Contacts of the helix formed by residues 413 - 426 (chain C) in PDB entry 5NTI
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 SER 413 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411C HIS 3.3 7.2 + - - -
412C PHE* 1.3 73.3 - - - +
414C GLU* 1.3 66.3 + - - +
415C ASP* 3.7 7.4 + - - +
416C GLU* 2.9 37.2 + - - +
417C ILE* 2.9 24.4 + - - +
453C HIS* 5.1 1.0 + - - -
459C ARG* 6.3 0.2 - - - -
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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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281C TYR* 3.5 26.9 - - + -
282C ARG* 3.4 31.0 - - + +
289C LEU* 3.4 28.9 - - + +
367C ARG* 2.8 40.3 + - - +
413C SER* 1.3 72.1 - - - +
415C ASP* 1.3 69.0 + - - +
417C ILE* 3.4 7.0 + - + +
418C ALA* 3.1 19.4 + - - +
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Residues in contact with ASP 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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274C VAL* 5.8 0.2 - - - +
278C CYS* 3.3 34.4 - - - +
282C ARG* 3.8 12.5 + - - +
413C SER* 3.3 5.9 + - - +
414C GLU* 1.3 84.7 - - - +
416C GLU* 1.3 62.4 + - - +
418C ALA* 3.4 3.9 - - - +
419C LEU* 3.3 30.1 + - - +
453C HIS* 3.5 31.5 - - - +
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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
----------------------------------------------------------
412C PHE* 3.8 17.8 - - + -
413C SER* 2.9 32.7 + - - +
415C ASP* 1.3 75.8 - - - +
417C ILE* 1.3 63.5 + - - +
419C LEU* 3.6 4.8 + - - -
420C TYR* 3.2 24.9 + - - +
450C PHE* 4.0 9.2 - - + -
453C HIS* 4.3 17.8 + - + -
454C LEU* 4.4 17.2 - - + +
457C THR* 4.0 10.4 + - - +
459C ARG* 2.8 50.7 + - - +
462C ILE* 4.4 0.9 - - - +
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Residues in contact with ILE 417 (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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281C TYR* 3.6 33.7 - - + +
363C VAL* 4.4 17.0 - - + +
364C ARG* 4.4 6.1 - - - -
366C CYS* 4.0 16.2 - - - -
367C ARG* 4.4 15.7 - - + +
412C PHE* 3.6 37.5 - - + +
413C SER 2.9 22.3 + - - +
414C GLU* 3.7 7.4 - - - +
416C GLU* 1.3 75.4 - - - +
418C ALA* 1.3 57.9 + - - +
420C TYR* 3.8 0.7 - - - +
421C THR* 2.9 45.0 + - + +
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Residues in contact with ALA 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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277C VAL* 3.4 14.7 - - + +
278C CYS* 4.0 18.6 - - - -
281C TYR* 3.5 33.8 - - + -
334C PHE* 3.9 1.9 - - - -
414C GLU 3.1 12.4 + - - +
415C ASP* 3.4 12.3 - - - +
416C GLU 3.2 0.2 - - - -
417C ILE* 1.3 76.7 - - - +
419C LEU* 1.3 57.7 + - - +
421C THR* 2.9 18.8 + - - -
422C ALA* 3.1 11.1 + - - +
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Residues in contact with LEU 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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274C VAL* 4.1 26.9 - - + +
277C VAL* 4.0 21.8 - - + -
278C CYS* 4.5 5.6 - - - -
415C ASP 3.3 20.2 + - - +
416C GLU* 4.3 2.0 - - - +
418C ALA* 1.3 73.9 - - - +
420C TYR* 1.3 60.7 + - - +
422C ALA* 3.5 3.7 + - - +
423C LEU* 3.1 33.3 + - - +
446C LEU* 5.3 5.3 - - + +
449C ALA* 4.2 19.7 - - + +
450C PHE* 3.7 28.0 - - + +
453C HIS* 3.9 36.1 - - + +
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Residues in contact with TYR 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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363C VAL* 3.6 40.6 - - + -
403C PHE* 5.1 2.1 - + - -
