Contacts of the helix formed by residues 412 - 426 (chain A) in PDB entry 4TMU
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 GLY 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A TYR* 3.0 23.2 + - - -
411A ASP* 1.3 72.3 - - - +
413A LEU* 1.3 63.0 + - - +
414A VAL 3.4 2.5 - - - -
415A ASP* 3.2 6.6 + - - +
416A ALA* 2.9 23.4 + - - +
508A LEU* 2.8 17.3 + - - -
510A LEU* 3.8 19.3 - - - +
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Residues in contact with LEU 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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411A ASP* 3.4 20.2 - - - +
412A GLY* 1.3 76.6 - - - +
414A VAL* 1.3 66.3 + - + +
416A ALA* 3.2 4.9 + - + +
417A GLN* 3.0 39.6 + - - +
501A PHE* 3.9 20.9 - - + +
504A GLY* 3.9 21.1 - - - +
505A GLU 5.3 1.1 - - - -
506A ALA 3.8 23.1 - - - +
507A PRO* 4.4 8.5 - - + -
508A LEU* 3.5 16.6 + - + +
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Residues in contact with VAL 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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411A ASP* 4.5 11.7 + - - +
412A GLY 3.4 0.6 - - - -
413A LEU* 1.3 77.8 - - + +
415A ASP* 1.3 66.9 + - - +
417A GLN* 3.2 21.5 + - - +
418A LYS* 3.1 47.8 + - + +
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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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410A TYR* 3.2 32.1 + - - +
411A ASP 5.0 1.0 + - - +
412A GLY* 3.2 9.7 + - - +
414A VAL* 1.3 76.8 - - - +
416A ALA* 1.3 66.7 + - - +
418A LYS* 3.4 5.2 + - - +
419A ALA* 3.0 20.8 + - - +
464A GLN* 3.3 19.1 + - - +
468A HIS* 3.4 16.9 + - - -
469A TRP* 3.3 27.0 - - + -
472A VAL* 4.3 14.1 - - + -
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Residues in contact with ALA 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 GLY 2.9 14.2 + - - +
413A LEU* 3.5 8.7 - - - +
415A ASP* 1.3 73.5 - - - +
417A GLN* 1.3 57.7 + - - +
419A ALA 3.3 0.3 + - - -
420A LEU* 2.7 48.6 + - + +
472A VAL* 4.5 2.2 - - - +
476A LEU* 4.1 23.6 - - + -
501A PHE* 4.9 5.6 - - + -
508A LEU* 3.7 24.0 - - + -
510A LEU* 5.2 1.1 - - + -
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Residues in contact with GLN 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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413A LEU* 3.0 26.3 + - - +
414A VAL* 3.2 22.4 + - - +
416A ALA* 1.3 76.6 - - - +
418A LYS* 1.3 54.9 + - + +
420A LEU* 4.7 0.2 - - - -
421A SER* 2.7 40.6 + - - -
501A PHE 3.3 18.8 + - - +
502A LEU* 3.7 19.5 + - + +
503A ARG 4.2 5.7 + - - -
504A GLY* 3.7 26.7 + - - -
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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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414A VAL* 3.1 33.4 + - + +
415A ASP* 3.7 9.7 + - - +
416A ALA 3.3 0.4 - - - -
417A GLN* 1.3 81.3 - - + +
419A ALA* 1.3 57.8 + - - +
421A SER* 3.9 4.1 - - - -
422A ALA* 2.9 30.7 + - - +
439A LEU* 3.6 5.1 - - + +
457A VAL* 5.2 1.5 - - - +
460A ILE* 3.4 61.2 + - + +
461A GLY* 5.1 0.4 - - - -
463A ASP* 4.7 10.9 + - - -
464A GLN* 5.3 2.2 + - - -
469A TRP* 3.8 24.5 - - + -
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Residues in contact with ALA 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 ASP 3.0 16.5 + - - +
416A ALA 3.8 2.0 - - - +
418A LYS* 1.3 76.4 - - - +
420A LEU* 1.3 63.8 + - - +
422A ALA* 3.4 3.3 + - - +
423A ILE* 3.1 29.8 + - + +
435A VAL* 4.6 1.0 - - - +
439A LEU* 4.2 11.6 - - + +
