Contacts of the helix formed by residues 407 - 414 (chain B) in PDB entry 3OY3
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 ALA 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405B TRP 3.7 0.8 + - - -
406B THR* 1.3 77.0 - - - +
408B PRO* 1.3 71.9 - - + +
409B GLU* 3.3 16.4 - - - +
410B SER* 2.9 19.6 + - - +
411B LEU* 3.0 10.9 + - - +
420B SER* 3.7 29.1 + - - -
423B TRP* 3.6 27.0 - - + -
483B ARG* 4.0 0.9 - - - +
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Residues in contact with PRO 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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406B THR 3.8 0.6 - - - +
407B ALA* 1.3 87.9 - - + +
409B GLU* 1.3 57.5 + - - +
411B LEU* 3.4 4.6 + - + -
412B ALA* 3.0 25.6 + - - +
413B TYR* 5.7 0.4 - - - -
423B TRP* 3.5 35.0 - - + -
449B TYR* 3.3 22.0 - - + -
452B LEU* 4.4 5.6 - - + -
478B TRP* 3.4 55.4 - - + +
483B ARG* 3.8 7.0 - - - +
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Residues in contact with GLU 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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407B ALA* 3.7 12.0 - - - +
408B PRO* 1.3 77.9 - - - +
410B SER* 1.3 58.6 + - - +
413B TYR* 3.0 43.6 + - + +
415B LYS* 3.4 31.7 + - + +
417B SER* 4.7 2.8 + - - -
420B SER* 3.8 10.9 + - - -
478B TRP 4.2 2.1 - - - +
480B PRO* 3.8 24.8 - - + +
483B ARG* 2.7 46.4 + - - -
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Residues in contact with SER 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B PHE* 3.9 10.3 - - - -
406B THR* 3.4 19.5 - - - -
407B ALA* 2.9 11.3 + - - +
409B GLU* 1.3 77.3 - - - +
411B LEU* 1.3 61.0 + - - +
414B ASN* 3.0 23.9 + - - -
415B LYS 2.6 25.8 + - - +
416B PHE* 3.5 17.9 - - - -
420B SER* 3.4 23.4 - - - -
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Residues in contact with LEU 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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396B HIS* 2.9 40.0 + - + +
397B ALA* 5.3 0.9 - - - +
401B PHE* 4.5 1.8 - - + -
403B ILE* 3.7 44.0 - - + +
406B THR* 3.6 40.1 - - + +
407B ALA 3.0 7.9 + - - +
408B PRO* 3.7 9.2 - - + +
410B SER* 1.3 78.6 - - - +
412B ALA* 1.3 59.7 + - - +
414B ASN 4.7 0.3 + - - -
448B VAL* 5.2 0.9 - - + -
449B TYR* 4.0 33.9 - - + +
452B LEU* 4.8 6.3 - - + -
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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 PRO 3.0 16.4 + - - +
411B LEU* 1.3 78.4 - - - +
413B TYR* 1.3 85.9 + - + +
414B ASN 3.8 0.4 - - - -
449B TYR* 3.7 26.2 - - + +
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Residues in contact with TYR 413 (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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409B GLU* 3.0 30.7 + - + +
412B ALA* 1.3 101.8 - - + +
414B ASN* 1.3 74.1 + - - +
415B LYS* 3.2 21.2 + - + +
449B TYR* 4.4 9.6 + - - -
478B TRP* 6.5 0.7 - + - -
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Residues in contact with ASN 414 (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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362B ARG* 5.4 3.8 + - - -
397B ALA* 4.2 15.2 + - + +
401B PHE* 3.4 30.5 - - - -
410B SER 3.0 14.8 + - - -
411B LEU 4.6 0.8 + - - -
412B ALA 3.8 0.4 - - - -
413B TYR* 1.3 81.3 - - - +
415B LYS* 1.3 60.6 + - - +
416B PHE* 3.8 17.6 + - - -
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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