Contacts of the helix formed by residues 401 - 411 (chain A) in PDB entry 1Y0P
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 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLY* 4.5 11.2 - - - +
237A GLY 5.1 1.6 - - - -
238A GLY* 4.1 20.4 - - - +
400A THR* 1.3 87.0 + - - +
402A ARG* 1.3 62.8 + - - +
403A ASP* 2.7 20.9 + - - -
404A LYS* 3.3 16.8 + - - +
405A ALA* 3.0 23.8 + - - +
543A ASN* 3.7 20.0 - - - +
545A LEU* 4.2 10.3 - - + -
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Residues in contact with ARG 402 (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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363A GLN* 2.9 36.5 + - + +
364A ALA 3.9 13.5 - - - +
365A HIS* 3.6 10.2 + - - +
366A PRO* 3.8 18.8 - - + +
378A GLU* 2.9 35.4 + - - +
400A THR 5.3 0.2 - - - +
401A THR* 1.3 74.4 - - - +
403A ASP* 1.3 60.9 + - - +
405A ALA* 4.1 0.6 - - - +
406A SER* 2.9 36.2 + - - -
504A HIS* 3.7 6.3 - - - -
543A ASN* 3.6 11.0 + - - +
544A ARG* 3.8 7.1 - - - +
546A GLY* 3.7 13.6 - - - +
1806A MEZ 2.8 68.8 + - - +
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Residues in contact with ASP 403 (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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199A GLY 4.8 1.2 - - - +
201A GLN* 3.2 27.0 + - - +
364A ALA 5.7 0.2 - - - -
401A THR* 2.7 28.5 + - - -
402A ARG* 1.3 79.6 - - - +
404A LYS* 1.3 76.4 + - + +
406A SER* 3.8 3.6 - - - -
407A ALA* 3.1 23.6 + - - +
542A ALA 4.9 1.1 - - - +
543A ASN* 3.4 26.5 + - + +
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Residues in contact with LYS 404 (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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201A GLN* 5.9 1.8 - - - +
396A VAL* 4.7 1.7 - - + +
400A THR* 3.9 23.6 - - + +
401A THR* 3.3 15.6 + - - +
403A ASP* 1.3 93.7 + - + +
405A ALA* 1.3 64.9 + - - +
407A ALA* 3.4 6.1 + - - +
408A ALA* 3.0 25.0 + - - +
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Residues in contact with ALA 405 (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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366A PRO* 3.8 25.6 - - + -
381A ARG* 4.5 11.7 - - - +
387A LEU* 5.6 2.7 - - + -
396A VAL* 4.6 8.0 - - + +
397A ASN 5.3 2.0 - - - +
398A GLU 5.4 0.9 - - - +
400A THR* 3.8 13.1 - - + +
401A THR 3.0 17.0 + - - +
402A ARG* 4.4 0.2 - - - -
404A LYS* 1.3 76.8 - - - +
406A SER* 1.3 61.9 + - - +
408A ALA* 3.3 6.9 + - - +
409A ILE* 3.0 30.1 + - + +
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ALA* 3.3 25.2 + - - -
365A HIS 3.9 0.9 - - - -
366A PRO* 3.4 15.8 - - - +
402A ARG 2.9 22.7 + - - -
403A ASP* 3.8 4.5 - - - -
405A ALA* 1.3 76.1 - - - +
407A ALA* 1.3 63.3 + - - +
409A ILE* 3.3 1.5 + - - -
410A LEU* 3.0 33.5 + - - +
501A PRO* 3.7 23.2 - - - +
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Residues in contact with ALA 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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403A ASP 3.1 17.5 + - - +
404A LYS* 3.6 7.4 - - - +
406A SER* 1.3 75.3 - - - +
408A ALA* 1.3 63.9 + - - +
410A LEU* 3.4 10.0 + - - +
411A ALA* 3.1 23.3 + - - +
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Residues in contact with ALA 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* 3.8 11.7 - - + +
396A VAL* 3.6 33.9 - - + -
404A LYS 3.0 16.8 + - - +
405A ALA 3.6 3.8 - - - +
406A SER 3.2 0.2 - - - -
407A ALA* 1.3 76.4 - - - +
409A ILE* 1.3 63.8 + - - +
411A ALA* 3.2 10.8 + - - +
412A GLN* 3.0 25.1 + - - +
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Residues in contact with ILE 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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366A PRO* 3.3 33.2 - - + +
367A THR* 4.2 6.5 - - + -
387A LEU* 4.1 22.7 - - + -
395A PHE* 3.9 23.6 - - + -
396A VAL* 5.5 0.2 - - + -
405A ALA* 3.0 17.2 + - + +
406A SER 3.8 3.6 - - - +
408A ALA* 1.3 77.0 - - - +
410A LEU* 1.3 63.0 + - - +
412A GLN* 3.1 19.5 + - - +
415A LYS 3.7 7.7 - - - +
416A SER* 3.8 12.3 + - - -
417A ALA* 3.9 6.7 - - + +
499A VAL* 3.8 22.9 - - + +
501A PRO* 4.0 15.7 - - + -
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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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333A PHE* 4.0 31.9 - - + -
406A SER* 3.0 26.2 + - - +
407A ALA* 3.8 7.4 - - - +
408A ALA 3.3 0.2 - - - -
409A ILE* 1.3 76.0 - - - +
411A ALA* 1.3 59.5 + - - +
412A GLN 3.5 1.2 + - - +
415A LYS* 3.5 53.6 - - + +
500A THR* 4.4 2.0 - - - +
501A PRO* 3.8 27.4 - - + -
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Residues in contact with ALA 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 ALA 3.1 12.9 + - - +
408A ALA* 3.5 12.6 - - - +
409A ILE 3.1 0.4 - - - -
410A LEU* 1.3 75.8 - - - +
412A GLN* 1.3 69.9 + - - +
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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