Contacts of the helix formed by residues 360 - 374 (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 PRO 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP* 4.1 8.7 - - - +
292A ARG* 3.7 4.0 - - - +
359A ARG* 1.3 95.9 - - + +
361A LEU* 1.3 66.8 - - - +
362A GLU* 3.3 16.4 - - + +
363A GLU* 3.1 28.8 + - + +
364A LEU 3.1 8.5 + - - -
502A SO4 3.7 26.7 - - - +
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Residues in contact with LEU 361 (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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291A GLU* 3.9 28.5 - - + +
292A ARG* 4.1 19.2 - - + +
295A GLY* 4.1 19.7 - - - -
296A MET 4.1 2.5 - - - +
360A PRO* 1.3 73.8 - - - +
362A GLU* 1.3 57.2 + - - +
364A LEU* 3.2 10.9 + - + -
365A LEU* 2.8 59.2 + - + +
502A SO4 3.1 23.1 + - - +
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Residues in contact with GLU 362 (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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360A PRO* 4.5 13.5 - - + +
361A LEU* 1.3 77.4 - - - +
363A GLU* 1.3 70.8 + - + +
365A LEU* 3.2 14.4 + - + +
366A GLU* 3.0 21.3 + - - +
502A SO4 5.0 0.8 + - - -
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Residues in contact with GLU 363 (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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28A ILE* 3.8 26.7 - - + +
359A ARG* 3.6 34.9 + - + +
360A PRO* 3.1 23.6 + - + +
362A GLU* 1.3 88.5 - - + +
364A LEU* 1.3 59.7 + - - +
366A GLU* 3.1 9.4 + - - +
367A ALA* 2.8 29.3 + - - +
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Residues in contact with LEU 364 (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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30A LEU* 3.5 36.1 - - + -
292A ARG* 3.4 42.4 - - + +
296A MET* 3.4 26.9 - - + +
356A ALA 4.5 0.2 - - - +
357A LEU* 3.9 24.0 - - + -
359A ARG* 3.4 20.2 - - + +
360A PRO 3.1 16.8 + - - +
361A LEU* 3.2 9.8 + - + +
363A GLU* 1.3 76.0 - - - +
365A LEU* 1.3 58.6 + - - +
367A ALA* 4.2 4.3 - - - -
368A ALA* 2.9 25.3 + - - +
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Residues in contact with LEU 365 (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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295A GLY* 4.3 18.4 - - - +
296A MET* 4.6 1.1 - - - +
299A ALA* 4.4 15.0 - - + +
361A LEU* 2.8 44.7 + - + +
362A GLU* 3.4 14.6 - - + +
363A GLU 3.1 0.2 - - - -
364A LEU* 1.3 76.7 - - - +
366A GLU* 1.3 66.2 + - - +
368A ALA* 3.1 5.6 + - - +
369A LYS* 3.0 21.5 + - - +
372A ARG* 5.5 0.2 + - - -
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Residues in contact with GLU 366 (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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28A ILE* 3.7 7.6 - - + -
362A GLU 3.0 12.6 + - - +
363A GLU* 3.4 9.6 - - - +
365A LEU* 1.3 74.0 - - - +
367A ALA* 1.3 64.8 + - - +
369A LYS* 2.9 42.2 + - - +
370A ARG* 2.7 59.4 + - - +
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Residues in contact with ALA 367 (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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28A ILE* 4.0 8.5 - - + +
30A LEU* 3.8 27.1 - - + -
296A MET* 4.0 2.7 - - + -
337A VAL* 3.6 27.0 - - + +
363A GLU 2.8 15.4 + - - +
364A LEU* 3.6 6.3 - - - +
366A GLU* 1.3 77.3 - - - +
368A ALA* 1.3 57.5 + - - +
370A ARG* 3.2 3.6 + - - +
371A ILE* 2.9 33.8 + - - +
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Residues in contact with ALA 368 (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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296A MET* 3.9 10.3 - - + +
299A ALA* 3.6 30.7 - - + -
300A LEU* 3.9 25.1 - - + +
364A LEU 2.9 14.9 + - - +
365A LEU* 3.1 9.4 + - - +
367A ALA* 1.3 76.2 - - - +
369A LYS* 1.3 63.1 + - - +
371A ILE* 3.3 3.2 + - - +
372A ARG* 3.0 26.4 + - - +
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Residues in contact with LYS 369 (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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365A LEU 3.0 10.3 + - - +
366A GLU* 2.9 36.8 + - - +
368A ALA* 1.3 78.2 - - - +
370A ARG* 1.3 54.9 + - - +
372A ARG* 3.1 30.5 + - - +
373A GLU* 3.0 56.0 + - + +
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Residues in contact with ARG 370 (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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26A GLY* 3.7 12.1 + - - -
28A ILE* 3.5 13.9 - - - +
332A LEU* 4.2 5.7 - - + +
335A ARG* 3.6 23.5 + - + +
336A GLY* 3.1 29.5 + - - -
337A VAL* 3.6 18.2 - - + -
366A GLU* 2.7 49.9 + - - +
367A ALA 3.2 5.8 + - - +
369A LYS* 1.3 72.7 - - + +
371A ILE* 1.3 62.6 + - - +
372A ARG 3.0 1.8 - - - -
373A GLU* 3.1 15.9 + - - +
374A ALA* 2.8 32.1 + - - +
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Residues in contact with ILE 371 (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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296A MET* 4.0 23.8 - - + -
300A LEU* 4.1 15.3 - - + -
303A VAL* 4.0 14.6 - - + -
304A LEU* 4.4 9.6 - - + -
328A PHE* 4.0 19.3 - - + -
332A LEU* 4.0 22.2 - - + -
337A VAL* 4.5 4.9 - - + -
339A LEU* 4.1 22.4 - - + -
355A ILE* 4.3 7.4 - - + -
367A ALA 2.9 22.3 + - - +
368A ALA 3.6 5.2 - - - +
369A LYS 3.3 0.2 - - - -
370A ARG* 1.3 75.9 - - - +
372A ARG* 1.3 62.8 + - - +
374A ALA* 3.6 1.6 + - - +
375A LEU* 3.5 25.5 + - + +
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Residues in contact with ARG 372 (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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299A ALA* 3.3 25.9 + - - +
301A LYS 5.5 2.0 - - - -
303A VAL* 3.3 33.1 - - + +
368A ALA* 3.0 27.6 + - - +
369A LYS* 3.2 36.7 - - - +
370A ARG 3.0 0.4 - - - -
371A ILE* 1.3 78.6 - - - +
373A GLU* 1.3 62.3 + - + +
375A LEU* 3.3 18.2 + - - +
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Residues in contact with GLU 373 (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* 5.3 0.2 + - - -
335A ARG* 4.2 17.8 + - - +
369A LYS* 3.0 39.9 + - + +
370A ARG* 3.1 21.3 + - - +
372A ARG* 1.3 73.9 - - + +
374A ALA* 1.3 58.7 + - - +
375A LEU* 3.0 12.0 + - - -
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Residues in contact with ALA 374 (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* 3.6 24.6 - - + -
331A ARG* 2.9 27.2 + - + +
332A LEU* 3.7 10.8 - - + -
335A ARG* 3.2 37.4 - - - +
370A ARG 2.8 14.4 + - - +
371A ILE 4.1 1.3 - - - +
372A ARG 3.3 0.2 - - - -
373A GLU* 1.3 75.7 - - - +
375A LEU* 1.3 59.4 + - - +
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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