Contacts of the helix formed by residues 413 - 426 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A HIS 3.6 1.2 + - - -
412A PHE* 1.3 75.6 - - - +
414A GLU* 1.3 65.2 + - - +
415A ASP* 3.9 7.9 + - - +
416A GLU* 3.1 33.8 + - - +
417A ILE* 3.0 23.4 + - - +
453A HIS* 4.9 2.4 + - - -
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Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TYR* 3.5 24.6 + - + -
282A ARG* 5.6 10.4 - - + +
285A CYS* 4.6 0.9 - - - -
289A LEU* 3.6 28.7 - - + +
367A ARG* 2.9 49.2 + - - +
413A SER* 1.3 72.9 - - - +
415A ASP* 1.3 62.9 + - - +
417A ILE* 3.3 6.8 + - - +
418A ALA* 2.9 29.3 + - - +
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Residues in contact with ASP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A CYS* 3.7 32.9 - - - +
282A ARG* 4.5 9.2 + - - +
413A SER* 3.3 5.9 + - - +
414A GLU* 1.3 79.9 - - - +
416A GLU* 1.3 56.6 + - - +
418A ALA* 3.4 4.3 - - - +
419A LEU* 3.0 35.4 + - - +
453A HIS* 3.6 31.3 + - + +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A PHE* 3.4 18.9 - - + -
413A SER* 3.1 34.9 + - - +
415A ASP* 1.3 75.6 - - - +
417A ILE* 1.3 55.1 + - - +
419A LEU* 3.4 2.3 + - - -
420A TYR* 2.8 37.1 + - - +
450A PHE* 3.7 11.8 - - + -
453A HIS* 4.5 11.3 + - + +
454A LEU* 3.7 19.5 - - + +
457A THR* 4.6 2.8 + - - -
459A ARG* 2.8 58.5 + - - +
462A ILE* 4.5 1.6 - - - -
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TYR* 3.3 26.5 - - + +
363A VAL* 4.5 8.1 - - + -
364A ARG* 4.9 7.0 - - - -
366A CYS* 3.9 16.2 - - - -
367A ARG* 3.8 25.4 - - + -
412A PHE* 3.4 38.4 - - + +
413A SER 3.0 10.7 + - - +
414A GLU* 3.7 12.1 - - - +
416A GLU* 1.3 72.3 - - - +
418A ALA* 1.3 54.0 + - - +
420A TYR* 4.3 5.4 - - - -
421A THR* 2.7 53.3 + - + +
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL* 3.5 14.1 - - + +
278A CYS* 3.9 19.5 - - - -
281A TYR* 3.4 33.8 - - + -
334A PHE* 3.8 2.9 - - - -
414A GLU 2.9 14.5 + - - +
415A ASP* 3.4 11.2 - - - +
416A GLU 3.3 0.2 - - - -
417A ILE* 1.3 75.8 - - - +
419A LEU* 1.3 57.1 + - - +
421A THR* 3.1 7.7 + - - -
422A ALA* 3.1 22.5 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A VAL* 4.3 10.1 - - + +
277A VAL* 3.9 26.7 - - + -
278A CYS* 4.2 9.2 - - - -
415A ASP 3.0 19.0 + - - +
416A GLU* 4.8 0.4 - - - -
418A ALA* 1.3 76.5 - - - +
420A TYR* 1.3 64.7 + - - +
422A ALA* 3.5 4.4 + - - +
423A LEU* 3.3 25.5 + - - +
446A LEU* 4.9 3.8 - - + +
449A ALA* 4.1 32.3 - - + +
450A PHE* 3.3 27.4 - - + +
453A HIS* 3.7 39.7 - - + -
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A VAL* 3.7 41.1 - - + -
403A PHE* 5.1 0.2 - - - -
407A LEU* 4.7 6.3 - - + -
412A PHE* 4.1 21.1 - + + -
416A GLU 2.8 23.7 + - - +
417A ILE* 3.8 3.1 - - - +
419A LEU* 1.3 74.2 - - - +
