Contacts of the helix formed by residues 324 - 335 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LEU* 4.1 1.3 - - - -
322A GLY 3.7 3.9 + - - +
323A VAL* 1.3 73.3 - - - +
325A ASP* 1.3 54.2 + - - +
326A LEU* 3.0 11.2 + - - +
327A GLU* 2.7 58.9 + - - +
328A PHE* 2.8 36.6 + - - +
343A ARG* 2.5 36.5 + - - +
351A GLY* 5.6 0.9 - - - +
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Residues in contact with ASP 325 (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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319A LEU* 3.4 21.6 - - + +
323A VAL 3.8 0.6 + - - -
324A ASP* 1.3 71.4 - - - +
326A LEU* 1.3 60.9 + - - +
328A PHE* 3.9 0.3 - - - +
329A GLY* 2.7 28.1 + - - -
341A PRO* 3.6 9.2 - - - +
342A GLY 3.4 4.8 + - - +
343A ARG* 2.9 55.7 + - - +
350A LYS* 3.7 0.5 - - - -
351A GLY 3.0 22.8 + - - +
352A PHE 3.1 25.6 - - - +
353A VAL* 4.2 4.9 - - + +
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Residues in contact with LEU 326 (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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8A SER* 5.2 4.0 - - - +
9A VAL* 3.7 43.7 - - + +
12A VAL* 4.1 28.9 - - + -
13A VAL* 4.5 3.4 - - + -
324A ASP* 3.0 9.6 + - - +
325A ASP* 1.3 84.1 - - - +
327A GLU* 1.3 66.0 + - + +
329A GLY* 3.6 0.3 - - - -
330A LEU* 3.0 22.1 + - + +
341A PRO* 4.1 17.7 - - + -
343A ARG* 4.8 11.4 - - - +
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Residues in contact with GLU 327 (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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324A ASP* 2.7 42.9 + - + +
326A LEU* 1.3 74.7 - - + +
328A PHE* 1.3 63.8 + - - +
330A LEU* 3.4 5.6 + - - +
331A ARG* 3.0 24.2 + - - +
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Residues in contact with PHE 328 (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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304A LEU* 5.5 0.2 - - + -
319A LEU* 3.6 24.2 - - + -
323A VAL* 4.4 10.5 - - + -
324A ASP 2.8 23.0 + - - +
325A ASP 3.9 2.2 - - - +
327A GLU* 1.3 72.6 - - - +
329A GLY* 1.3 55.9 + - - +
331A ARG* 3.1 12.4 + - + +
332A LEU* 2.7 62.0 + - + +
339A LEU* 4.6 5.6 - - + -
353A VAL* 4.5 9.6 - - + -
371A ILE* 4.0 20.4 - - + -
374A ALA* 3.6 39.5 - - + -
375A LEU* 3.6 30.1 - - + -
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Residues in contact with GLY 329 (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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13A VAL* 5.2 5.8 - - - -
325A ASP 2.7 22.4 + - - -
326A LEU 3.6 1.6 - - - -
327A GLU 3.2 0.4 - - - -
328A PHE* 1.3 79.3 - - - +
330A LEU* 1.3 60.9 + - - +
332A LEU* 3.3 8.1 + - - +
333A VAL* 3.2 27.6 + - - +
337A VAL 4.7 0.2 - - - +
339A LEU* 5.5 11.1 + - - +
341A PRO* 4.6 11.9 - - - -
353A VAL* 5.8 2.2 - - - -
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Residues in contact with LEU 330 (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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12A VAL* 3.8 28.5 - - + +
13A VAL* 5.3 4.4 - - - +
16A ALA* 3.5 28.5 - - + -
326A LEU 3.0 15.6 + - - +
327A GLU* 3.9 4.9 - - - +
329A GLY* 1.3 70.7 - - - +
331A ARG* 1.3 68.4 + - - +
333A VAL* 3.2 15.0 + - - +
334A GLU* 3.5 27.0 + - + +
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Residues in contact with ARG 331 (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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327A GLU 3.0 17.8 + - - +
328A PHE* 3.4 14.5 - - + +
330A LEU* 1.3 80.4 - - - +
332A LEU* 1.3 59.5 + - - +
334A GLU* 3.5 25.9 + - - +
335A ARG* 2.6 52.7 + - - +
373A GLU 5.3 0.2 + - - -
374A ALA* 2.9 29.5 + - + +
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Residues in contact with LEU 332 (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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328A PHE* 2.7 36.1 + - + +
329A GLY* 3.6 5.8 - - - +
330A LEU 3.1 0.2 - - - -
331A ARG* 1.3 71.4 - - - +
333A VAL* 1.3 63.8 + - - +
334A GLU 3.1 1.6 - - - -
335A ARG* 2.9 19.8 + - + +
336A GLY 3.1 8.7 + - - -
337A VAL* 3.1 36.6 + - + +
339A LEU* 3.4 41.1 - - + -
370A ARG 4.2 4.3 - - - +
371A ILE* 4.0 20.2 - - + +
374A ALA* 3.7 26.0 - - + -
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Residues in contact with VAL 333 (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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13A VAL* 4.5 10.5 - - + -
16A ALA* 3.5 42.8 - - + +
17A LYS* 3.9 11.2 - - + +
20A ALA* 4.3 7.8 - - + +
25A VAL* 5.8 1.6 - - - +
27A LEU* 3.5 20.5 - - + +
329A GLY 3.2 15.5 + - - +
330A LEU* 3.2 9.2 + - - +
332A LEU* 1.3 76.5 - - - +
334A GLU* 1.3 60.7 + - + +
336A GLY* 2.9 16.3 + - - -
337A VAL 3.4 13.5 - - - +
338A ALA* 4.0 18.2 - - + -
339A LEU 5.1 0.9 - - - +
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Residues in contact with GLU 334 (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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16A ALA* 5.8 1.1 - - + -
20A ALA* 5.8 2.2 - - - -
330A LEU* 3.5 29.6 + - + +
331A ARG* 3.5 25.2 - - - +
332A LEU 3.1 0.4 - - - -
333A VAL* 1.3 78.9 - - + +
335A ARG* 1.3 60.9 + - + +
336A GLY 3.6 0.5 + - - -
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Residues in contact with ARG 335 (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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331A ARG* 2.6 50.6 + - - +
332A LEU* 2.9 17.6 + - + +
334A GLU* 1.3 79.7 - - + +
336A GLY* 1.3 56.4 + - - +
337A VAL* 3.7 0.4 - - - -
370A ARG* 3.6 26.0 + - + +
373A GLU* 4.2 20.0 + - - +
374A ALA* 3.2 37.0 - - - +
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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