Contacts of the helix formed by residues 413 - 426 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411D HIS 3.7 0.6 + - - -
412D PHE* 1.3 75.9 - - - +
414D GLU* 1.3 65.6 + - - +
415D ASP* 3.8 6.6 + - - +
416D GLU* 3.1 33.2 + - - +
417D ILE* 3.1 25.1 + - - +
453D HIS* 4.8 2.3 + - - -
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Residues in contact with GLU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D TYR* 3.3 24.5 + - + -
282D ARG* 5.8 8.1 - - + +
285D CYS* 5.7 0.2 - - - -
289D LEU* 3.7 34.4 + - + +
367D ARG* 2.9 43.5 + - - +
413D SER* 1.3 74.5 - - - +
415D ASP* 1.3 64.7 + - - +
417D ILE* 3.4 4.2 + - - +
418D ALA* 3.0 23.7 + - - +
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Residues in contact with ASP 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D CYS* 3.5 35.6 - - - +
281D TYR* 5.9 0.9 - - - -
282D ARG* 3.8 14.5 + - - +
413D SER* 3.3 5.3 + - - +
414D GLU* 1.3 82.5 - - - +
416D GLU* 1.3 57.6 + - - +
418D ALA* 3.3 5.2 - - - +
419D LEU* 3.1 33.2 + - - +
453D HIS* 3.7 27.1 - - - +
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Residues in contact with GLU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D HIS 4.0 0.3 - - - +
412D PHE* 3.4 17.4 - - + -
413D SER* 3.1 32.0 + - - +
415D ASP* 1.3 76.0 - - - +
417D ILE* 1.3 60.0 + - - +
419D LEU* 3.4 1.4 + - - -
420D TYR* 3.0 29.9 + - - +
450D PHE* 3.5 13.4 - - + -
453D HIS* 4.0 18.4 + - + -
454D LEU* 3.2 24.5 - - + +
457D THR* 4.4 2.9 + - - -
459D ARG* 2.7 47.8 + - - +
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Residues in contact with ILE 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D TYR* 3.4 26.2 - - + +
363D VAL* 4.7 5.6 - - + +
364D ARG* 4.7 12.8 - - - -
366D CYS* 4.1 15.5 - - - -
367D ARG* 3.7 26.0 - - + +
412D PHE* 3.6 30.1 - - + +
413D SER 3.1 21.7 + - - +
414D GLU* 3.8 8.1 - - - +
416D GLU* 1.3 71.7 - - - +
418D ALA* 1.3 57.3 + - - +
420D TYR* 3.4 5.7 + - - +
421D THR* 2.8 51.5 + - + +
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Residues in contact with ALA 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D VAL* 3.5 14.3 - - + +
278D CYS* 4.1 17.5 - - - -
281D TYR* 3.5 33.6 - - + -
334D PHE* 4.1 1.0 - - - -
414D GLU 3.0 13.2 + - - +
415D ASP* 3.3 12.8 - - - +
416D GLU 3.2 0.2 - - - -
417D ILE* 1.3 75.4 - - - +
419D LEU* 1.3 56.7 + - - +
421D THR* 2.9 20.9 + - - -
422D ALA* 3.0 12.6 + - - +
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Residues in contact with LEU 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D VAL* 4.1 16.2 - - + -
277D VAL* 4.0 21.1 - - + -
278D CYS* 4.6 6.3 - - - -
415D ASP 3.1 19.6 + - - +
416D GLU 3.9 0.9 - - - +
417D ILE 3.4 0.2 - - - -
418D ALA* 1.3 76.4 - - - +
420D TYR* 1.3 65.5 + - - +
422D ALA* 3.6 3.2 + - - +
423D LEU* 3.2 23.4 + - - +
446D LEU* 5.0 8.3 - - + +
449D ALA* 4.0 29.6 - - + +
450D PHE* 3.6 29.8 - - + +
453D HIS* 3.6 40.6 - - + +
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Residues in contact with TYR 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D VAL* 3.5 34.0 - - + +
403D PHE* 3.9 14.9 - - - -
407D LEU* 3.7 20.0 - - + -