469A TRP* 4.3 8.3 - - + -
472A VAL* 4.3 12.6 - - + -
473A ILE* 4.1 25.8 - - + -
476A LEU* 4.3 6.3 - - + -
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Residues in contact with LEU 420 (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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416A ALA* 2.7 31.3 + - + +
419A ALA* 1.3 71.0 - - - +
421A SER* 1.3 59.7 + - - +
423A ILE* 3.2 6.7 + - - +
424A ALA* 2.9 28.1 + - - +
476A LEU* 4.1 9.0 - - + -
481A VAL* 3.5 25.6 - - + -
482A VAL* 3.4 23.1 - - + -
494A LEU* 3.3 31.0 - - + +
498A ALA* 4.0 9.9 - - + +
501A PHE* 3.9 25.6 - - + -
502A LEU* 3.9 19.3 - - + +
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Residues in contact with SER 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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417A GLN* 2.7 26.6 + - - -
418A LYS* 3.9 4.7 - - - -
420A LEU* 1.3 73.6 - - - +
422A ALA* 1.3 61.0 + - - +
424A ALA* 3.2 7.6 + - - +
425A ARG* 3.0 27.9 + - - +
457A VAL* 3.6 19.9 - - - +
502A LEU* 3.4 16.6 - - - +
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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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418A LYS 2.9 19.7 + - - +
419A ALA 3.5 5.6 - - - +
420A LEU 3.2 0.2 - - - -
421A SER* 1.3 78.1 - - - +
423A ILE* 1.3 61.5 + - - +
425A ARG* 3.5 1.9 + - - +
426A VAL* 3.4 27.4 + - - +
435A VAL* 4.3 11.3 - - + +
438A VAL* 4.9 6.0 - - + +
439A LEU* 3.8 24.2 - - + -
457A VAL* 4.0 21.8 - - + +
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Residues in contact with ILE 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 ALA* 3.1 21.3 + - + +
420A LEU* 3.2 8.0 + - + +
422A ALA* 1.3 74.0 - - - +
424A ALA* 1.3 64.3 + - - +
426A VAL* 3.5 11.5 - - + +
428A GLN* 3.2 22.3 + - + -
435A VAL* 3.7 22.9 - - + -
473A ILE* 5.0 9.9 - - + -
476A LEU* 6.1 0.2 - - + -
482A VAL* 4.2 24.9 - - + -
492A LEU* 3.2 50.5 - - + +
493A GLN 4.8 0.2 - - - -
494A LEU* 4.1 17.7 - - + -
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Residues in contact with ALA 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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420A LEU 2.9 13.4 + - - +
421A SER* 3.2 13.4 + - - +
423A ILE* 1.3 77.1 - - - +
425A ARG* 1.3 59.6 + - + +
427A GLU* 2.9 25.6 + - - +
428A GLN* 4.9 3.7 - - - +
494A LEU* 4.1 17.7 - - + +
502A LEU* 4.4 9.9 - - + -
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Residues in contact with ARG 425 (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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421A SER* 3.0 16.7 + - - +
422A ALA 4.0 3.8 - - - +
423A ILE 3.4 0.2 - - - -
424A ALA* 1.3 81.4 - - + +
426A VAL* 1.3 58.1 + - + +
427A GLU* 3.1 14.4 + - - +
452A HIS* 5.3 1.0 + - - -
455A LEU* 4.0 38.7 - - + +
456A LYS* 5.8 2.2 - - - +
457A VAL* 4.4 21.5 - - + -
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Residues in contact with VAL 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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422A ALA 3.4 14.7 + - - +
423A ILE* 3.5 19.5 - - + +
425A ARG* 1.3 75.2 - - + +
427A GLU* 1.3 67.4 + - - +
428A GLN* 3.2 4.1 + - - +
429A ARG* 3.6 3.0 + - - +
430A PHE* 3.4 42.8 - - + +
434A TYR* 4.7 3.4 - - + -
435A VAL* 4.3 16.6 - - + -
438A VAL* 4.6 20.2 - - + -
452A HIS* 4.3 28.9 - - + +
455A LEU* 5.0 4.3 - - + -
457A VAL* 6.3 0.2 - - + -
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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