Contacts of the helix formed by residues 413 - 424 (chain D) in PDB entry 6O0T
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 LYS 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 SER 3.5 7.8 + - - +
412D TRP* 1.3 78.7 - - - +
414D GLU* 1.3 69.4 + - + +
415D ALA* 3.2 4.0 - - + +
416D GLU* 3.2 24.0 + - - +
417D VAL* 3.4 12.6 + - - +
439D ASP* 4.1 9.9 - - - -
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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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413D LYS* 1.3 77.7 - - + +
415D ALA* 1.3 63.8 + - - +
417D VAL* 3.2 3.6 + - - +
418D GLN* 3.0 31.8 + - + +
433D PHE 5.8 1.1 - - - +
434D ARG* 4.2 17.1 - - + +
437D GLN* 3.4 45.2 - - - +
438D VAL 3.8 24.5 - - - +
439D ASP* 4.3 5.1 - - + +
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Residues in contact with ALA 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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413D LYS* 3.2 3.6 - - + +
414D GLU* 1.3 77.9 - - - +
416D GLU* 1.3 69.9 + - - +
418D GLN* 3.3 8.5 + - - +
419D THR* 3.1 26.7 + - - -
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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 SER 5.3 1.0 - - - +
412D TRP* 3.4 48.2 - - + +
413D LYS* 3.2 28.6 + - - +
415D ALA* 1.3 82.3 - - - +
417D VAL* 1.3 57.5 + - - +
419D THR* 3.5 6.5 + - - -
420D TRP* 3.0 27.9 + - - +
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Residues in contact with VAL 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D TRP* 4.3 7.9 - - + -
413D LYS 3.4 6.0 + - - +
414D GLU 3.2 8.1 + - - +
416D GLU* 1.3 76.0 - - - +
418D GLN* 1.3 66.8 + - - +
420D TRP* 3.2 6.6 + - + +
421D LEU* 3.0 29.3 + - + +
433D PHE* 4.0 28.7 - - + -
438D VAL* 3.7 16.6 - - + +
439D ASP 3.6 32.5 - - - +
440D GLY 4.0 1.8 - - - +
443D LEU* 3.9 24.0 - - + -
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Residues in contact with GLN 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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414D GLU* 3.0 23.8 + - + +
415D ALA* 3.6 9.6 - - - +
417D VAL* 1.3 78.0 - - - +
419D THR* 1.3 62.3 + - - +
421D LEU* 3.4 6.4 + - - +
422D GLN* 3.3 34.5 + - - +
430D CYS* 2.9 49.1 + - - +
431D GLU* 5.6 1.0 - - - +
433D PHE* 3.7 13.9 + - - +
434D ARG* 3.4 33.0 - - + +
438D VAL 5.9 0.4 + - - -
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Residues in contact with THR 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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415D ALA 3.1 16.2 + - - -
416D GLU* 3.8 7.8 - - - -
417D VAL 3.3 0.2 - - - -
418D GLN* 1.3 75.6 - - - +
420D TRP* 1.3 63.1 + - - +
422D GLN* 3.2 14.5 + - + +
423D GLN* 3.1 45.1 + - + +
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Residues in contact with TRP 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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412D TRP* 3.7 16.6 - + + -
416D GLU 3.0 18.3 + - - +
417D VAL* 3.2 4.2 + - + +
419D THR* 1.3 78.8 - - - +
421D LEU* 1.3 85.5 + - + +
423D GLN* 3.3 13.4 + - + +
424D ILE* 3.2 55.7 + - + +
443D LEU* 3.8 24.0 - - + -
466D PHE* 3.6 31.9 - + - -
469D GLU* 3.9 24.3 + - + -
470D LEU* 4.1 18.8 - - + -
473D LEU* 3.9 35.0 - - + +
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Residues in contact with LEU 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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417D VAL* 3.0 22.1 + - + +
418D GLN* 3.7 9.9 - - - +
419D THR 3.3 0.2 - - - -
420D TRP* 1.3 99.2 - - + +
422D GLN* 1.3 59.4 + - - +
424D ILE* 3.3 7.9 - - + +
426D PHE* 2.8 50.4 + - + +
429D TYR* 3.9 9.2 - - + +
430D CYS* 4.1 15.0 - - - -
433D PHE* 3.5 47.6 - - + -
466D PHE* 3.9 16.2 - - + -
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Residues in contact with GLN 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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418D GLN* 3.3 25.9 + - - +
419D THR* 3.2 13.1 + - + +
421D LEU* 1.3 78.1 - - - +
423D GLN* 1.3 62.2 + - + +
425D GLY* 3.3 12.6 + - - -
427D SER* 3.8 23.0 + - - +
430D CYS* 3.9 17.4 - - - -
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Residues in contact with GLN 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 THR* 3.1 36.8 + - + +
420D TRP* 3.3 13.9 + - + +
422D GLN* 1.3 76.0 - - + +
424D ILE* 1.3 62.3 + - + +
425D GLY 3.4 0.4 + - - -
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Residues in contact with ILE 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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420D TRP* 3.3 67.1 - - + +
421D LEU* 3.3 15.5 - - + +
423D GLN* 1.3 80.3 - - + +
425D GLY* 1.3 58.7 + - - +
426D PHE* 3.4 35.8 - - + -
465D ARG* 4.9 5.4 + - - -
466D PHE* 4.5 3.6 - - + -
469D GLU* 4.0 37.4 - - + +
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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