412D PHE* 3.8 21.3 - + + -
416D GLU 3.0 18.2 + - - +
417D ILE* 3.8 3.8 - - - +
419D LEU* 1.3 76.9 - - - +
421D THR* 1.3 57.7 + - - +
423D LEU* 3.1 10.2 + - + +
424D VAL* 2.9 37.5 + - + +
450D PHE* 3.8 17.4 - + + -
466D LEU* 3.8 29.2 - - + -
467D PRO* 3.6 24.1 + - - +
472D LEU* 4.5 5.5 - - + +
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Residues in contact with THR 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D TYR* 4.3 4.9 - - + -
334D PHE* 3.7 13.0 - - - -
360D VAL* 3.8 28.7 - - + +
363D VAL* 3.6 29.4 - - + -
364D ARG* 4.2 10.0 + - + -
417D ILE* 2.8 31.5 + - + +
418D ALA* 2.9 22.2 + - - -
420D TYR* 1.3 72.3 - - - +
422D ALA* 1.3 56.5 + - - +
424D VAL* 3.2 10.4 + - - +
425D LEU* 3.0 27.7 + - - +
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Residues in contact with ALA 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D VAL* 3.9 23.1 - - + -
334D PHE* 4.1 16.1 - - + -
338D LEU* 4.1 13.0 - - + -
418D ALA 3.0 17.6 + - - +
419D LEU 3.7 5.4 - - - +
421D THR* 1.3 76.8 + - - +
423D LEU* 1.3 57.3 + - - +
425D LEU* 3.4 2.3 + - - +
426D ILE* 3.0 34.8 + - - +
446D LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D LEU 3.2 11.4 + - - +
420D TYR* 3.1 15.8 + - + +
422D ALA* 1.3 74.9 - - - +
424D VAL* 1.3 64.4 + - - +
426D ILE 3.2 19.5 - - - +
427D ASN* 4.2 3.1 + - - +
443D GLN* 3.5 35.4 - - + +
446D LEU* 3.7 18.3 - - + +
447D GLU* 3.6 26.7 - - + +
450D PHE* 4.0 26.5 - - + -
463D LEU* 5.3 3.8 - - + -
466D LEU* 5.3 7.0 - - + -
469D LYS* 5.5 7.0 - - - -
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Residues in contact with VAL 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D GLY 4.6 0.4 - - - +
359D GLU* 3.5 47.2 - - + +
360D VAL* 4.0 7.4 - - + +
363D VAL* 4.3 9.2 - - + -
420D TYR* 2.9 40.6 + - + +
421D THR* 3.2 10.7 + - - +
423D LEU* 1.3 79.0 - - - +
425D LEU* 1.3 59.4 + - - +
427D ASN* 3.8 7.0 + - - +
430D ARG* 3.3 19.2 + - - -
472D LEU* 4.0 15.3 - - + -
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Residues in contact with LEU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D VAL* 5.3 1.1 - - + +
334D PHE* 4.7 8.7 - - + -
335D ALA* 3.7 31.0 - - + -
338D LEU* 4.4 11.2 - - + -
341D PHE* 3.9 15.3 - - + -
352D LEU* 3.4 47.3 - - + +
353D LEU* 3.8 24.2 - - + +
356D GLY* 4.7 8.7 - - - -
360D VAL* 4.2 15.3 - - + -
421D THR 3.0 14.1 + - - +
422D ALA* 3.8 4.7 - - - +
423D LEU 3.3 0.2 - - - -
424D VAL* 1.3 79.5 - - - +
426D ILE* 1.3 66.5 + - + +
427D ASN* 3.1 7.1 + - - +
430D ARG* 5.0 1.4 + - - -
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Residues in contact with ILE 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D LEU* 5.1 6.5 - - + -
341D PHE* 3.8 31.6 - - + -
344D LEU* 4.3 1.8 - - + -
352D LEU* 4.2 10.8 - - + -
422D ALA 3.0 18.0 + - - +
423D LEU* 3.2 13.0 - - - +
425D LEU* 1.3 80.3 - - + +
427D ASN* 1.3 57.5 + - - +
428D ALA 4.1 0.2 - - - -
439D VAL* 3.8 19.3 - - + +
442D LEU* 3.8 27.1 - - + -
443D GLN* 3.5 42.5 - - - +
446D LEU* 3.6 18.2 - - + -
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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