Contacts of the helix formed by residues 324 - 331 (chain B) in PDB entry 6VW1
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 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B ASN 5.1 1.3 - - - +
323B MET* 1.3 76.1 - - - +
325B GLN* 1.3 62.9 + - - +
326B GLY* 3.5 5.2 + - - -
327B PHE* 2.8 42.0 + - - +
328B TRP* 3.0 12.9 + - - -
354B GLY 4.9 8.8 + - - +
356B PHE* 4.5 13.8 + - + +
383B MET* 3.7 23.8 - - + +
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Residues in contact with GLN 325 (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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323B MET 3.8 1.8 + - - -
324B THR* 1.3 73.4 - - - +
326B GLY* 1.3 57.5 + - - +
328B TRP* 3.4 8.6 + - - +
329B GLU* 2.9 52.7 + - - +
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Residues in contact with GLY 326 (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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324B THR* 3.0 7.3 + - - -
325B GLN* 1.3 78.2 - - - +
327B PHE* 1.3 57.8 + - - +
329B GLU* 4.5 5.4 - - - -
330B ASN* 2.9 46.4 + - - +
355B ASP* 5.2 4.5 - - - -
356B PHE 4.3 3.8 - - - +
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Residues in contact with PHE 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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308B PHE* 4.4 7.0 - + - -
323B MET* 3.4 45.8 - - + -
324B THR* 2.8 26.1 + - - +
326B GLY* 1.3 76.2 - - - +
328B TRP* 1.3 89.0 + + - +
331B SER* 2.8 61.5 + - - +
333B LEU* 4.5 2.7 - - + -
356B PHE* 3.3 27.3 + - + +
357B ARG* 3.7 4.5 - - - -
358B ILE* 3.4 35.9 - - + -
376B MET* 4.1 8.5 - - + -
379B ILE* 5.1 1.1 - - + -
383B MET* 5.3 0.2 - - + -
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Residues in contact with TRP 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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305B GLN* 4.1 22.4 + - - -
308B PHE* 3.7 29.4 - - + -
309B LYS* 3.5 37.6 - - + +
312B GLU* 3.1 42.4 + - + -
323B MET* 3.6 13.1 - - + +
324B THR 3.0 22.3 + - - -
325B GLN* 4.0 8.5 - - - +
327B PHE* 1.3 94.8 - + - +
329B GLU* 1.3 63.1 + - + +
331B SER* 4.7 4.6 + - - +
333B LEU* 3.9 25.8 - - + -
376B MET* 5.0 0.4 - - + -
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Residues in contact with GLU 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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325B GLN* 2.9 41.2 + - - +
326B GLY* 4.0 5.9 - - - +
328B TRP* 1.3 82.1 - - + +
330B ASN* 1.3 69.2 + - - +
331B SER 3.7 2.2 - - - +
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Residues in contact with ASN 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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48B TRP* 3.1 20.8 + - - -
326B GLY* 2.9 29.0 + - - +
329B GLU* 1.3 86.6 + - - +
331B SER* 1.3 67.8 + - - +
332B MET* 5.0 0.2 - - - +
355B ASP* 4.6 4.3 - - - +
357B ARG* 3.6 40.5 + - - +
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Residues in contact with SER 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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48B TRP* 4.1 5.6 - - - -
327B PHE* 2.8 48.0 + - - -
328B TRP* 4.6 3.4 - - - +
329B GLU 3.7 3.2 - - - +
330B ASN* 1.3 82.9 + - - +
332B MET* 1.3 59.7 + - - +
333B LEU* 3.9 22.1 + - - +
357B ARG* 3.4 3.8 - - - +
358B ILE 3.1 20.5 + - - -
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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