421A THR* 1.3 56.2 + - - +
423A LEU* 3.0 13.5 + - + +
424A VAL* 2.9 37.6 + - + +
450A PHE* 4.0 16.0 - + + -
466A LEU* 3.8 37.9 - - + -
467A PRO* 3.5 26.3 + - + +
472A LEU* 4.1 15.2 - - - +
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Residues in contact with THR 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TYR* 4.2 5.5 - - - -
334A PHE* 3.8 12.7 - - - -
360A VAL* 3.8 30.6 - - + +
363A VAL* 3.6 34.3 - - + -
364A ARG* 4.4 4.7 + - + -
417A ILE* 2.7 37.8 + - + +
418A ALA* 3.1 12.3 + - - -
420A TYR* 1.3 71.9 - - - +
422A ALA* 1.3 55.4 + - - +
424A VAL* 3.2 8.9 + - - +
425A LEU* 3.0 28.2 + - - +
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL* 4.1 8.7 - - + -
334A PHE* 4.1 9.8 - - + -
338A LEU* 4.0 28.0 - - + -
418A ALA 3.1 18.1 + - - +
419A LEU 3.5 7.0 - - - +
421A THR* 1.3 77.0 + - - +
423A LEU* 1.3 56.6 + - - +
425A LEU* 3.4 1.8 + - - +
426A ILE* 2.9 34.7 + - - +
446A LEU* 4.3 16.4 - - + -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A LEU 3.3 7.1 + - - +
420A TYR* 3.0 15.5 + - + +
422A ALA* 1.3 76.2 - - - +
424A VAL* 1.3 65.1 + - - +
426A ILE* 3.1 19.9 - - - +
427A ASN* 4.2 4.3 + - - +
443A GLN* 3.7 17.9 - - + +
446A LEU* 3.8 12.1 - - + +
447A GLU* 3.6 42.4 - - + +
450A PHE* 3.4 44.0 - - + -
451A HIS* 6.1 0.2 - - - +
469A LYS* 5.1 9.1 + - - -
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A GLY 4.5 0.9 - - - +
359A GLU* 3.6 38.5 - - + +
360A VAL* 3.9 16.4 - - + +
363A VAL* 4.2 4.7 - - + -
420A TYR* 2.9 48.0 + - + +
421A THR* 3.4 12.8 - - - +
423A LEU* 1.3 78.5 - - - +
425A LEU* 1.3 60.7 + - - +
427A ASN* 3.9 5.2 + - - +
430A ARG* 3.2 26.0 + - - -
469A LYS* 6.5 0.4 - - - +
472A LEU* 4.1 12.3 - - + -
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A VAL* 5.3 2.5 - - + +
334A PHE* 4.6 9.0 - - + -
335A ALA* 3.6 28.3 - - + -
338A LEU* 3.8 22.9 - - + -
341A PHE* 4.2 8.5 - - + -
352A LEU* 3.4 46.2 - - + +
353A LEU* 3.8 23.8 - - + -
356A GLY* 4.7 11.4 - - - +
360A VAL* 4.3 9.6 - - + -
421A THR 3.0 15.7 + - - +
422A ALA 3.7 3.4 - - - +
424A VAL* 1.3 80.6 - - - +
426A ILE* 1.3 63.1 + - + +
427A ASN* 3.2 8.0 + - - +
430A ARG* 4.8 1.9 + - - -
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Residues in contact with ILE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LEU* 4.1 12.3 - - + -
341A PHE* 3.6 31.6 - - + -
344A LEU* 5.2 0.2 - - + -
352A LEU* 3.9 12.1 - - + -
422A ALA 2.9 20.2 + - - +
423A LEU* 3.1 13.9 - - - +
425A LEU* 1.3 76.2 - - + +
427A ASN* 1.3 58.1 + - - +
428A ALA 4.1 0.2 - - - -
439A VAL* 4.0 18.2 - - + +
442A LEU* 4.0 24.2 - - + -
443A GLN* 3.4 41.0 - - - +
446A LEU* 3.6 18.8 - - + -
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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