Contacts of the helix formed by residues 402 - 412 (chain B) in PDB entry 1ASZ
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 TYR 402 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400B LEU 3.6 0.2 + - - -
401B THR* 1.3 70.6 - - - +
403B LYS* 1.3 65.5 + - - +
405B GLY* 3.2 3.1 + - - +
406B ILE* 3.0 47.0 + - + +
418B ASP 3.9 16.8 - - - -
420B GLU 2.5 27.5 + - - -
421B ASP* 4.7 0.2 + - - -
422B LEU* 3.7 23.7 + - + -
445B LEU* 3.7 25.4 - - + -
446B ASP 2.9 8.0 + - - +
447B LYS 3.8 19.6 + - - +
448B PHE* 3.9 32.1 - + + +
449B PRO* 3.1 28.5 - - + -
452B ILE* 3.3 14.1 - - + +
466B TYR* 4.8 5.6 - + + -
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Residues in contact with LYS 403 (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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401B THR* 3.0 13.8 + - - +
402B TYR* 1.3 75.8 - - - +
404B GLU* 1.3 81.7 + - - +
406B ILE* 2.7 11.1 + - - +
407B GLU* 2.6 67.5 + - + +
418B ASP 5.9 0.7 - - - -
466B TYR* 4.7 20.9 + - + +
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Residues in contact with GLU 404 (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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400B LEU* 3.2 22.1 - - + +
401B THR* 2.7 45.0 + - - +
403B LYS* 1.3 94.4 + - - +
405B GLY* 1.3 63.9 + - - +
407B GLU* 3.5 11.8 - - - +
408B MET* 2.8 35.4 + - + +
438B TYR* 6.1 0.7 - - - -
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Residues in contact with GLY 405 (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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400B LEU* 4.7 2.8 - - - +
401B THR 3.1 11.9 + - - -
402B TYR* 3.2 5.4 + - - -
403B LYS 2.9 1.4 + - - -
404B GLU* 1.3 80.8 - - - +
406B ILE* 1.3 62.9 + - - +
408B MET* 3.2 4.3 + - - +
409B LEU* 3.1 23.4 + - - +
422B LEU* 6.0 0.2 - - - -
430B LEU* 3.8 30.5 - - - +
445B LEU* 4.3 7.6 - - - -
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Residues in contact with ILE 406 (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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402B TYR* 3.0 41.1 - - + +
403B LYS* 2.7 12.7 + - - +
405B GLY* 1.3 68.7 - - - +
407B GLU* 1.3 66.1 + - - +
409B LEU* 3.1 3.8 + - - +
410B ARG* 2.9 51.8 + - - +
416B ILE* 3.4 33.4 - - + +
417B GLY 5.6 0.4 - - - -
418B ASP* 4.2 18.8 - - - +
420B GLU 4.8 4.7 - - - +
422B LEU* 4.1 21.1 - - + -
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Residues in contact with GLU 407 (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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403B LYS* 2.6 47.6 + - + +
404B GLU* 3.5 12.0 - - - +
406B ILE* 1.3 73.7 - - - +
408B MET* 1.3 59.3 + - + +
410B ARG* 3.8 8.5 - - - +
411B ALA* 2.9 35.4 + - + +
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Residues in contact with MET 408 (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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400B LEU* 4.4 13.9 - - + -
404B GLU* 2.8 23.9 + - + +
405B GLY 3.5 3.6 - - - +
407B GLU* 1.3 79.2 - - + +
409B LEU* 1.3 64.7 + - - +
411B ALA* 3.2 15.1 + - - +
412B ALA* 3.3 14.0 + - - +
430B LEU* 4.1 22.2 - - + -
433B LEU* 3.9 25.6 - - + +
434B VAL* 5.5 3.1 - - - -
437B LYS* 3.2 48.0 - - + +
438B TYR* 3.8 14.6 - - + +
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Residues in contact with LEU 409 (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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405B GLY 3.1 12.0 + - - +
406B ILE* 3.1 4.5 + - + +
408B MET* 1.3 77.5 - - - +
410B ARG* 1.3 61.6 + - - +
412B ALA* 3.0 8.2 + - - +
414B LYS* 2.9 31.8 + - + +
416B ILE* 3.4 23.8 - - + -
422B LEU* 4.1 13.2 - - + -
426B ASN* 3.0 42.0 - - + +
429B PHE* 3.5 31.6 - - + -
430B LEU* 3.9 27.1 - - + +
433B LEU* 4.6 2.9 - - + -
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Residues in contact with ARG 410 (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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406B ILE* 2.9 23.2 + - - +
407B GLU* 3.9 6.7 - - - +
409B LEU* 1.3 71.7 - - - +
411B ALA* 1.3 54.3 - - - +
412B ALA 2.5 17.4 + - - -
413B GLY* 2.7 15.4 + - - -
414B LYS 3.1 17.3 - - - +
415B GLU* 5.1 0.7 - - - -
416B ILE* 2.7 48.9 + - - +
417B GLY* 3.7 2.2 - - - -
418B ASP* 3.2 43.4 + - - +
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Residues in contact with ALA 411 (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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407B GLU* 2.9 24.1 + - + +
408B MET* 3.2 7.6 + - - +
410B ARG* 1.3 73.5 - - - +
412B ALA* 1.3 57.7 + - - +
413B GLY 3.7 0.7 - - - -
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Residues in contact with ALA 412 (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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408B MET 3.5 9.9 - - - +
409B LEU 3.3 8.7 - - - +
410B ARG 2.5 6.1 + - - -
411B ALA* 1.3 76.6 - - - +
413B GLY* 1.3 57.7 + - - +
414B LYS* 3.0 17.7 + - - +
429B PHE* 4.1 23.2 - - + -
433B LEU* 4.2 12.6 - - + -
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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