Contacts of the helix formed by residues 324 - 335 (chain B) in PDB entry 2DOU
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 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B LEU* 4.1 1.3 - - - -
322B GLY 3.3 4.0 + - - +
323B VAL* 1.3 72.9 - - - +
325B ASP* 1.3 59.2 + - - +
326B LEU* 2.8 29.1 + - - +
327B GLU* 2.9 24.3 + - + +
328B PHE* 2.8 31.5 + - - +
343B ARG* 3.2 20.3 + - - -
351B GLY* 6.0 0.2 - - - -
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Residues in contact with ASP 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.4 22.3 - - + +
323B VAL 4.0 1.0 + - - -
324B ASP* 1.3 70.7 + - - +
326B LEU* 1.3 61.6 + - - +
328B PHE* 4.0 0.6 - - - +
329B GLY* 2.9 25.5 + - - -
341B PRO* 3.4 15.1 - - + +
342B GLY 4.4 1.1 - - - +
343B ARG* 2.9 50.9 + - - +
350B LYS* 3.7 4.5 - - - +
351B GLY* 2.9 25.2 + - - +
352B PHE 3.3 24.0 - - - +
353B VAL* 4.3 5.5 - - + +
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Residues in contact with LEU 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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9B VAL* 3.4 36.1 - - + +
12B VAL* 4.9 10.8 - - + -
13B VAL* 4.3 7.0 - - + -
324B ASP* 2.8 11.8 + - - +
325B ASP* 1.3 76.5 - - - +
327B GLU* 1.3 68.1 + - - +
329B GLY* 3.2 1.0 + - - -
330B LEU* 3.0 47.9 + - + +
341B PRO* 4.1 11.0 - - + -
343B ARG* 3.3 23.3 - - - +
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Residues in contact with GLU 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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324B ASP* 2.9 25.8 + - + +
326B LEU* 1.3 76.0 - - - +
328B PHE* 1.3 58.0 + - - +
330B LEU* 3.1 14.1 + - - +
331B ARG* 2.8 29.6 + - - +
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Residues in contact with PHE 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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303B VAL* 6.3 0.2 - - + -
304B LEU* 6.3 0.2 - - + -
319B LEU* 4.1 24.2 - - + -
320B PRO* 6.2 0.9 - - + -
323B VAL* 3.8 25.6 - - + -
324B ASP 2.8 22.9 + - - +
325B ASP 4.0 2.0 - - - +
327B GLU* 1.3 71.2 - - - +
329B GLY* 1.3 58.9 + - - +
331B ARG* 3.1 11.3 + - + +
332B LEU* 2.6 61.4 + - + +
339B LEU* 4.9 4.3 - - + -
353B VAL* 4.7 6.3 - - + -
371B ILE* 4.2 21.1 - - + -
374B ALA* 3.0 44.9 - - + -
375B LEU* 4.5 8.3 - - + -
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Residues in contact with GLY 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 5.0 3.4 - - - -
325B ASP 2.9 19.2 + - - -
326B LEU 3.7 1.1 - - - -
328B PHE* 1.3 78.8 - - - +
330B LEU* 1.3 59.0 + - - +
332B LEU* 3.2 9.7 + - - +
333B VAL* 2.9 35.0 + - - +
337B VAL 4.6 0.5 - - - +
339B LEU* 5.4 11.7 + - - -
341B PRO* 5.0 9.4 - - - -
353B VAL* 5.9 2.2 - - - -
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Residues in contact with LEU 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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12B VAL* 3.7 29.2 - - + -
13B VAL* 4.0 15.2 - - + +
16B ALA* 4.0 21.8 - - + -
326B LEU* 3.0 30.4 + - + +
327B GLU* 3.3 10.1 - - - +
329B GLY* 1.3 75.5 - - - +
331B ARG* 1.3 64.3 + - - +
333B VAL* 2.9 22.6 + - + +
334B GLU* 3.3 12.4 + - - +
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Residues in contact with ARG 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 GLU 2.8 17.2 + - - +
328B PHE* 3.5 15.0 - - + +
330B LEU* 1.3 73.1 - - - +
332B LEU* 1.3 63.1 + - - +
334B GLU* 3.4 20.0 + - - +
335B ARG* 3.2 63.7 + - - +
374B ALA* 4.7 14.5 + - - +
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Residues in contact with LEU 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 PHE* 2.6 34.2 + - + +
329B GLY* 3.4 4.7 - - - +
331B ARG* 1.3 71.4 - - - +
333B VAL* 1.3 66.8 + - - +
335B ARG* 2.9 21.1 + - + +
337B VAL* 3.2 45.4 + - + +
339B LEU* 3.4 38.4 - - + -
370B ARG* 4.5 2.5 - - + +
371B ILE* 3.9 25.8 - - + +
374B ALA* 3.8 24.2 - - + +
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Residues in contact with VAL 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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13B VAL* 4.2 25.4 - - + +
16B ALA* 2.9 34.5 - - + +
17B LYS* 3.8 2.2 - - + -
20B ALA* 4.0 8.6 - - + +
25B VAL* 5.3 1.0 - - - +
27B LEU* 3.4 24.6 - - + +
329B GLY 2.9 24.5 + - - +
330B LEU* 2.9 10.7 + - - +
332B LEU* 1.3 75.4 - - - +
334B GLU* 1.3 57.4 + - - +
336B GLY* 2.7 26.3 + - - -
337B VAL 3.4 13.2 - - - +
338B ALA* 4.5 7.0 - - + -
339B LEU 5.3 0.2 - - - +
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Residues in contact with GLU 334 (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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16B ALA* 3.9 21.5 - - - +
19B LYS* 6.0 0.7 - - - +
20B ALA* 4.5 3.8 + - - +
23B ARG* 2.5 42.6 + - - +
25B VAL* 4.6 8.5 - - - +
330B LEU 3.3 12.1 + - - +
331B ARG* 3.6 14.4 - - - +
332B LEU 3.3 0.4 - - - -
333B VAL* 1.3 77.0 - - - +
335B ARG* 1.3 61.8 + - + +
336B GLY 3.6 0.7 + - - -
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ARG* 3.2 57.6 + - - +
332B LEU* 2.9 15.4 + - + +
333B VAL 2.9 1.4 - - - -
334B GLU* 1.3 80.5 - - + +
336B GLY* 1.3 55.9 + - - +
337B VAL 3.7 0.4 - - - -
370B ARG* 3.5 26.9 + - + +
373B GLU* 4.4 20.3 + - - +
374B ALA* 3.6 33.4 - - - +
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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