Contacts of the helix formed by residues 412 - 425 (chain A) in PDB entry 5ODS
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 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A PRO 4.1 7.0 - - - -
406A ALA* 4.8 3.8 - - - -
411A THR* 1.3 82.9 + - - +
413A PRO* 1.3 68.4 - - - +
414A LEU* 3.4 19.0 - - - +
415A LEU* 2.8 48.2 + - - +
416A GLN* 2.8 17.2 + - - +
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Residues in contact with PRO 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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377A TYR* 3.7 40.6 - - + -
401A PHE* 3.4 19.7 - - + -
404A VAL* 3.4 29.4 - - + +
405A PRO* 3.6 18.8 - - + +
407A GLN* 6.2 3.6 - - + -
410A GLN 5.6 1.1 - - - +
411A THR* 5.0 1.3 - - - -
412A SER* 1.3 83.2 - - - +
414A LEU* 1.3 55.7 + - - +
416A GLN* 3.4 17.0 + - + +
417A TYR* 3.0 22.3 + - - +
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Residues in contact with LEU 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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398A ILE* 5.3 2.2 - - + +
401A PHE* 3.3 41.1 + - + +
402A GLN* 4.3 27.1 - - + +
404A VAL 4.1 12.8 - - - +
405A PRO 5.8 0.4 - - - -
412A SER* 3.1 22.3 - - - +
413A PRO* 1.3 75.9 - - - +
415A LEU* 1.3 67.1 + - - +
417A TYR* 3.3 4.0 + - - +
418A PHE* 3.0 46.1 + - + -
434A GLU 5.7 2.5 - - - +
438A PRO* 5.2 14.6 - - + -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR* 4.2 8.3 - - - +
412A SER* 2.8 34.9 + - - +
414A LEU* 1.3 79.3 - - - +
416A GLN* 1.3 62.3 + - + +
418A PHE* 3.5 7.2 + - - +
419A GLY* 3.0 20.3 + - - -
435A LEU* 6.4 2.9 - - + -
439A VAL* 6.3 3.4 - - + -
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Residues in contact with GLN 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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377A TYR* 4.6 13.5 - - - +
378A SER* 3.5 34.9 + - - +
381A ALA* 4.7 1.3 - - - -
410A GLN* 4.3 15.6 + - - +
411A THR 5.2 1.8 - - - +
412A SER 2.8 16.5 + - - +
413A PRO* 3.5 22.3 - - + +
415A LEU* 1.3 78.4 - - + +
417A TYR* 1.3 61.9 + - - +
419A GLY* 3.2 7.1 + - - -
420A ILE* 3.1 26.3 + - + +
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Residues in contact with TYR 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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381A ALA* 3.8 22.6 - - + +
384A ALA* 3.7 23.0 - - + +
385A ALA 4.9 1.3 - - - -
392A LEU 3.7 17.8 + - - -
393A ARG* 4.0 13.5 - - - +
394A THR 4.7 1.4 + - - -
397A THR* 3.8 12.3 - - + +
398A ILE* 4.0 26.6 - - + +
401A PHE* 3.7 33.4 - + + -
413A PRO 3.0 13.5 + - - +
414A LEU* 3.3 10.7 + - - +
416A GLN* 1.3 76.7 - - - +
418A PHE* 1.3 72.0 + + - +
420A ILE* 3.3 8.2 - - + +
421A LEU* 3.2 52.3 + - + +
431A GLU* 4.3 1.6 + - - -
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Residues in contact with PHE 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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398A ILE* 4.1 25.4 - - + -
402A GLN* 6.2 0.2 - - - -
414A LEU* 3.0 42.4 + - + +
415A LEU* 3.9 6.3 - - - +
417A TYR* 1.3 84.4 - + - +
419A GLY* 1.3 67.4 + - - +
421A LEU* 3.1 20.4 + - + +
422A LEU* 3.3 21.2 + - + +
427A LEU* 4.3 14.3 - - + +
431A GLU* 3.5 41.7 - - + -
434A GLU* 4.2 13.9 - - + -
435A LEU* 3.8 37.2 - - + -
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Residues in contact with GLY 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 LEU 3.0 15.4 + - - -
416A GLN* 3.2 5.1 + - - -
418A PHE* 1.3 76.3 - - - +
420A ILE* 1.3 56.9 + - - +
422A LEU* 3.2 13.6 - - - +
423A ASP* 3.1 22.6 - - - +
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Residues in contact with ILE 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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378A SER* 5.0 8.3 - - - +
381A ALA* 3.6 37.5 - - + +
382A LYS* 4.6 18.8 - - + +
385A ALA* 4.0 16.2 - - + -
416A GLN* 3.1 15.9 - - + +
417A TYR* 3.3 23.6 - - + +
418A PHE 3.3 0.2 - - - -
419A GLY* 1.3 74.4 - - - +
421A LEU* 1.3 69.1 + - - +
423A ASP* 3.0 28.1 + - - +
424A GLN* 3.5 13.3 + - - +
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Residues in contact with LEU 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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385A ALA* 4.9 13.9 - - + +
393A ARG* 3.2 39.9 + - + +
417A TYR* 3.2 56.6 + - + +
418A PHE* 3.1 12.0 + - + +
420A ILE* 1.3 84.3 - - + +
422A LEU* 1.3 63.9 + - - +
424A GLN* 3.1 24.7 + - + +
425A GLY 3.6 5.7 + - - +
427A LEU* 3.7 13.8 - - + +
431A GLU* 3.5 15.7 - - - +
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Residues in contact with LEU 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 PHE 3.3 13.7 + - - +
419A GLY* 3.2 14.8 - - - +
421A LEU* 1.3 76.3 - - - +
423A ASP* 1.3 85.8 + - - +
424A GLN 3.1 0.2 - - - -
425A GLY* 3.0 24.1 + - - +
427A LEU* 4.2 25.9 - - + +
435A LEU* 4.7 7.6 - - + -
451A TRP* 3.7 30.7 - - + +
456A LYS* 3.9 40.9 + - + +
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Residues in contact with ASP 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 GLY 3.1 23.2 - - - +
420A ILE* 3.0 17.6 + - + +
422A LEU* 1.3 87.5 - - - +
424A GLN* 1.3 66.9 + - - +
456A LYS* 5.1 2.6 + - - +
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Residues in contact with GLN 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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385A ALA* 4.0 25.9 - - + +
386A ASN* 3.4 30.3 + - - +
420A ILE* 3.5 23.4 + - - +
421A LEU* 3.5 10.3 - - + +
422A LEU 3.1 0.4 - - - -
423A ASP* 1.3 87.0 + - - +
425A GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 4.7 4.0 - - - +
421A LEU 3.6 4.3 + - - +
422A LEU* 3.0 27.8 + - - +
424A GLN* 1.3 80.9 - - - +
426A GLN* 1.3 63.1 + - - -
427A LEU 3.6 0.5 + - - -
456A LYS* 4.0 4.2 - - - +
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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