407C LEU* 4.7 11.0 - - + -
412C PHE* 3.9 17.0 - + + -
416C GLU 3.2 19.4 + - - +
417C ILE 3.9 2.7 - - - +
419C LEU* 1.3 75.1 - - - +
421C THR* 1.3 60.3 + - - +
423C LEU* 3.2 13.3 + - + +
424C VAL* 2.9 41.9 + - + +
450C PHE* 4.2 21.5 - + + -
466C LEU* 4.1 24.4 - - + +
467C PRO* 3.9 27.5 + - + +
472C LEU* 4.7 8.9 - - + +
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Residues in contact with THR 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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281C TYR* 4.6 4.0 - - - -
334C PHE* 3.9 12.8 - - - -
360C VAL* 3.8 33.6 - - + +
363C VAL* 3.7 28.5 - - + -
364C ARG* 4.2 6.3 + - + -
417C ILE* 2.9 32.4 + - + +
418C ALA* 2.9 15.8 + - - -
420C TYR* 1.3 72.4 - - - +
422C ALA* 1.3 59.4 + - - +
424C VAL* 3.3 7.8 + - - +
425C LEU* 3.0 31.0 + - - +
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Residues in contact with ALA 422 (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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277C VAL* 3.7 19.1 - - + -
334C PHE* 4.2 13.4 - - + -
338C LEU* 4.4 9.0 - - + -
418C ALA 3.1 18.7 + - - +
419C LEU 3.5 6.7 - - - +
421C THR* 1.3 75.8 + - - +
423C LEU* 1.3 57.9 + - - +
425C LEU* 3.6 1.1 + - - +
426C ILE* 2.9 34.7 + - - +
446C LEU* 4.0 21.1 - - + -
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Residues in contact with LEU 423 (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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419C LEU 3.1 17.7 + - - +
420C TYR* 3.5 14.4 - - + +
421C THR 3.2 0.2 - - - -
422C ALA* 1.3 75.2 - - - +
424C VAL* 1.3 66.1 + - + +
426C ILE 3.1 20.9 - - - +
427C ASN* 4.0 3.1 + - - +
443C GLN* 3.7 12.0 - - + +
446C LEU* 3.5 30.3 - - + +
447C GLU* 3.6 30.1 - - + +
450C PHE* 3.7 38.8 - - + -
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Residues in contact with VAL 424 (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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356C GLY 4.5 0.7 - - - +
359C GLU* 3.5 41.7 - - + +
360C VAL* 4.1 13.5 - - + -
363C VAL* 4.5 3.8 - - + -
420C TYR* 2.9 38.3 + - + +
421C THR* 3.7 7.6 - - - +
423C LEU* 1.3 76.5 - - + +
425C LEU* 1.3 62.4 + - - +
427C ASN* 3.8 7.2 + - - +
430C ARG* 3.3 19.1 + - - -
472C LEU* 3.8 22.2 - - + -
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Residues in contact with LEU 425 (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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331C VAL* 5.4 1.6 - - + +
334C PHE* 4.5 10.1 - - + -
335C ALA* 3.9 26.0 - - + -
338C LEU* 3.9 23.1 - - + -
341C PHE* 4.3 9.6 - - + -
352C LEU* 3.6 44.0 - - + +
353C LEU* 3.8 22.7 - - + +
356C GLY* 4.6 12.1 - - - -
360C VAL* 4.2 11.0 - - + -
421C THR 3.0 16.7 + - - +
422C ALA 3.8 2.7 - - - +
424C VAL* 1.3 81.1 - - - +
426C ILE* 1.3 62.5 + - + +
427C ASN* 2.9 9.0 + - - +
430C ARG* 4.9 1.4 + - - -
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Residues in contact with ILE 426 (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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338C LEU* 4.2 14.4 - - + -
341C PHE* 3.7 30.3 - - + -
344C LEU* 4.8 0.4 - - + -
352C LEU* 3.9 12.1 - - + -
422C ALA 2.9 20.4 + - - +
423C LEU* 3.1 13.3 - - - +
425C LEU* 1.3 72.8 - - + +
427C ASN* 1.3 58.1 + - - +
428C ALA 4.1 0.2 - - - -
439C VAL* 3.8 17.7 - - + +
442C LEU* 3.9 26.2 - - + -
443C GLN* 3.6 42.8 - - - +
446C LEU* 3.7 17.0 - - + -
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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