Contacts of the helix formed by residues 400 - 411 (chain B) in PDB entry 1OH7
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 PHE 400 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372B PHE* 4.4 11.2 - + + -
375B LEU* 4.0 8.3 - - + -
396B LYS 5.6 0.7 - - - -
397B MET 3.7 21.5 - - - -
398B GLY* 4.0 8.3 - - - -
399B GLU* 1.3 83.6 - - - +
401B ALA* 1.3 64.2 + - - +
402B GLU 3.2 2.9 + - - -
403B LEU* 3.3 25.7 + - + +
404B ARG* 3.0 20.1 + - - +
538B HIS* 4.7 8.1 - + + -
541B ALA* 3.5 45.8 - - + -
542B LEU* 3.9 26.0 - - + -
545B SER* 3.8 10.3 - - - -
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Residues in contact with ALA 401 (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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399B GLU* 3.3 14.2 - - + +
400B PHE* 1.3 76.1 - - - +
402B GLU* 1.3 70.7 + - + +
404B ARG* 3.3 40.7 + - - +
405B ASP* 2.9 27.2 + - - +
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Residues in contact with GLU 402 (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 PHE 3.2 0.8 - - - -
401B ALA* 1.3 87.8 - - + +
403B LEU* 1.3 64.5 + - + +
405B ASP* 3.9 19.5 - - - +
406B LEU* 3.1 23.9 + - - +
409B ARG* 5.6 0.5 + - - -
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Residues in contact with LEU 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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372B PHE* 3.9 14.4 - - + -
400B PHE* 3.3 30.2 + - + +
401B ALA 3.3 0.2 - - - -
402B GLU* 1.3 80.3 - - + +
404B ARG* 1.3 65.1 + - - +
405B ASP 3.2 1.1 - - - -
406B LEU* 3.3 10.6 + - + +
407B LEU* 3.2 29.1 + - - +
534B LEU* 4.1 11.9 - - + +
535B LEU* 4.2 22.7 - - + +
538B HIS* 3.5 43.3 - - + +
542B LEU* 4.5 15.0 - - + -
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Residues in contact with ARG 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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369B ARG* 4.5 4.4 - - + +
372B PHE* 3.8 32.5 + - + -
373B GLN* 4.2 21.3 - - + +
376B PRO* 3.6 28.1 - - - +
399B GLU* 4.2 8.3 + - - +
400B PHE 3.0 13.6 + - - +
401B ALA* 3.3 40.5 + - - +
403B LEU* 1.3 76.4 - - - +
405B ASP* 1.3 59.2 + - - +
407B LEU* 3.5 3.1 + - - +
408B GLU* 3.1 55.6 + - + +
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Residues in contact with ASP 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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401B ALA 2.9 16.6 + - - +
402B GLU* 4.0 22.1 - - - +
403B LEU 3.2 0.2 - - - -
404B ARG* 1.3 76.7 - - + +
406B LEU* 1.3 64.5 + - - +
408B GLU* 3.3 18.8 + - - +
409B ARG* 3.1 56.6 + - - +
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Residues in contact with LEU 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 GLU 3.1 20.3 + - - +
403B LEU* 3.6 11.9 - - + +
404B ARG 3.3 0.4 - - - -
405B ASP* 1.3 78.4 + - - +
407B LEU* 1.3 57.6 + - + +
409B ARG* 3.6 23.8 + - - +
410B ALA* 3.0 27.2 + - - +
429B TYR* 4.0 19.0 - - + +
531B LEU* 3.9 18.2 - - + -
534B LEU* 3.7 37.0 - - + -
535B LEU* 3.8 28.9 - - + -
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Residues in contact with LEU 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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365B LEU* 3.8 40.6 - - + +
368B MET* 4.4 11.4 - - - -
369B ARG* 3.3 45.5 + - + +
372B PHE* 4.3 12.6 - - + -
403B LEU 3.2 17.2 + - - +
404B ARG 4.2 0.7 - - - +
406B LEU* 1.3 73.1 - - + +
408B GLU* 1.3 64.2 + - - +
409B ARG 3.2 1.3 - - - -
410B ALA* 3.7 5.2 - - - -
411B ILE* 3.4 20.2 + - + +
531B LEU* 4.0 23.8 - - + -
535B LEU* 4.2 17.7 - - + -
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Residues in contact with GLU 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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369B ARG* 3.9 9.2 + - - +
373B GLN* 3.4 31.3 + - - +
404B ARG* 3.1 47.9 + - + +
405B ASP* 3.3 23.6 + - - +
407B LEU* 1.3 77.6 - - - +
409B ARG* 1.3 62.4 + - + +
411B ILE 3.6 10.6 - - - +
426B ALA* 4.8 2.4 - - - +
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Residues in contact with ARG 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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402B GLU 5.6 0.4 + - - -
405B ASP* 3.1 39.6 + - - +
406B LEU* 4.0 30.1 - - - +
408B GLU* 1.3 80.5 - - + +
410B ALA* 1.3 58.4 + - - +
411B ILE 3.7 0.2 - - - -
426B ALA* 3.4 10.4 - - - +
427B SER 5.4 0.2 - - - +
428B GLY 5.2 0.2 - - - -
429B TYR* 3.0 45.8 + - + +
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Residues in contact with ALA 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 LEU 3.0 18.9 + - - +
407B LEU* 3.6 2.6 + - - -
408B GLU 3.5 0.4 - - - -
409B ARG* 1.3 78.8 - - - +
411B ILE* 1.3 68.2 + - + +
425B ILE* 3.1 18.7 - - - +
426B ALA 2.9 20.0 + - - -
429B TYR* 3.8 17.9 - - + -
531B LEU* 3.7 29.6 - - + -
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Residues in contact with ILE 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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362B PRO* 4.6 4.7 - - + +
365B LEU* 3.6 44.0 - - + -
366B ALA* 5.0 2.9 - - + -
369B ARG* 3.1 19.3 + - - +
407B LEU* 3.4 18.0 + - + +
408B GLU 3.6 12.1 - - - +
410B ALA* 1.3 92.8 - - + +
412B ILE* 1.3 70.7 + - - +
413B ASP* 5.2 0.3 - - - +
415B PRO* 3.9 21.8 - - + -
424B VAL* 3.3 15.3 - - + +
425B ILE* 4.8 2.5 - - + -
426B ALA* 3.8 7.9 - - - +
528B TYR* 4.5 9.4 - - + -
531B LEU* 3.8 11.0 - - + -
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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