Contacts of the helix formed by residues 401 - 416 (chain C) in PDB entry 5ZR1
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 PRO 401 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ASP* 6.1 0.4 - - - +
399C GLU* 4.5 15.5 - - + +
400C ASN* 1.3 87.3 - - - +
402C ILE* 1.3 62.3 + - - +
403C ASN 3.2 2.7 - - - -
404C GLY* 3.6 4.6 + - - +
405C HIS* 3.2 23.4 + - - +
455C PHE* 4.3 21.8 - - + -
458C ILE* 6.0 7.0 - - + -
460C THR* 6.3 0.4 - - + -
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Residues in contact with ILE 402 (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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293C ASN* 5.1 5.8 - - - +
400C ASN* 3.0 19.2 + - - +
401C PRO* 1.3 79.3 - - - +
403C ASN* 1.3 65.6 + - - +
405C HIS* 4.0 5.1 - - - +
406C ALA* 3.0 28.9 + - - +
428C TYR* 4.2 22.1 - - + +
431C LEU* 3.8 38.8 - - + +
432C LEU* 3.7 32.1 - - + -
455C PHE* 4.4 18.8 - - + -
457C PRO* 4.8 7.0 - - + -
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Residues in contact with ASN 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLN* 4.5 6.6 + - - +
285C LEU* 4.0 28.2 - - + +
286C ASP* 5.7 0.2 - - - +
288C VAL* 3.9 6.2 + - - +
289C ASP* 3.2 47.6 + - + +
290C GLY* 3.7 5.9 - - - +
292C LEU 4.3 7.9 + - - +
293C ASN* 5.1 5.7 - - - +
294C LEU* 5.4 0.7 - - - +
400C ASN* 3.9 11.3 + - - +
401C PRO* 3.2 0.8 - - + -
402C ILE* 1.3 83.3 - - - +
404C GLY* 1.3 59.3 + - - +
406C ALA* 4.3 2.3 - - - +
407C LYS* 3.6 18.5 + - - +
428C TYR* 3.5 24.2 + - - -
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Residues in contact with GLY 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C ASP* 4.6 7.5 + - - -
401C PRO* 3.6 6.1 + - - +
402C ILE 3.4 0.2 - - - -
403C ASN* 1.3 78.8 - - - +
405C HIS* 1.3 60.7 + - - +
407C LYS* 3.4 16.4 + - - +
408C PHE* 2.8 26.7 + - - +
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Residues in contact with HIS 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C PRO* 3.2 19.1 + - + +
402C ILE* 3.4 7.2 + - - +
404C GLY* 1.3 75.9 - - - +
406C ALA* 1.3 59.7 + - - +
408C PHE* 3.2 22.8 + + - +
409C VAL* 2.8 44.7 + - + +
431C LEU* 4.1 15.4 - - + +
436C LEU* 4.5 0.2 - - + -
452C ARG 5.4 1.0 + - - -
453C LEU* 3.5 28.4 + - - -
454C HIS 4.7 1.4 + - - -
455C PHE* 3.5 36.7 - + + +
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Residues in contact with ALA 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLN* 4.9 0.7 - - - +
285C LEU* 5.2 5.2 - - + -
402C ILE 3.0 18.9 + - - +
403C ASN 4.3 3.4 - - - +
404C GLY 3.3 0.2 - - - -
405C HIS* 1.3 75.5 + - - +
407C LYS* 1.3 58.5 + - - +
409C VAL* 3.4 5.3 + - - +
410C ALA* 3.0 29.8 + - - +
424C LEU* 4.0 17.0 - - + +
427C LEU* 4.6 2.8 - - + +
428C TYR* 4.0 21.1 - - + -
431C LEU* 3.8 20.4 - - + +
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Residues in contact with LYS 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLN* 3.4 40.9 + - + +
286C ASP* 4.5 11.7 + - - +
289C ASP* 5.7 3.2 + - - -
403C ASN 3.6 7.7 + - - +
404C GLY* 3.4 16.1 + - - +
405C HIS 3.4 0.4 - - - -
406C ALA* 1.3 77.2 - - - +
408C PHE* 1.3 62.1 + - - +
410C ALA* 4.1 3.8 - - - +
411C ARG* 3.2 28.5 + - + +
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Residues in contact with PHE 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C GLY 2.8 18.2 + - - +
405C HIS* 3.3 28.9 - + + +
406C ALA 3.2 0.4 - - - -
