Contacts of the helix formed by residues 405 - 419 (chain A) in PDB entry 5T0I
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 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A GLU* 2.7 33.9 + - - +
367A ASP* 4.5 9.9 - - + +
368A ILE* 4.2 4.9 - - + -
403A ILE* 4.2 3.5 - - - +
404A ALA* 1.3 74.5 - - - +
406A GLU* 1.3 89.1 + - + +
407A LYS* 3.4 24.8 + - - +
408A ASP* 2.7 34.9 + - - +
409A PHE* 3.1 14.3 - - - -
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Residues in contact with GLU 406 (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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367A ASP* 2.8 34.8 - - - +
368A ILE* 3.4 24.1 - - + +
369A ARG* 3.0 42.5 + - - +
372A LEU* 4.1 11.4 - - - +
405A THR* 1.3 81.6 - - + +
407A LYS* 1.3 72.7 + - + +
408A ASP 3.0 1.4 + - - -
409A PHE* 3.6 16.4 - - + -
410A LEU* 3.0 35.1 + - + +
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Residues in contact with LYS 407 (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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367A ASP* 5.4 2.8 + - - -
405A THR* 3.5 27.3 + - + +
406A GLU* 1.3 84.5 - - + +
408A ASP* 1.3 76.1 + - - +
410A LEU* 3.6 15.6 - - + +
411A GLU* 3.5 20.6 + - - +
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Residues in contact with ASP 408 (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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395A PHE* 6.1 0.3 - - - -
401A ARG* 3.9 32.7 + - - +
403A ILE* 4.6 0.3 - - - +
404A ALA* 3.7 5.9 - - - -
405A THR* 2.7 42.4 + - - +
406A GLU 3.0 1.8 + - - -
407A LYS* 1.3 98.4 + - - +
409A PHE* 1.3 61.1 + - - +
411A GLU* 3.6 11.1 + - - +
412A ALA* 4.0 4.2 + - - +
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Residues in contact with PHE 409 (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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355A PHE* 6.3 0.2 - + - -
368A ILE* 3.9 20.6 - - + -
370A PHE* 5.2 7.6 - + - -
373A LEU* 3.6 23.1 - - + -
388A VAL* 3.7 25.1 - - + +
389A CYS* 6.0 4.7 - - - -
391A GLU* 4.6 3.1 - - + -
392A ALA* 3.6 44.9 - - + +
395A PHE* 6.1 0.7 - - - -
401A ARG* 5.4 2.5 - - - +
404A ALA* 3.7 15.0 - - + -
405A THR 3.1 30.3 - - - -
406A GLU* 3.6 18.2 - - + -
408A ASP* 1.3 74.2 - - + +
410A LEU* 1.3 66.8 + - - +
411A GLU 3.1 2.5 - - - -
412A ALA* 2.8 12.9 + - - +
413A VAL* 2.7 35.1 + - + +
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Residues in contact with LEU 410 (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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372A LEU* 4.2 27.4 - - + -
373A LEU* 3.6 31.5 - - + +
376A LEU* 5.0 9.0 - - + +
406A GLU* 3.0 38.4 + - + +
407A LYS* 3.6 14.6 - - + +
409A PHE* 1.3 78.9 - - + +
411A GLU* 1.3 67.0 + - - +
413A VAL* 3.6 11.5 - - - +
414A ASN* 3.0 35.4 + - - +
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Residues in contact with GLU 411 (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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407A LYS 3.5 18.0 + - - +
408A ASP 3.7 6.1 - - - +
409A PHE 3.1 0.4 - - - -
410A LEU* 1.3 86.3 - - - +
412A ALA* 1.3 55.0 + - - +
414A ASN* 2.7 37.2 + - - +
415A LYS* 3.9 3.8 + - - +
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Residues in contact with ALA 412 (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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391A GLU* 5.0 11.6 - - + +
395A PHE* 3.5 37.0 - - + -
