Contacts of the helix formed by residues 362 - 370 (chain A) in PDB entry 1FR8
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 ARG 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A TYR* 3.4 45.4 + - - +
314A TRP* 4.8 15.6 + - - +
315A GLY 3.3 18.4 + - - -
320A ASP* 6.4 0.2 - - - -
323A ASN* 4.0 6.2 - - - +
360A PHE* 3.4 31.6 + - + +
361A ASP* 1.3 77.4 - - - +
363A ILE* 1.3 60.8 + - - +
364A ALA 3.4 3.6 - - - +
365A HIS* 3.3 27.9 + - + -
366A THR* 2.9 31.4 + - - +
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Residues in contact with ILE 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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323A ASN* 3.8 18.2 - - - +
327A PHE* 3.7 16.3 - - + -
359A ARG* 4.2 7.4 - - - +
361A ASP* 3.4 24.7 + - - +
362A ARG* 1.3 73.1 - - - +
364A ALA* 1.3 66.2 + - - +
366A THR* 3.4 0.3 + - - -
367A LYS* 3.2 23.0 + - - +
314B TRP* 3.4 72.0 - - + +
360B PHE* 5.4 0.7 - - + -
362B ARG* 3.8 17.3 - - - +
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ARG* 4.5 0.6 - - - +
363A ILE* 1.3 78.8 - - - +
365A HIS* 1.3 58.8 + - - +
367A LYS* 3.4 14.9 + - - +
368A GLU* 2.9 32.0 + - - +
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Residues in contact with HIS 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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310A ASN* 6.1 5.2 - - + -
311A TYR* 4.0 23.5 + + - -
320A ASP* 4.5 1.4 + - - -
362A ARG* 3.3 35.1 + - + +
363A ILE 3.2 0.2 - - - -
364A ALA* 1.3 81.3 - - - +
366A THR* 1.3 52.1 + - - +
368A GLU* 3.3 5.2 + - + +
369A THR* 2.6 68.3 + - + +
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Residues in contact with THR 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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311A TYR* 4.5 0.3 + - - -
320A ASP* 2.8 29.4 + - - +
323A ASN* 3.3 30.8 + - + -
324A ARG* 3.5 33.2 - - + +
327A PHE* 4.2 0.7 - - + -
362A ARG* 2.9 21.2 + - - +
363A ILE 4.0 2.0 - - - -
364A ALA 3.3 0.4 - - - -
365A HIS* 1.3 69.7 - - - +
367A LYS* 1.3 64.3 + - - +
369A THR* 3.1 5.1 + - - -
370A MET* 2.7 43.5 + - + +
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Residues in contact with LYS 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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327A PHE* 3.3 39.3 - - + -
363A ILE* 3.2 13.3 + - - +
364A ALA* 3.7 13.2 + - - +
366A THR* 1.3 78.2 - - - +
368A GLU* 1.3 63.4 + - - +
370A MET* 3.7 12.6 + - + +
371A LEU* 5.3 5.4 + - - +
402B SER 4.0 19.7 - - - +
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Residues in contact with GLU 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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364A ALA 2.9 19.5 + - - +
365A HIS* 3.5 7.9 - - + +
367A LYS* 1.3 80.5 - - - +
369A THR* 1.3 66.1 + - + +
371A LEU* 5.1 2.4 + - - +
372A SER* 4.7 3.1 + - - -
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Residues in contact with THR 369 (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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310A ASN* 6.0 0.2 - - - -
320A ASP* 4.7 2.6 + - - -
324A ARG* 4.8 2.1 + - - -
365A HIS* 2.6 58.3 + - + +
366A THR* 3.8 3.1 + - - -
368A GLU* 1.3 83.4 - - + +
370A MET* 1.3 66.4 + - - +
371A LEU 3.3 2.9 - - - -
372A SER* 2.9 23.4 + - - +
373A ASP* 2.9 23.1 + - - +
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Residues in contact with MET 370 (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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304A ILE* 4.0 9.9 - - - +
305A ASN* 3.2 15.7 - - + +
324A ARG* 3.4 52.5 + - + +
327A PHE* 3.2 42.6 - - + -
328A ARG* 4.3 20.6 - - - +
366A THR* 2.7 30.7 + - + +
367A LYS* 3.7 11.2 - - + +
368A GLU 3.7 0.8 - - - -
369A THR* 1.3 72.6 + - - +
371A LEU* 1.3 66.6 + - + +
372A SER 3.3 0.3 + - - -
373A ASP 3.4 9.4 - - - +
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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