407C LYS* 1.3 75.5 - - - +
409C VAL* 1.3 64.8 + - - +
411C ARG* 3.5 29.9 + - - +
412C PHE* 3.1 30.4 + + + +
452C ARG* 3.9 33.2 - - - -
453C LEU* 3.7 24.5 - - + -
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Residues in contact with VAL 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C HIS* 2.8 46.8 + - + +
406C ALA* 3.4 6.5 + - - +
407C LYS 3.4 0.2 - - - -
408C PHE* 1.3 74.8 - - + +
410C ALA* 1.3 55.8 + - - +
412C PHE* 4.5 3.3 - - - -
413C LEU* 2.7 51.8 + - + +
427C LEU* 3.9 28.3 - - + -
431C LEU* 5.6 1.6 - - + -
436C LEU* 4.5 16.4 - - + -
440C LEU* 5.1 1.1 - - + -
453C LEU* 4.0 25.8 - - + -
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Residues in contact with ALA 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLN* 5.6 0.7 - - - +
406C ALA 3.0 19.0 + - - +
407C LYS* 4.2 5.4 - - - +
409C VAL* 1.3 76.6 - - - +
411C ARG* 1.3 61.4 + - - +
413C LEU* 4.9 1.3 - - - -
414C GLU* 3.3 22.2 + - - +
422C PHE* 3.9 22.0 - - + -
424C LEU* 3.7 25.1 - - + -
427C LEU* 4.3 6.5 - - + +
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Residues in contact with ARG 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C LYS* 3.2 22.1 + - + +
408C PHE* 3.5 35.5 + - - +
410C ALA* 1.3 76.1 - - - +
412C PHE* 1.3 71.3 + - - +
414C GLU* 3.3 5.8 + - + +
415C GLU* 3.2 35.8 + - + +
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Residues in contact with PHE 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PHE* 3.1 29.6 + + + +
409C VAL* 3.9 2.9 - - - +
411C ARG* 1.3 85.9 - - - +
413C LEU* 1.3 62.3 + - - +
415C GLU* 4.5 8.1 - - - -
416C GLU* 3.3 52.7 + - + +
417C LEU* 5.2 3.1 - - + -
449C TYR* 3.5 39.5 - + + -
452C ARG* 3.2 31.9 - - - -
453C LEU* 3.7 33.7 - - + -
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Residues in contact with LEU 413 (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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409C VAL* 2.7 31.5 + - + +
410C ALA* 4.6 2.0 - - - +
412C PHE* 1.3 75.6 - - + +
414C GLU* 1.3 64.1 + - - +
417C LEU* 3.9 14.8 - - + +
419C ILE* 3.7 47.8 + - + +
422C PHE* 4.1 23.6 - - + -
427C LEU* 5.3 5.2 - - + -
439C TYR* 6.2 0.4 - - + -
440C LEU* 3.8 39.0 - - + -
443C TRP* 5.2 8.7 - - + -
446C CYS* 4.4 11.0 - - - -
453C LEU* 5.3 2.7 - - + -
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Residues in contact with GLU 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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410C ALA 3.3 19.4 + - - +
411C ARG* 3.3 8.0 + - - +
412C PHE 3.2 0.6 - - - -
413C LEU* 1.3 78.1 - - - +
415C GLU* 1.3 65.0 + - + +
418C ASN* 3.0 38.1 + - - +
419C ILE 2.8 25.0 + - - +
420C THR* 4.1 14.1 + - - +
422C PHE* 3.5 14.7 - - - -
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Residues in contact with GLU 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ARG* 3.2 27.4 + - + +
412C PHE* 4.4 8.7 - - - +
414C GLU* 1.3 81.9 - - + +
416C GLU* 1.3 92.2 + - - +
418C ASN* 4.3 3.7 + - - +
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Residues in contact with GLU 416 (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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412C PHE* 3.3 43.4 + - + +
415C GLU* 1.3 101.8 - - - +
417C LEU* 1.3 76.5 + - + +
418C ASN* 3.7 0.9 + - - +
449C TYR* 3.5 23.2 + - + -
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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