Contacts of the helix formed by residues 414 - 430 (chain F) 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 THR 414 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356C ARG* 4.5 2.9 - - - +
410F ASN* 5.4 5.8 - - - +
412F LEU 4.8 4.3 - - - +
413F VAL* 1.3 84.1 - - - +
415F ASP* 1.3 59.6 + - - +
416F ASP* 2.4 27.0 + - - -
417F GLN* 3.2 25.6 + - - +
418F TYR* 2.9 27.9 + - - +
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Residues in contact with ASP 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C LYS* 5.3 4.7 - - - +
356C ARG* 3.7 35.4 + - - +
414F THR* 1.3 76.4 - - - +
416F ASP* 1.3 58.1 + - - +
418F TYR* 3.7 9.1 + - - +
419F ASN* 3.0 24.4 + - - +
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Residues in contact with ASP 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F ARG* 5.6 4.0 - - - +
338F LYS* 4.0 34.2 + - + +
414F THR* 2.4 33.7 + - - -
415F ASP* 1.3 73.2 - - - +
417F GLN* 1.3 65.5 + - - +
418F TYR 3.3 0.2 - - - -
419F ASN* 3.3 24.9 + - + +
420F ILE* 3.4 10.9 + - - +
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Residues in contact with GLN 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C MET* 5.5 0.2 - - - +
337F ARG 3.2 24.6 + - - +
338F LYS* 4.5 15.8 + - + +
340F PRO* 4.9 10.5 - - - +
413F VAL* 3.3 31.4 - - + +
414F THR* 3.2 26.3 + - - +
416F ASP* 1.3 86.6 + - - +
418F TYR* 1.3 59.4 + - - +
420F ILE* 3.7 10.3 - - + +
421F TRP* 3.3 24.4 + - - +
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Residues in contact with TYR 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C LYS 5.5 5.2 - - - -
355C SER* 3.4 41.4 + - - -
356C ARG* 4.1 19.3 - - + -
360C PHE* 4.9 0.9 - - - -
361C MET* 4.0 13.2 - - + -
381C LEU* 4.7 3.1 - - - +
413F VAL* 3.9 7.8 - - + +
414F THR 2.9 19.2 + - - +
415F ASP* 4.0 12.1 - - - +
417F GLN* 1.3 74.3 - - - +
419F ASN* 1.3 63.7 + - - +
421F TRP* 3.6 31.8 - + - -
422F LYS* 3.0 59.6 + - + +
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Residues in contact with ASN 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415F ASP 3.0 16.7 + - - +
416F ASP* 3.3 18.4 + - - +
418F TYR* 1.3 78.7 - - - +
420F ILE* 1.3 65.5 + - - +
422F LYS* 3.4 4.5 + - - +
423F LYS* 3.3 38.9 + - - +
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Residues in contact with ILE 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F LYS 6.0 2.2 - - - +
416F ASP 3.4 9.6 + - - +
417F GLN* 3.7 14.1 - - + +
419F ASN* 1.3 79.0 - - + +
421F TRP* 1.3 67.3 + - - +
423F LYS* 4.5 15.3 - - + -
424F ARG* 3.3 23.6 + - + +
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Residues in contact with TRP 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C PHE* 5.7 2.2 - + - -
361C MET* 3.6 52.7 + - + +
364C VAL* 3.6 33.9 - - + -
365C GLU* 4.6 6.7 + - + +
381C LEU* 5.3 2.7 - - + -
417F GLN 3.3 19.8 + - - +
418F TYR* 3.6 40.8 - + - +
419F ASN 3.3 0.2 - - - -
420F ILE* 1.3 79.1 - - + +
422F LYS* 1.3 78.1 + - + +
424F ARG* 3.4 12.0 + - - +
425F ILE* 3.1 59.2 + - + +
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Residues in contact with LYS 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C LEU* 3.4 43.2 - - + +
382C THR* 5.3 10.4 - - + +
418F TYR* 3.0 56.8 + - + +
419F ASN* 3.7 5.6 - - - +
420F ILE 3.3 0.2 - - - -
421F TRP* 1.3 84.5 - - + +
423F LYS* 1.3 65.0 + - + +
425F ILE* 4.4 2.8 - - + +
426F GLU* 3.4 25.3 + - + +
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Residues in contact with LYS 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419F ASN* 3.3 29.3 + - - +
420F ILE* 4.0 18.8 - - + +
421F TRP 3.3 0.2 - - - -
422F LYS* 1.3 79.2 - - + +
424F ARG* 1.3 62.2 + - - +
426F GLU* 3.7 3.9 + - - +
427F MET* 3.5 25.8 + - - +
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Residues in contact with ARG 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C GLU* 6.2 2.0 - - - +
420F ILE* 3.3 17.7 + - + +
421F TRP* 3.4 14.2 + - - +
422F LYS 3.3 0.4 - - - -
423F LYS* 1.3 81.4 - - - +
425F ILE* 1.3 81.8 + - - +
427F MET* 3.4 6.4 + - - +
428F ASP* 3.0 37.3 + - + +
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Residues in contact with ILE 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C VAL* 4.2 16.4 - - + -
365C GLU* 5.5 8.5 - - + -
368C ILE* 3.9 25.4 - - + -
377C ILE* 5.2 0.2 - - + -
381C LEU* 5.6 4.0 - - + -
421F TRP* 3.1 49.8 + - + +
422F LYS* 4.5 4.5 - - + +
424F ARG* 1.3 102.6 - - - +
426F GLU* 1.3 52.1 + - - +
428F ASP* 2.9 10.7 + - - +
429F LEU* 2.6 54.7 + - + +
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Residues in contact with GLU 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C LEU* 6.4 0.9 - - + -
422F LYS* 3.4 19.7 + - + +
423F LYS* 4.1 3.4 - - - +
424F ARG 3.3 0.8 - - - -
425F ILE* 1.3 78.6 - - - +
427F MET* 1.3 83.0 + - - +
429F LEU* 3.3 23.4 - - + +
430F ALA* 3.2 26.0 + - - +
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Residues in contact with MET 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423F LYS 3.5 13.6 + - - +
424F ARG* 3.4 8.6 + - - +
425F ILE 3.3 0.2 - - - -
426F GLU* 1.3 97.2 - - - +
428F ASP* 1.3 59.6 + - - +
430F ALA 3.4 26.7 - - - +
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Residues in contact with ASP 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C ILE* 3.4 33.0 - - + +
372C ALA 5.5 1.2 - - - +
424F ARG* 3.0 30.9 + - + +
425F ILE* 2.9 17.1 + - + +
427F MET* 1.3 75.6 - - - +
429F LEU* 1.3 63.8 + - - +
430F ALA 5.0 0.4 - - - -
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Residues in contact with LEU 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C ILE* 3.7 14.4 - - + -
372C ALA 4.3 13.3 - - - +
374C ALA* 3.7 46.0 + - + +
377C ILE* 3.9 17.0 - - + -
378C LEU* 4.8 17.9 - - + -
381C LEU* 5.3 6.3 - - + -
425F ILE* 2.6 47.5 + - + +
426F GLU* 3.3 24.5 - - + +
428F ASP* 1.3 76.3 - - - +
430F ALA* 1.3 61.1 + - + +
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Residues in contact with ALA 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C ALA* 5.1 7.0 - - + -
426F GLU* 3.2 12.5 + - - +
427F MET* 3.4 27.7 - - - +
428F ASP 5.1 0.3 - - - -
429F LEU* 1.3 81.5 - - + +
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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