408A ASP 4.0 2.6 + - - +
409A PHE* 2.8 15.3 + - - +
411A GLU* 1.3 76.6 - - - +
413A VAL* 1.3 59.4 + - - +
415A LYS* 3.3 14.9 + - - +
416A VAL* 2.9 28.5 + - - +
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Residues in contact with VAL 413 (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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373A LEU* 3.7 32.5 - - + -
376A LEU* 5.8 0.4 - - + -
377A CYS* 4.9 7.2 - - + -
388A VAL* 3.7 45.5 - - + +
391A GLU* 5.7 3.1 - - + -
409A PHE* 2.7 24.5 + - + +
410A LEU* 3.1 10.2 + - - +
412A ALA* 1.3 71.4 - - - +
414A ASN* 1.3 65.6 + - - +
415A LYS 3.1 1.3 - - - -
416A VAL* 3.1 14.6 + - + +
417A ILE* 3.1 34.1 + - + +
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Residues in contact with ASN 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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373A LEU* 5.3 0.8 - - - +
376A LEU* 4.9 14.9 - - + +
410A LEU* 3.0 25.1 + - - +
411A GLU* 2.7 41.0 + - - +
413A VAL* 1.3 76.9 - - - +
415A LYS* 1.3 70.6 + - - +
417A ILE* 3.2 15.7 - - + +
418A LYS* 3.1 29.7 - - + +
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Residues in contact with LYS 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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391A GLU* 5.8 2.2 + - - -
395A PHE* 4.7 21.6 - - - -
411A GLU 4.2 2.9 - - - +
412A ALA* 3.3 22.0 + - - +
413A VAL 3.1 0.6 - - - -
414A ASN* 1.3 84.3 + - - +
416A VAL* 1.3 58.6 + - - +
417A ILE 3.2 2.5 - - - -
418A LYS* 4.9 1.1 - - - -
419A SER* 2.5 57.9 + - - +
420A TYR* 5.2 5.7 - - - -
349B ARG* 5.4 7.1 - - - +
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Residues in contact with VAL 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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384A GLU* 4.3 10.3 - - + +
387A SER* 4.6 13.9 - - - +
388A VAL* 5.4 3.6 - - + +
391A GLU* 4.7 16.6 - - + +
412A ALA 2.9 13.5 + - - +
413A VAL* 3.1 34.0 + - + +
415A LYS* 1.3 79.9 - - - +
417A ILE* 1.3 65.7 + - + +
419A SER* 4.0 0.4 - - - -
420A TYR* 3.0 56.2 - - + +
347B ILE 4.5 9.2 - - - +
348B ASP 4.3 8.7 - - - +
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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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376A LEU* 3.2 28.5 - - + +
377A CYS* 4.0 23.8 - - + -
378A PRO* 5.4 3.4 - - + -
384A GLU* 3.4 25.1 - - + +
413A VAL* 3.2 17.5 - - + +
414A ASN* 3.2 22.2 - - + +
416A VAL* 1.3 86.6 - - + +
418A LYS* 1.3 86.9 + - + +
420A TYR* 4.0 1.0 - - - +
421A ALA* 3.2 26.0 + - - +
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Residues in contact with LYS 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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376A LEU 5.5 1.2 + - - -
378A PRO* 6.0 3.4 - - - +
414A ASN* 3.1 18.8 - - + +
415A LYS* 3.3 3.0 + - - +
417A ILE* 1.3 96.3 - - + +
419A SER* 1.3 60.6 + - - +
420A TYR 3.2 1.6 - - - -
421A ALA* 2.9 22.5 + - + +
422A LYS* 3.2 17.3 + - - +
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Residues in contact with SER 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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415A LYS* 2.5 44.3 + - - +
418A LYS* 1.3 74.1 - - - +
420A TYR* 1.3 77.7 + - - +
421A ALA 3.6 0.2 + - - -
422A LYS* 3.7 41.7 + - - +
423A PHE* 3.9 7.6 - - - -
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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