Contacts of the helix formed by residues 326 - 333 (chain B) in PDB entry 6RUT
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 THR 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B PRO* 5.8 2.2 - - + +
325B LEU* 1.3 75.3 - - - +
327B THR* 1.3 65.6 + - - +
328B ASP* 3.7 6.2 + - - +
329B GLN* 3.1 43.2 + - - +
330B ILE* 3.2 14.0 + - - +
410B ASP* 3.7 40.8 - - + +
446B PRO* 4.3 1.8 - - - -
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B THR* 1.3 72.4 - - - +
328B ASP* 1.4 64.3 + - - +
330B ILE* 3.2 12.7 + - - +
331B ALA* 3.2 13.8 + - - +
363B PRO* 3.7 27.3 - - + +
364B LYS* 4.4 10.3 - - + -
367B VAL* 3.7 22.9 - - + -
410B ASP* 2.6 31.9 + - - -
444B ALA* 3.3 3.6 - - + +
445B LEU 3.1 30.1 + - - +
446B PRO* 4.0 1.6 - - - +
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B THR* 3.3 7.4 + - - +
327B THR* 1.4 77.1 - - - +
329B GLN* 1.4 61.9 + - + +
331B ALA* 3.3 6.1 + - - +
332B ARG* 3.1 48.2 + - - +
364B LYS* 3.4 33.1 + - - +
410B ASP* 4.4 4.2 + - - +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP* 6.3 1.4 - - - +
111B ASN* 5.4 2.7 - - - +
112B LEU* 3.8 35.4 - - + +
324B LEU 4.5 1.2 - - - +
325B LEU* 3.3 25.1 - - + +
326B THR* 3.1 50.2 + - - +
328B ASP* 1.4 76.3 - - + +
330B ILE* 1.3 55.8 + - - +
332B ARG* 3.6 12.0 - - - +
333B GLU* 2.9 35.6 + - - +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B LEU* 3.9 21.1 - - + +
326B THR 3.2 16.6 + - - +
327B THR* 3.2 6.0 + - - +
329B GLN* 1.3 71.5 - - - +
331B ALA* 1.3 64.6 + - - +
333B GLU* 3.2 23.5 - - - +
334B LYS* 4.2 5.7 - - - -
336B MET* 4.2 6.3 - - - +
337B GLY* 3.7 28.6 + - - +
363B PRO* 3.7 19.0 - - + +
445B LEU 4.4 5.2 - - - +
446B PRO* 3.9 5.4 - - + -
447B PHE* 3.4 38.8 - - + +
450B TYR* 4.0 17.0 - - + -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B THR 3.2 7.4 + - - +
328B ASP 3.3 7.6 + - - +
330B ILE* 1.3 75.8 - - - +
332B ARG* 1.3 56.9 + - - +
334B LYS* 2.9 30.0 + - - +
362B ASP* 3.5 26.0 - - - +
363B PRO* 3.8 11.6 - - + +
364B LYS* 3.8 28.0 - - + -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ASP* 3.1 49.5 + - - +
329B GLN* 3.6 11.7 - - - +
331B ALA* 1.3 76.3 - - - +
333B GLU* 1.4 79.7 + - - +
334B LYS* 3.6 8.0 + - - +
364B LYS* 4.8 8.1 - - - +
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 3.6 38.8 - - + +
116B ASN* 5.1 4.9 - - - +
325B LEU* 5.9 0.2 - - + -
329B GLN* 2.9 16.9 + - - +
330B ILE 3.2 12.7 + - - +
332B ARG* 1.4 95.7 - - - +
334B LYS* 1.3 52.5 + - - +
335B GLY* 3.1 6.3 - - - +
336B MET* 2.8 42.7 + - + +
337B GLY 3.6 1.0 + - - -
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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