Contacts of the helix formed by residues 413 - 426 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B HIS 3.6 0.8 + - - -
412B PHE* 1.3 77.1 - - - +
414B GLU* 1.3 63.8 + - - +
415B ASP* 3.7 9.3 + - - +
416B GLU* 2.9 38.7 + - - +
417B ILE* 3.1 25.0 + - - +
453B HIS* 4.9 2.4 + - - -
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TYR* 3.4 29.9 + - + -
282B ARG* 5.6 9.8 - - + +
285B CYS* 4.7 0.9 - - - -
289B LEU* 3.9 31.4 - - + +
367B ARG* 2.8 47.9 + - - +
413B SER* 1.3 74.6 - - - +
415B ASP* 1.3 60.8 + - - +
417B ILE* 3.4 9.9 + - - +
418B ALA* 3.0 24.9 + - - +
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Residues in contact with ASP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B CYS* 3.2 33.4 - - - +
282B ARG* 4.1 10.9 + - - +
413B SER* 3.3 6.3 + - - +
414B GLU* 1.3 81.3 - - - +
416B GLU* 1.3 57.4 + - - +
418B ALA* 3.3 4.0 - - - +
419B LEU* 3.1 34.4 + - - +
453B HIS* 3.6 32.0 + - + +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B HIS 4.2 0.2 - - - +
412B PHE* 3.6 17.2 - - + -
413B SER* 2.9 38.0 + - - +
415B ASP* 1.3 75.1 - - - +
417B ILE* 1.3 60.7 + - - +
419B LEU* 3.5 1.6 + - - -
420B TYR* 2.9 32.2 + - - +
450B PHE* 3.9 11.5 - - + -
453B HIS* 4.6 10.9 - - + -
454B LEU* 3.4 30.1 - - + +
457B THR* 4.5 2.9 + - - -
459B ARG* 3.0 45.9 + - - +
462B ILE* 4.2 3.1 - - + -
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TYR* 3.3 25.8 - - + +
363B VAL* 4.5 9.4 - - + +
364B ARG* 4.7 10.1 - - - -
366B CYS* 4.1 11.0 - - - -
367B ARG* 3.8 23.8 - - + +
412B PHE* 3.6 34.3 - - + +
413B SER 3.1 17.0 + - - +
414B GLU* 3.8 12.8 - - - +
416B GLU* 1.3 73.0 - - - +
418B ALA* 1.3 54.2 + - - +
420B TYR* 4.4 5.4 - - - -
421B THR* 2.7 50.2 + - + +
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.5 12.4 - - + +
278B CYS* 3.9 19.5 - - - -
281B TYR* 3.5 35.6 - - + -
334B PHE* 3.9 2.4 - - - -
414B GLU 3.0 14.1 + - - +
415B ASP* 3.3 12.6 - - - +
416B GLU 3.3 0.2 - - - -
417B ILE* 1.3 76.0 - - - +
419B LEU* 1.3 60.4 + - - +
421B THR* 3.0 16.2 + - - -
422B ALA* 3.2 8.5 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 4.2 17.0 - - + +
277B VAL* 3.9 28.3 - - + -
278B CYS* 4.6 4.0 - - - -
415B ASP 3.1 18.3 + - - +
416B GLU* 4.1 0.7 - - - +
418B ALA* 1.3 76.8 - - - +
420B TYR* 1.3 65.0 + - - +
422B ALA* 3.5 4.0 - - - +
423B LEU* 3.3 26.2 + - - +
446B LEU* 5.1 5.0 - - + +
449B ALA* 4.1 26.9 - - + +
450B PHE* 3.5 29.2 - - + +
453B HIS* 3.8 36.8 - - + -
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Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B VAL* 3.6 37.5 - - + +
403B PHE* 4.8 1.4 - - - -
407B LEU* 4.2 16.1 - - + +
412B PHE* 4.1 17.5 - + + -
