Contacts of the helix formed by residues 347 - 355 (chain A) in PDB entry 1FO4
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 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A VAL* 3.6 20.1 - - - +
301A ALA 3.5 10.1 + - - -
302A ALA 3.4 22.2 - - - -
303A CYS 3.3 5.4 - - - -
305A LEU* 4.1 4.5 - - - +
345A VAL 3.5 0.6 + - - -
346A ALA* 1.3 74.8 - - - +
348A LEU* 1.3 64.5 + - - +
349A GLY* 4.3 0.2 - - - -
350A GLY* 3.1 15.1 + - - -
351A ASN* 3.2 17.5 + - - +
3006A FAD 2.8 33.6 + - - -
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Residues in contact with LEU 348 (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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299A PHE* 3.8 27.8 - - + -
300A GLY 4.6 3.4 - - - +
301A ALA 3.6 4.0 + - - +
303A CYS* 3.2 9.9 + - + +
305A LEU* 4.1 15.3 - - + +
308A VAL* 3.8 33.9 - - + -
347A SER* 1.3 71.2 - - - +
349A GLY* 1.3 68.6 + - - +
351A ASN* 3.2 4.6 + - - +
352A ILE* 3.1 29.6 + - + +
361A LEU* 4.2 5.4 - - + -
365A PHE* 3.5 36.6 - - + -
407A ILE* 4.4 25.8 - - + -
409A ILE* 5.1 3.1 - - + -
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Residues in contact with GLY 349 (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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301A ALA* 2.7 30.4 + - - +
347A SER* 4.3 0.2 - - - -
348A LEU* 1.3 73.2 - - - +
350A GLY* 1.3 54.9 + - - +
352A ILE 3.4 0.3 + - - -
353A ILE* 2.9 36.2 + - - +
404A LEU* 3.9 21.8 - - - -
3006A FAD 3.9 11.9 - - - -
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Residues in contact with GLY 350 (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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347A SER* 3.1 11.4 + - - -
348A LEU 3.2 0.4 - - - -
349A GLY* 1.3 76.8 - - - +
351A ASN* 1.3 53.3 + - - +
354A THR* 2.6 37.9 + - - -
3006A FAD 3.4 49.8 + - - +
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Residues in contact with ASN 351 (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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305A LEU* 5.3 0.9 - - + -
337A PHE* 3.6 3.0 - - - -
347A SER 3.2 7.0 + - - +
348A LEU 3.2 8.0 + - - +
350A GLY* 1.3 76.9 - - - +
352A ILE* 1.3 66.4 + - + +
354A THR* 3.6 2.9 + - - -
355A ALA 3.6 8.7 + - - -
356A SER* 4.8 0.3 + - - -
359A SER* 2.8 28.5 + - - -
361A LEU* 3.2 38.7 - - + +
362A ASN* 3.4 12.6 + - - +
3006A FAD 2.9 58.5 + - - +
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Residues in contact with ILE 352 (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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348A LEU* 3.1 18.5 + - + +
349A GLY 3.9 2.2 - - - +
351A ASN* 1.3 77.5 - - + +
353A ILE* 1.3 63.7 + - + +
355A ALA* 3.2 9.2 + - - -
362A ASN* 3.3 15.7 + - - +
365A PHE* 3.8 29.4 - - + -
372A LEU* 4.2 7.4 - - + -
385A MET* 3.6 21.5 - - + -
389A PHE* 4.0 17.0 - - + -
390A PHE* 3.6 16.9 - - + -
396A THR* 4.1 0.5 - - - +
404A LEU* 3.9 16.8 - - + -
407A ILE* 3.6 32.1 - - + -
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Residues in contact with ILE 353 (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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349A GLY 2.9 18.1 + - - +
352A ILE* 1.3 79.5 - - + +
354A THR* 1.3 65.8 + - - +
355A ALA* 2.9 8.3 + - - +
389A PHE* 4.5 6.5 - - + -
394A ARG 4.5 5.7 - - - +
396A THR* 4.1 17.7 - - + +
398A LEU* 3.5 31.9 - - + -
404A LEU* 4.2 18.6 - - + -
3006A FAD 3.5 48.4 + - + +
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Residues in contact with THR 354 (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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263A GLU* 3.2 37.7 - - + +
267A GLU* 5.2 0.9 - - - +
350A GLY 2.6 27.3 + - - -
351A ASN 3.8 5.6 - - - -
352A ILE 3.3 0.2 - - - -
353A ILE* 1.3 76.8 - - - +
355A ALA* 1.3 67.9 + - - +
356A SER* 4.0 13.2 - - - +
394A ARG* 3.4 39.7 - - - +
3006A FAD 3.6 20.6 + - - +
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Residues in contact with ALA 355 (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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351A ASN 3.6 2.2 + - - -
352A ILE 3.2 9.8 + - - +
353A ILE 2.9 9.4 - - - +
354A THR* 1.3 81.6 - - - +
356A SER* 1.3 64.6 + - - +
357A PRO* 3.7 3.1 - - - +
362A ASN* 4.1 4.5 - - - +
390A PHE* 3.7 33.7 - - + -
394A ARG* 3.7 29.8 + - - +
395A LYS 4.2 0.9 - - - +
396A THR* 3.9 7.6 - - + -
461A ASP 5.2 1.2 - - - +
462A ARG* 5.4 3.3 - - - +
463A THR* 5.8 1.1 - - - -
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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