Contacts of the helix formed by residues 406 - 421 (chain C) in PDB entry 4XZV
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 406 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C TYR* 4.3 17.5 - - + -
387C CYS* 2.0 65.3 - - - -
388C PHE* 3.9 4.3 - - - -
391C TRP* 4.8 7.2 - - + -
405C PRO* 1.3 81.1 - - + +
407C THR* 1.3 66.6 + - - +
408C ASP* 3.0 4.8 + - - +
409C LEU* 3.6 12.4 + - + +
410C PHE* 3.4 19.4 + - - +
40D GLN* 6.2 1.8 - - - +
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Residues in contact with THR 407 (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 PRO* 3.4 23.6 - - - +
406C CYS* 1.3 78.5 - - - +
408C ASP* 1.3 67.0 + - - +
410C PHE* 3.4 16.1 - - - +
411C LYS* 3.4 7.8 + - + +
40D GLN* 5.5 4.7 + - - +
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Residues in contact with ASP 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C PRO 5.5 2.9 - - - +
406C CYS* 4.8 2.2 - - - -
407C THR* 1.3 77.4 - - - +
409C LEU* 1.3 74.3 + - + +
411C LYS* 3.1 22.2 + - - +
412C ARG* 3.8 18.3 + - - +
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Residues in contact with LEU 409 (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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380C MET 4.8 1.4 - - - +
383C GLU* 4.0 28.9 - - + +
384C TYR* 4.3 16.8 - - + +
387C CYS* 4.1 20.9 - - + -
390C ARG* 6.1 0.7 - - - +
406C CYS* 3.6 14.6 + - - +
407C THR 3.6 0.2 - - - -
408C ASP* 1.3 85.4 - - + +
410C PHE* 1.3 65.0 + - - +
412C ARG* 3.6 42.3 + - - +
413C TYR* 3.4 16.8 + - - +
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Residues in contact with PHE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP 4.8 2.7 - - - -
384C TYR* 3.2 48.9 - + + -
406C CYS 3.4 9.5 + - - +
407C THR* 3.4 12.1 - - - +
409C LEU* 1.3 77.4 - - - +
411C LYS* 1.3 75.9 + - + +
413C TYR* 2.8 21.2 + + - +
414C GLN* 2.8 54.9 + - + -
35D GLY* 3.7 13.9 - - - -
36D VAL 3.7 15.0 - - - -
38D VAL* 3.8 24.7 - - + -
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Residues in contact with LYS 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.0 23.1 + - - -
282A ASN* 5.9 1.5 + - - +
283A TYR* 3.1 25.7 + - - -
407C THR* 3.4 7.1 + - + +
408C ASP* 3.1 12.9 + - - +
410C PHE* 1.3 85.5 - - + +
412C ARG* 1.3 63.5 - - + +
414C GLN* 3.3 15.4 + - - +
415C GLN* 3.1 41.1 + - + +
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Residues in contact with ARG 412 (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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49C GLN* 2.6 60.4 + - + +
52C ALA* 4.9 0.3 - - - +
53C THR* 6.1 2.2 - - - -
380C MET* 3.4 23.1 - - + +
383C GLU* 4.3 16.2 - - - +
408C ASP* 3.8 17.3 + - - +
409C LEU* 3.6 42.3 + - - +
410C PHE 3.2 0.2 - - - -
411C LYS* 1.3 79.7 - - + +
413C TYR* 1.3 62.2 + - - +
415C GLN* 3.6 7.0 + - - +
416C CYS* 3.3 15.6 + - - +
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Residues in contact with TYR 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C SER* 5.2 0.4 - - - -
377C CYS* 4.1 5.6 - - + -
380C MET* 3.8 21.9 - - + +
381C LYS* 3.2 46.4 - - + +
384C TYR* 3.3 33.2 - + + -
385C ASP* 4.4 2.0 + - - -
409C LEU 3.4 8.7 + - - +
410C PHE* 2.8 16.4 + + - +
412C ARG* 1.3 71.8 - - - +
414C GLN* 1.3 69.5 + - - +
416C CYS* 2.9 14.7 + - - +
417C VAL* 3.1 36.3 + - + +
34D LEU* 2.8 33.8 - - + +
35D GLY 3.3 25.0 + - - -
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Residues in contact with GLN 414 (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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30A ASP* 2.8 57.9 + - - +
410C PHE* 2.8 39.4 + - + +
411C LYS* 3.6 19.3 - - - +
413C TYR* 1.3 76.9 - - - +
415C GLN* 1.3 61.0 + - - +
417C VAL* 3.4 10.2 - - + +
