3.4 38.9 + - + +
456C PHE* 2.9 17.9 + - + +
457C GLU* 3.6 5.4 - - - +
459C MET* 1.3 76.3 - - - +
461C ALA* 1.3 60.6 + - - +
464C MET* 2.8 44.9 + - + +
465C HIS* 4.3 1.9 + - - -
476C TRP* 3.8 12.3 - - + -
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ARG* 3.5 18.0 - - - +
457C GLU* 3.0 20.0 + - + +
458C GLN* 4.2 3.6 - - - +
460C ALA* 1.3 77.1 - - - +
462C ALA* 1.3 62.6 + - - +
465C HIS* 3.8 13.9 + - - -
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Residues in contact with ALA 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 GLN 3.3 17.1 + - - +
459C MET* 3.3 8.5 + - - +
460C ALA 3.2 0.6 - - - -
461C ALA* 1.3 79.8 - - - +
463C SER* 1.3 60.5 + - - +
465C HIS* 3.6 9.6 + - - -
466C ARG* 3.1 20.1 + - - +
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Residues in contact with SER 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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459C MET* 3.1 9.2 + - - +
460C ALA 3.4 0.6 + - - -
461C ALA 3.4 0.2 - - - -
462C ALA* 1.3 81.3 - - - +
464C MET* 1.3 68.2 + - - +
465C HIS* 3.1 6.5 - - - -
466C ARG* 3.0 50.1 + - - +
467C VAL 4.0 1.6 + - - -
476C TRP* 3.0 24.4 + - - -
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Residues in contact with MET 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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436C LEU* 3.6 52.3 - - + +
437C PRO* 4.5 6.1 - - + -
440C ARG* 4.0 26.0 - - + +
456C PHE* 4.2 11.9 - - + -
460C ALA* 2.8 33.7 + - + +
463C SER* 1.3 73.2 + - - +
465C HIS* 1.3 60.7 + - - +
466C ARG 3.1 1.8 + - - -
467C VAL* 3.1 22.8 + - + +
476C TRP* 3.2 48.3 - - + +
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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
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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