Contacts of the helix formed by residues 361 - 368 (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 LEU 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A LEU* 3.9 28.5 - - + -
330A VAL* 4.4 23.1 - - + -
333A GLN* 4.2 19.3 - - + -
334A LEU* 4.5 10.8 - - + -
337A PHE* 4.0 17.7 - - + -
348A LEU* 4.2 14.6 - - + -
351A ASN* 3.2 22.9 - - - +
359A SER* 3.3 1.4 + - - -
360A ASP* 1.3 82.7 - - - +
362A ASN* 1.3 62.3 + - - +
363A PRO 3.3 2.0 - - - -
364A VAL* 2.9 9.6 + - + +
365A PHE* 2.8 43.6 + - + -
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Residues in contact with ASN 362 (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* 3.4 14.9 + - - -
352A ILE* 3.3 31.6 + - - +
355A ALA* 4.1 6.7 - - - +
356A SER 4.6 0.2 - - - +
359A SER* 3.1 24.4 + - - +
361A LEU* 1.3 76.4 - - - +
363A PRO* 1.3 62.4 - - + +
365A PHE* 4.1 4.9 - - - -
366A MET* 2.8 32.4 + - - +
385A MET* 3.6 15.3 - - - +
390A PHE* 3.6 22.4 - - + -
463A THR* 3.6 17.9 + - - +
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Residues in contact with PRO 363 (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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359A SER 2.9 26.5 - - - +
360A ASP 3.8 5.4 - - - +
361A LEU 3.4 3.8 - - - -
362A ASN* 1.3 94.5 - - + +
364A VAL* 1.3 57.1 + - - +
367A ALA* 3.1 28.9 + - - +
435A THR* 4.3 4.3 - - + -
436A CYS* 4.1 7.0 - - - +
437A GLY* 3.7 9.6 - - - +
455A CYS* 3.4 27.9 - - + +
457A GLY* 4.0 16.6 - - - +
463A THR* 3.6 24.5 - - + +
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 4.8 4.7 - - + -
329A GLY 4.6 0.2 - - - +
330A VAL* 3.7 31.2 - - + +
333A GLN* 3.9 18.6 - - + -
360A ASP 3.7 17.5 - - - +
361A LEU* 2.9 11.1 + - + +
363A PRO* 1.3 75.2 - - - +
365A PHE* 1.3 65.3 + - + +
366A MET 3.2 0.2 - - - -
367A ALA 3.5 0.3 + - - -
368A SER* 2.8 27.5 + - - -
418A PHE* 3.7 20.5 - - + -
420A ALA* 3.9 15.9 - - + -
436A CYS 4.1 9.2 - - - +
437A GLY* 4.1 7.2 - - - -
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Residues in contact with PHE 365 (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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330A VAL* 4.2 16.2 - - + -
348A LEU* 3.5 33.0 - - + -
352A ILE* 3.8 31.2 - - + -
361A LEU* 2.8 48.1 + - + +
362A ASN* 4.1 3.1 - - - -
364A VAL* 1.3 79.8 - - + +
366A MET* 1.3 58.0 + - - +
368A SER* 3.3 0.6 + - - -
369A GLY* 3.1 6.4 + - - -
370A THR* 2.8 55.0 + - + -
385A MET* 3.6 19.9 - - + +
407A ILE* 5.1 1.6 - - + -
409A ILE* 4.1 25.6 - - + -
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Residues in contact with MET 366 (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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362A ASN 2.8 18.6 + - - +
363A PRO* 3.9 3.6 - - + +
365A PHE* 1.3 73.0 - - - +
367A ALA* 1.3 65.5 + - - +
368A SER 3.0 1.8 - - - -
369A GLY* 3.0 11.6 + - - -
385A MET* 3.5 17.0 - - - +
386A ASP* 3.5 33.7 - - - +
387A HIS* 3.7 19.3 - - - +
390A PHE* 3.6 27.1 - - + -
453A ALA* 5.3 1.0 - - - +
455A CYS* 3.6 26.4 - - + -
463A THR* 3.7 22.2 - - + +
464A ILE 4.3 5.4 - - - -
465A SER* 4.0 10.5 - - - -
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Residues in contact with ALA 367 (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 PRO 3.1 12.4 + - - +
364A VAL 4.0 0.9 - - - +
365A PHE 3.5 0.2 - - - -
366A MET* 1.3 78.7 - - - +
368A SER* 1.3 58.3 + - - +
369A GLY 3.4 0.8 + - - -
418A PHE* 3.8 11.2 - - + -
437A GLY 3.3 33.2 - - - +
438A MET* 4.1 0.7 - - - +
439A ARG* 3.1 25.9 + - - +
453A ALA* 3.8 20.1 - - - +
455A CYS* 3.6 14.1 - - - -
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Residues in contact with SER 368 (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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326A VAL* 3.7 33.3 - - - +
364A VAL* 2.8 21.0 + - - +
365A PHE* 3.3 1.0 + - - -
366A MET 3.0 0.2 - - - -
367A ALA* 1.3 75.9 - - - +
369A GLY* 1.3 65.5 + - - +
370A THR* 3.0 20.5 + - - -
410A PRO* 3.4 16.0 - - - +
418A PHE* 4.0 8.3 - - - -
439A ARG* 4.0 13.0 + - - +
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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