Contacts of the helix formed by residues 355 - 367 (chain A) in PDB entry 6FY5
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 ASP 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A LYS* 4.4 6.8 - - - +
354A PHE* 1.3 88.8 - - + +
356A SER* 1.3 66.9 + - - +
357A GLU* 3.3 12.9 + - - +
358A SER* 3.0 39.1 + - - +
359A ILE* 2.9 25.6 + - - +
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Residues in contact with SER 356 (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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354A PHE 3.6 4.3 + - - -
355A ASP* 1.3 75.5 + - - +
357A GLU* 1.4 61.6 + - - +
359A ILE* 3.3 10.4 + - - +
360A GLY* 3.0 20.3 + - - -
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Residues in contact with GLU 357 (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 LYS* 4.6 12.3 - - + +
355A ASP* 3.3 11.7 + - - +
356A SER* 1.4 77.2 - - - +
358A SER* 1.3 63.9 + - - +
360A GLY* 3.2 2.8 + - - +
361A ILE* 3.0 42.8 + - + +
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS* 3.2 33.4 + - - +
353A LEU* 4.0 22.2 - - - -
355A ASP* 3.0 31.3 + - - +
357A GLU* 1.3 73.5 - - - +
359A ILE* 1.4 61.5 + - - +
361A ILE* 3.2 7.0 + - - +
362A TYR* 3.0 27.2 + - - +
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Residues in contact with ILE 359 (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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186A LEU* 3.7 28.7 - - + -
199A LEU* 4.2 3.0 - - + +
201A GLN* 3.4 25.6 - - - +
353A LEU* 3.8 25.8 - - + -
354A PHE* 4.0 11.4 - - - +
355A ASP 2.9 25.1 + - - +
356A SER* 3.5 11.9 - - - +
358A SER* 1.4 75.2 - - - +
360A GLY* 1.3 58.3 + - - +
362A TYR* 3.2 4.3 + - - +
363A VAL* 2.9 42.8 + - + +
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Residues in contact with GLY 360 (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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356A SER 3.0 14.8 + - - -
357A GLU* 3.2 3.8 + - - -
359A ILE* 1.3 76.2 - - - +
361A ILE* 1.4 56.7 + - - +
363A VAL* 3.3 9.2 + - - +
364A GLN* 2.9 39.7 + - - +
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Residues in contact with ILE 361 (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 LYS* 3.5 34.5 - - + +
324A GLN* 3.8 32.3 - - + +
327A ALA* 3.8 15.5 - - + -
357A GLU* 3.0 40.6 + - + +
358A SER* 3.2 8.0 + - - +
360A GLY* 1.4 72.6 - - - +
362A TYR* 1.3 61.0 + - + +
364A GLN* 3.3 16.5 + - - +
365A GLU* 2.9 31.2 + - + +
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Residues in contact with TYR 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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199A LEU* 3.5 34.5 - - + -
323A LYS 5.6 0.2 - - - -
326A ALA 4.5 0.7 + - - -
327A ALA* 3.7 24.3 + - + -
330A THR* 3.8 23.0 + - - +
331A LEU* 4.2 25.8 - - + -
351A PHE* 3.8 24.4 - + - -
353A LEU* 4.1 13.7 - - + -
358A SER* 3.0 17.5 + - - +
359A ILE 3.7 4.3 - - - +
361A ILE* 1.3 73.3 - - + +
363A VAL* 1.4 56.9 + - - +
365A GLU* 4.0 3.7 - - - +
366A MET* 2.8 39.0 + - - +
1001A EDO 3.4 40.9 - - - -
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Residues in contact with VAL 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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186A LEU* 6.2 0.7 - - + -
187A SER* 4.7 14.8 - - - +
189A LYS* 6.1 0.2 - - - -
199A LEU* 3.6 17.7 - - + -
359A ILE* 2.9 28.6 + - + +
360A GLY* 3.3 11.9 + - - +
362A TYR* 1.4 75.4 - - - +
364A GLN* 1.3 64.7 + - + +
366A MET* 3.9 4.1 - - - +
367A ALA* 3.2 23.0 + - + +
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Residues in contact with GLN 364 (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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360A GLY 2.9 22.7 + - - +
361A ILE* 3.3 20.3 + - - +
363A VAL* 1.3 76.8 - - + +
365A GLU* 1.3 69.2 + - - +
367A ALA* 3.4 19.5 - - - +
368A LYS* 3.6 18.7 - - - +
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Residues in contact with GLU 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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324A GLN* 3.6 25.6 + - - +
327A ALA* 4.0 20.9 - - + -
328A GLN* 3.6 33.3 - - - +
331A LEU* 3.7 19.3 - - + -
361A ILE* 2.9 22.0 + - + +
362A TYR 4.0 1.3 - - - +
364A GLN* 1.3 78.6 - - - +
366A MET* 1.4 64.0 + - - +
368A LYS* 3.1 51.5 + - - +
369A LEU* 3.7 10.4 - - - +
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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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187A SER* 4.3 6.5 - - - +
188A SER* 4.2 2.7 - - - -
189A LYS* 3.6 40.3 - - + +
197A LEU* 3.5 35.2 - - + +
199A LEU* 3.2 48.9 - - + -
331A LEU* 3.8 24.0 - - + -
351A PHE* 5.0 1.3 - - + -
362A TYR* 2.8 16.9 + - - +
363A VAL* 3.9 4.0 - - - +
365A GLU* 1.4 70.1 - - - +
367A ALA* 1.3 65.2 + - - +
369A LEU* 3.1 28.7 + - + +
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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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189A LYS* 4.5 12.9 - - - +
363A VAL* 3.2 13.1 + - + +
364A GLN* 3.4 15.7 - - - +
365A GLU 3.2 0.6 - - - -
366A MET* 1.3 75.9 - - - +
368A LYS* 1.3 60.6 + - + +
369A LEU 3.6 5.5 + - - +
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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