416B GLU 2.9 20.6 + - - +
417B ILE* 3.9 2.7 - - - +
419B LEU* 1.3 74.7 - - - +
421B THR* 1.3 58.5 + - - +
423B LEU* 3.0 11.5 + - + +
424B VAL* 3.0 37.8 + - + +
450B PHE* 4.2 17.2 - + + -
466B LEU* 4.0 32.7 - - + +
467B PRO* 4.0 25.5 + - - +
472B LEU* 4.6 10.0 - - - +
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Residues in contact with THR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TYR* 4.4 5.1 - - + -
334B PHE* 3.9 11.7 - - - -
360B VAL* 3.8 34.5 - - + +
363B VAL* 3.6 29.6 - - + -
364B ARG* 4.2 5.8 + - + -
417B ILE* 2.7 37.7 + - + +
418B ALA* 3.0 14.9 + - - -
420B TYR* 1.3 68.7 - - - +
422B ALA* 1.3 65.4 + - - +
424B VAL* 3.2 9.3 + - - +
425B LEU* 3.0 23.7 + - - +
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B VAL* 3.9 17.7 - - + -
334B PHE* 4.1 10.7 - - + -
338B LEU* 4.2 13.0 - - + -
418B ALA 3.2 15.4 + - - +
419B LEU* 3.5 10.8 - - - +
421B THR* 1.3 76.8 + - - +
423B LEU* 1.3 58.2 + - - +
425B LEU* 3.4 1.8 + - - +
426B ILE* 2.8 34.9 + - - +
446B LEU* 4.2 21.1 - - + -
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LEU 3.3 12.7 + - - +
420B TYR* 3.0 14.1 + - + +
422B ALA* 1.3 77.4 - - - +
424B VAL* 1.3 65.4 - - - +
426B ILE* 3.0 22.1 - - - +
427B ASN* 4.1 4.3 + - - +
443B GLN* 3.7 16.8 - - + +
446B LEU* 3.7 12.8 - - + +
447B GLU* 3.6 40.8 - - + +
450B PHE* 3.6 42.0 - - + -
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Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLY 4.3 1.3 - - - +
359B GLU* 3.5 38.8 - - + +
360B VAL* 3.9 16.8 - - + +
363B VAL* 4.2 9.2 - - + -
420B TYR* 3.0 40.5 + - + +
421B THR* 3.4 12.3 - - - +
423B LEU* 1.3 78.0 - - - +
425B LEU* 1.3 59.4 + - - +
427B ASN* 3.9 7.1 + - - +
430B ARG* 3.2 25.1 + - - -
472B LEU* 4.2 13.0 - - + -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B VAL* 5.3 1.6 - - + +
334B PHE* 4.6 9.0 - - + -
335B ALA* 3.8 26.7 - - + -
338B LEU* 3.9 24.2 - - + -
341B PHE* 4.3 4.9 - - + -
352B LEU* 3.5 43.4 - - + +
353B LEU* 3.7 27.8 - - + +
356B GLY* 4.7 11.4 - - - -
360B VAL* 4.4 9.9 - - + -
421B THR 3.0 12.7 + - - +
422B ALA 3.6 5.6 - - - +
424B VAL* 1.3 80.9 - - - +
426B ILE* 1.3 68.7 + - + +
427B ASN* 3.0 9.0 + - - +
430B ARG* 4.8 1.4 + - - -
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 4.1 9.4 - - + -
341B PHE* 3.6 31.2 - - + -
352B LEU* 3.9 11.9 - - + -
422B ALA 2.8 22.9 + - - +
423B LEU* 3.0 14.9 - - - +
425B LEU* 1.3 75.8 - - + +
427B ASN* 1.3 58.5 + - - +
428B ALA 4.1 0.2 - - - -
439B VAL* 3.9 18.6 - - + +
442B LEU* 3.8 23.8 - - + -
443B GLN* 3.6 43.0 - - - +
446B LEU* 3.5 20.0 - - + -
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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