418C GLN* 2.8 57.8 + - + +
36D VAL* 3.0 22.9 - - - +
37D ASP* 3.7 0.2 - - - +
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Residues in contact with GLN 415 (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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26A LYS* 3.0 28.3 + - - +
30A ASP* 3.4 10.0 - - - +
52C ALA* 4.3 9.2 + - + +
53C THR* 4.3 28.0 - - + +
411C LYS* 3.1 46.9 + - + +
412C ARG* 3.8 6.1 - - - +
413C TYR 3.1 0.2 - - - -
414C GLN* 1.3 76.1 - - - +
416C CYS* 1.3 65.2 + - - +
418C GLN* 3.1 8.4 + - - +
419C LYS* 3.0 24.9 + - - +
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Residues in contact with CYS 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PRO 4.6 2.7 - - - -
52C ALA* 3.6 20.4 - - + +
73C SER* 4.8 6.5 - - - -
75C LEU* 5.4 1.8 - - - -
376C ALA* 3.9 12.8 - - - -
377C CYS* 2.0 60.4 - - + -
380C MET* 3.7 26.2 - - - -
412C ARG 3.3 2.6 + - - +
413C TYR 2.9 9.6 + - - +
415C GLN* 1.3 81.5 - - - +
417C VAL* 1.3 59.3 + - - +
419C LYS* 3.4 9.7 + - - +
420C ALA* 3.5 10.6 + - - +
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Residues in contact with VAL 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C SER* 4.1 0.9 - - - +
374C GLY* 4.4 6.6 + - - +
377C CYS* 3.4 29.2 - - + -
413C TYR* 3.1 26.3 + - + +
414C GLN* 3.4 16.4 - - + +
416C CYS* 1.3 74.1 - - - +
418C GLN* 1.3 67.0 + - + +
419C LYS 3.2 0.9 - - - -
420C ALA* 3.4 2.8 + - - +
421C ILE* 2.8 39.5 + - + +
34D LEU* 3.5 45.1 - - + -
35D GLY 5.9 0.2 - - - +
36D VAL* 5.5 5.2 - - + -
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Residues in contact with GLN 418 (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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26A LYS* 3.1 13.3 + - - +
29A LYS* 3.5 29.0 + - + +
30A ASP* 2.9 18.9 + - - +
414C GLN* 2.8 47.6 + - - +
415C GLN* 3.8 8.7 + - - +
417C VAL* 1.3 82.2 - - + +
419C LYS* 1.3 59.2 + - - +
421C ILE* 3.8 16.2 - - + +
422C LYS* 3.3 23.2 + - - +
36D VAL* 4.3 15.2 - - + +
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Residues in contact with LYS 419 (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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51C ALA 3.4 21.2 + - - -
52C ALA* 3.5 24.8 + - - +
54C GLY* 4.5 6.9 - - - +
73C SER 4.2 13.7 - - - +
74C GLY* 4.2 18.8 + - - -
75C LEU* 4.1 8.8 - - + +
268C ALA* 5.9 1.4 - - - +
269C ALA* 5.3 6.1 - - - +
415C GLN 3.0 15.7 + - - +
416C CYS* 3.7 6.7 - - - +
417C VAL 3.2 0.2 - - - -
418C GLN* 1.3 75.9 - - - +
420C ALA* 1.3 63.6 + - - +
422C LYS* 3.2 15.7 - - + +
423C GLU* 3.1 17.9 - - - +
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Residues in contact with ALA 420 (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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72C GLN 5.1 0.2 - - - +
73C SER* 4.7 11.3 + - - -
373C VAL* 4.4 5.6 - - + +
374C GLY* 3.8 25.8 - - - -
375C GLU* 4.1 15.0 - - - +
416C CYS 3.5 6.2 + - - +
417C VAL 3.4 7.3 + - - +
419C LYS* 1.3 75.4 - - - +
421C ILE* 1.3 57.3 + - - +
422C LYS 2.9 11.3 + - - -
423C GLU* 3.1 29.3 + - - +
424C LYS* 4.1 13.6 + - - +
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Residues in contact with ILE 421 (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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373C VAL* 4.0 20.9 - - + -
417C VAL* 2.8 42.3 + - + +
418C GLN* 3.8 17.0 - - + +
419C LYS 3.4 0.4 - - - -
420C ALA* 1.3 70.7 - - - +
422C LYS* 1.3 61.4 + - - +
423C GLU 3.4 0.4 - - - -
424C LYS* 3.0 24.9 - - + +
425C GLU 4.5 17.3 - - - +
34D LEU* 4.8 7.2 - - + -
36D VAL* 4.8 9.6 - - + -
54D LEU* 4.4 20.6 - - + -
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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