Contacts of the helix formed by residues 400 - 411 (chain B) in PDB entry 5FI4
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 SER 400 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B TYR* 3.6 26.3 - - - +
398B PHE* 3.9 1.7 - - - +
399B SER* 1.3 77.5 - - - +
401B VAL* 1.3 62.9 + - - +
402B VAL* 3.8 9.6 + - - +
403B GLU* 3.2 24.9 + - - +
404B LEU* 3.5 14.4 + - - +
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TRP* 4.1 21.3 - - + -
334B TYR* 5.8 2.7 - - + -
357B VAL* 4.4 15.5 - - + -
368B TYR* 4.1 23.6 - - + -
383B ILE* 4.6 12.3 - - + -
390B TYR* 3.8 33.0 - - + +
400B SER* 1.3 71.8 - - - +
402B VAL* 1.4 57.2 + - + +
404B LEU* 3.2 8.5 + - + +
405B ILE* 2.9 39.3 + - + +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLN 5.9 3.4 - - - +
331B ALA* 4.3 12.6 - - + -
333B TRP* 3.8 26.2 - - + -
400B SER* 4.1 8.1 - - - +
401B VAL* 1.4 77.7 - - + +
403B GLU* 1.4 55.4 + - - +
406B ASN* 2.9 56.8 + - - +
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B THR 4.9 1.0 - - - +
398B PHE* 3.7 18.2 - - + -
399B SER* 3.1 40.4 + - - -
400B SER* 3.2 25.3 + - - +
401B VAL 3.3 0.2 - - - -
402B VAL* 1.4 76.3 - - - +
404B LEU* 1.4 54.7 + - - +
406B ASN* 4.0 3.2 - - - +
407B HIS* 3.1 31.8 + - + +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ILE* 3.7 33.4 - - + -
390B TYR* 4.3 2.2 - - + -
391B GLY* 3.8 23.8 - - - +
392B PHE* 3.8 27.8 - - + -
398B PHE* 3.6 37.4 - - + -
400B SER 3.5 10.3 + - - +
401B VAL* 3.2 10.0 + - - +
403B GLU* 1.4 76.2 - - - +
405B ILE* 1.3 66.1 + - + +
407B HIS* 3.8 0.9 - - - +
408B TYR* 3.3 46.1 + - + +
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TRP* 3.6 48.7 - - + +
355B PHE* 3.6 22.4 - - + -
357B VAL* 3.7 20.0 - - + -
370B LEU* 3.9 23.1 - - + -
383B ILE* 4.6 10.1 - - + -
392B PHE* 5.5 1.3 - - + -
401B VAL* 2.9 22.2 + - + +
404B LEU* 1.3 79.3 - - + +
406B ASN* 1.4 55.4 + - - +
408B TYR* 3.0 7.8 + - - -
409B ARG* 2.8 33.2 + - - +
424B LEU* 3.6 12.4 - - + +
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Residues in contact with ASN 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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333B TRP* 4.2 17.2 + - - -
402B VAL* 2.9 42.9 + - - +
403B GLU* 4.4 3.4 - - - +
405B ILE* 1.4 70.7 - - - +
407B HIS* 1.4 59.8 + - - +
409B ARG* 3.4 25.7 + - - +
410B ASN* 3.2 24.2 + - - +
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Residues in contact with HIS 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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398B PHE* 3.2 34.8 - + + -
403B GLU 3.1 21.0 + - - +
404B LEU 3.8 2.5 - - - +
405B ILE 3.2 0.2 - - - -
406B ASN* 1.4 77.8 - - - +
408B TYR* 1.3 75.1 + + - +
409B ARG 3.3 0.2 - - - -
410B ASN* 3.6 2.4 + - - +
411B GLU* 3.1 31.3 + - + +
415B GLN* 2.9 35.6 + - - -
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Residues in contact with TYR 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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392B PHE* 3.8 16.2 - + - -
398B PHE* 4.5 4.9 - + - -
404B LEU* 3.3 40.1 + - + +
405B ILE 3.0 7.8 + - - +
407B HIS* 1.3 87.1 - + - +
409B ARG* 1.3 60.6 + - - +
410B ASN 3.3 1.3 - - - -
411B GLU 2.9 27.7 - - - +
412B SER 3.8 5.6 - - - -
413B LEU* 3.6 26.4 - - + +
415B GLN* 3.2 43.8 + - + +
416B TYR* 3.7 22.1 + - + +
423B LYS* 3.8 1.0 - - - -
424B LEU* 3.0 35.7 + - + -
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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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332B GLU* 3.5 25.5 + - - +
333B TRP* 3.8 22.6 - - - +
355B PHE* 4.2 10.8 - - - -
405B ILE* 2.8 16.2 + - - +
406B ASN* 3.5 24.7 + - - +
407B HIS 3.3 0.6 - - - -
408B TYR* 1.3 77.9 - - - +
410B ASN* 1.4 64.7 + - - +
423B LYS* 4.5 7.7 - - - +
424B LEU* 3.3 31.0 + - + +
425B LEU* 5.1 4.8 + - - +
427B PRO* 3.5 21.9 - - - +
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Residues in contact with ASN 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ASN* 3.2 21.3 + - - +
407B HIS 4.4 1.8 - - - +
409B ARG* 1.4 87.4 + - - +
411B GLU* 1.4 57.8 + - + +
412B SER 4.5 0.3 + - - -
423B LYS* 5.2 4.1 - - - +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B HIS* 3.1 33.1 + - + +
408B TYR* 2.9 31.5 - - - +
410B ASN* 1.4 77.8 - - - +
412B SER* 1.4 66.6 + - - +
415B GLN* 4.2 12.3 - - - +
423B LYS* 4.5 2.2 - - - -
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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