Contacts of the helix formed by residues 364 - 372 (chain A) in PDB entry 6FD3
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 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A GLY 4.5 0.5 - - - +
363A GLY* 1.3 76.3 - - - -
365A LEU* 1.3 65.7 + - - +
366A THR* 3.3 21.0 + - - -
367A ASP* 3.0 31.8 + - - +
368A VAL* 3.6 3.1 + - - +
405A SER 3.9 2.5 - - - -
406A ASP* 3.5 22.0 + - - -
408A ILE 3.2 11.7 - - - -
409A LEU* 4.4 0.9 - - - +
410A LEU* 4.1 8.0 - - - +
603A ADP 3.7 19.7 + - - -
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Residues in contact with LEU 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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364A SER* 1.3 73.5 - - - +
366A THR* 1.3 62.6 + - - +
368A VAL* 3.1 10.7 + - + +
369A VAL* 2.9 36.5 + - + +
374A MET* 4.1 19.7 - - + -
382A VAL* 4.1 27.8 - - + -
405A SER* 3.3 14.1 + - - +
408A ILE* 2.8 24.6 + - + -
410A LEU* 4.1 17.3 - - + +
466A MET* 4.1 32.8 - - + -
470A MET* 4.1 10.8 - - + -
543A LEU* 6.2 0.7 - - + -
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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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364A SER* 3.0 10.6 + - - -
365A LEU* 1.3 78.0 - - - +
367A ASP* 1.3 63.9 + - - +
369A VAL* 3.9 3.8 - - + -
370A THR* 2.8 45.9 + - + +
405A SER* 2.6 27.0 + - - +
406A ASP* 2.8 35.3 + - - +
469A GLU* 5.4 0.9 - - - +
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Residues in contact with ASP 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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362A GLY 4.5 4.4 - - - +
363A GLY* 3.7 8.8 - - - -
364A SER* 3.0 34.4 + - - +
366A THR* 1.3 81.8 - - - +
368A VAL* 1.3 63.0 + - + +
370A THR* 3.4 4.4 + - - -
371A GLU* 3.3 28.9 + - - +
550A ALA* 3.4 9.2 - - + +
551A LYS* 6.0 3.9 - - + +
554A ILE* 3.6 28.7 - - + +
603A ADP 5.5 0.5 + - - -
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLY 5.3 1.6 - - - +
364A SER 3.6 1.7 + - - +
365A LEU* 3.1 13.3 + - + +
367A ASP* 1.3 79.0 - - + +
369A VAL* 1.3 60.0 + - - +
372A THR* 2.8 47.3 + - - +
374A MET* 3.9 30.3 - - + -
410A LEU* 3.7 26.2 - - + -
543A LEU* 5.8 3.8 - - + -
546A LEU* 4.3 9.4 - - + +
547A ILE* 3.9 29.8 - - + +
550A ALA* 4.1 6.1 - - + -
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Residues in contact with VAL 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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365A LEU* 2.9 34.1 + - + +
366A THR* 3.6 12.3 - - - +
368A VAL* 1.3 77.3 - - - +
370A THR* 1.3 70.1 + - + +
372A THR 3.6 12.5 - - - +
374A MET* 4.0 8.3 - - - -
405A SER* 4.4 8.5 - - - +
469A GLU* 3.6 22.4 - - + +
470A MET* 3.8 37.9 - - + +
473A GLY* 3.7 21.0 - - - +
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Residues in contact with THR 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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366A THR* 2.8 38.9 + - + +
367A ASP* 3.4 8.8 + - - -
369A VAL* 1.3 79.2 - - + +
371A GLU* 1.3 74.2 + - - +
473A GLY* 3.9 20.2 - - - +
554A ILE* 5.4 1.0 - - - +
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Residues in contact with GLU 371 (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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367A ASP 3.3 18.4 + - - +
368A VAL 3.3 1.6 + - - -
370A THR* 1.3 92.2 + - - +
372A THR* 1.3 61.2 + - + +
550A ALA* 3.8 30.3 - - + +
553A ALA* 3.4 24.9 - - + +
554A ILE* 3.8 19.8 + - + +
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Residues in contact with THR 372 (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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368A VAL* 2.8 38.2 + - - +
369A VAL* 3.6 13.7 - - - +
371A GLU* 1.3 89.4 - - + +
373A CYS* 1.3 68.4 + - - +
374A MET* 4.0 1.7 + - - +
546A LEU* 3.6 48.2 - - + +
549A ALA* 4.3 9.4 - - + -
550A ALA* 4.2 7.0 - - + +
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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