Contacts of the helix formed by residues 325 - 333 (chain B) in PDB entry 3R2W
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 LEU 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL* 4.8 3.6 - - + -
219B PHE* 4.2 10.1 - - + -
225B LEU* 3.9 34.2 - - + +
228B PHE* 4.7 12.8 - - + -
229B ILE* 4.2 13.2 - - + +
233B LYS* 3.9 26.0 - - + +
234B GLU 3.1 25.2 + - - +
235B TYR* 3.7 8.7 - - - +
236B ILE* 3.6 28.3 - - + -
323B ILE 3.6 1.2 + - - -
324B SER* 1.3 68.9 - - - +
326B ALA* 1.3 67.0 + - - +
328B VAL* 2.8 20.7 + - - +
329B LYS* 3.2 12.5 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 3.9 20.0 - - + +
234B GLU* 4.2 4.4 + - - +
324B SER* 3.4 11.0 - - - +
325B LEU* 1.3 79.0 - - - +
327B ALA* 1.3 59.2 + - - +
328B VAL 3.6 0.2 + - - -
329B LYS* 3.7 6.6 - - - +
330B ARG* 3.6 24.6 + - - +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLU* 3.3 37.0 - - + +
324B SER* 2.5 28.5 + - - +
326B ALA* 1.3 72.5 - - + +
328B VAL* 1.3 61.9 + - - +
330B ARG* 3.6 11.8 + - - +
331B LEU* 3.1 32.0 + - - +
368B PHE* 4.1 10.1 - - + -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TYR* 4.7 32.3 - - + +
219B PHE* 6.3 0.2 - - + -
220B TYR* 5.4 0.9 - - + -
225B LEU* 3.7 28.0 - - + -
236B ILE* 4.8 10.3 - - + -
323B ILE* 4.5 14.6 - - + -
324B SER 3.6 13.0 - - - +
325B LEU* 2.8 15.4 + - - +
327B ALA* 1.3 75.6 - - - +
329B LYS* 1.3 68.6 + - - +
331B LEU* 2.7 17.2 + - + +
332B GLN* 2.9 22.3 + - + -
337B ILE* 6.3 2.0 - - + -
368B PHE* 5.1 6.1 - - + -
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Residues in contact with LYS 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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220B TYR* 4.9 1.6 - - + -
225B LEU* 3.8 22.3 - - + +
226B ASP* 2.9 32.3 + - - +
229B ILE* 4.9 20.7 - - + +
325B LEU 3.2 5.8 + - - +
326B ALA* 3.7 11.4 - - - +
328B VAL* 1.3 78.1 - - - +
330B ARG* 1.3 65.8 + - + +
331B LEU 2.7 2.4 + - - -
332B GLN 3.3 6.9 + - - -
333B GLU* 3.2 50.3 + - + +
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Residues in contact with ARG 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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266B GLU* 2.5 31.3 + - - -
326B ALA 3.6 9.6 + - - +
327B ALA* 3.6 20.4 + - - +
328B VAL 3.4 0.4 - - - -
329B LYS* 1.3 78.1 - - + +
331B LEU* 1.3 74.6 - - - +
333B GLU* 5.0 2.9 - - - +
334B GLN* 3.1 36.8 - - - +
369B GLU* 4.6 17.5 + - - +
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Residues in contact with LEU 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 ALA 3.1 18.4 - - - +
328B VAL* 2.7 11.3 + - - +
329B LYS 2.7 4.9 + - - -
330B ARG* 1.3 93.7 - - - +
332B GLN* 1.3 58.3 + - - +
333B GLU 3.6 0.2 - - - -
334B GLN 3.4 1.3 + - - -
335B ASN 3.1 7.3 + - - -
336B ALA* 3.1 57.5 + - + +
337B ILE* 3.8 12.6 - - + -
367B SER* 3.8 24.9 - - - +
368B PHE* 4.0 34.8 - - + -
369B GLU* 5.5 0.9 - - - +
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Residues in contact with GLN 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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216B TYR* 3.8 11.5 - - - +
217B ALA* 3.4 35.8 - - - +
220B TYR* 4.0 38.5 - - + -
328B VAL* 2.9 23.2 + - + +
329B LYS 4.6 0.4 - - - +
331B LEU* 1.3 68.0 - - - +
333B GLU* 1.3 54.0 + - - +
334B GLN 2.6 16.5 + - - -
335B ASN* 2.9 28.8 + - - +
337B ILE* 2.8 32.9 - - + +
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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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220B TYR* 3.2 41.3 + - + +
226B ASP* 4.4 2.1 - - - +
329B LYS* 3.2 54.6 + - - +
330B ARG* 5.2 1.6 - - - -
332B GLN* 1.3 72.4 - - - +
334B GLN* 1.3 66.9 + - + +
335B ASN* 5.1 0.9 - - - -
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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