Contacts of the helix formed by residues 40 - 51 (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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 1.3 91.2 - - + +
41A GLU* 1.3 60.6 + - - +
42A ALA* 4.7 2.7 - - + +
43A PRO* 3.0 32.4 - - + +
44A LEU* 4.2 7.6 - - - +
232A TYR* 3.5 21.3 - - + +
234A LEU* 5.4 0.2 - - + -
277A THR* 3.7 36.3 - - + +
281A VAL* 4.7 6.1 - - + -
285A TYR* 3.4 16.6 - - + +
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Residues in contact with GLU 41 (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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39A PRO 3.7 1.4 + - - -
40A PRO* 1.3 71.7 - - - +
42A ALA* 1.3 67.8 + - - +
44A LEU* 3.0 27.1 + - + +
45A LYS* 3.1 27.6 + - + +
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Residues in contact with ALA 42 (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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40A PRO* 4.7 2.4 - - + +
41A GLU* 1.3 76.4 - - - +
43A PRO* 1.3 70.8 - - + +
45A LYS* 3.1 10.0 + - - +
46A ALA* 2.9 22.5 + - - +
273A GLU* 3.3 29.9 - - + +
277A THR* 6.1 0.4 - - - +
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Residues in contact with PRO 43 (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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40A PRO* 3.0 36.3 - - + +
42A ALA* 1.3 94.3 - - + +
44A LEU* 1.3 61.2 + - - +
46A ALA* 3.1 4.0 + - - +
47A LEU* 3.0 23.0 + - - +
234A LEU* 4.1 14.4 - - + -
270A MET* 3.8 32.6 - - + +
273A GLU* 3.9 9.4 - - + -
274A ALA* 3.8 27.1 - - + +
277A THR* 4.6 1.8 - - - +
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Residues in contact with LEU 44 (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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39A PRO* 4.2 10.3 - - + +
40A PRO 4.2 10.5 - - - +
41A GLU* 3.0 15.5 + - + +
43A PRO* 1.3 75.5 - - - +
45A LYS* 1.3 61.2 + - + +
47A LEU* 3.3 4.0 + - - +
48A ALA* 2.8 29.7 + - - +
234A LEU* 4.4 6.5 - - + -
237A PHE* 3.7 33.0 - - + -
270A MET* 3.8 12.1 - - + -
51B LEU* 4.1 17.6 - - + +
57B TYR* 3.4 36.3 - - + +
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Residues in contact with LYS 45 (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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41A GLU* 3.1 27.4 + - + +
42A ALA* 3.1 9.4 + - - +
44A LEU* 1.3 76.1 - - + +
46A ALA* 1.3 66.7 + - - +
48A ALA* 3.6 8.3 - - + +
49A GLU* 2.9 26.2 + - - +
52B ASN* 5.5 7.1 - - - +
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Residues in contact with ALA 46 (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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42A ALA 2.9 12.1 + - - +
43A PRO 3.4 9.2 - - - +
45A LYS* 1.3 78.0 - - - +
47A LEU* 1.3 62.7 + - - +
49A GLU* 3.2 6.8 + - - +
50A ALA* 3.0 21.7 + - - +
266A GLY 4.8 1.8 - - - -
269A ARG* 4.0 28.6 - - + +
270A MET* 4.2 2.0 - - - -
273A GLU* 4.2 12.6 - - + +
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Residues in contact with LEU 47 (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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43A PRO 3.0 11.9 + - - +
44A LEU 3.6 6.7 - - - +
46A ALA* 1.3 74.3 - - - +
48A ALA* 1.3 67.6 + - - +
50A ALA* 3.1 10.8 + - - +
51A LEU* 3.3 17.9 + - + +
237A PHE* 3.6 37.7 - - + -
264A TYR* 3.6 20.9 - - + -
266A GLY 3.3 37.4 + - - +
267A VAL* 3.7 8.3 - - + +
270A MET* 3.7 13.0 - - + +
47B LEU* 6.1 3.4 - - + -
51B LEU* 3.8 17.7 - - + -
264B TYR* 5.2 3.4 - - + -
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Residues in contact with ALA 48 (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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44A LEU 2.8 21.4 + - - +
45A LYS* 3.3 12.1 + - + +
47A LEU* 1.3 72.0 - - - +
49A GLU* 1.3 62.6 + - - +
51A LEU* 3.1 25.9 + - + +
52A ASN* 4.0 6.9 + - - -
48B ALA* 6.1 2.0 - - + -
51B LEU* 3.5 21.6 - - + +
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Residues in contact with GLU 49 (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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45A LYS 2.9 17.5 + - - +
46A ALA* 3.5 7.0 - - - +
48A ALA* 1.3 74.5 - - - +
50A ALA* 1.3 65.3 + - - +
52A ASN* 3.2 27.6 + - - +
53A ASP* 3.9 4.2 + - - +
269A ARG* 5.3 0.4 - - - -
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Residues in contact with ALA 50 (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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46A ALA 3.0 11.6 + - - +
47A LEU 3.1 6.9 + - - +
49A GLU* 1.3 76.6 - - - +
51A LEU* 1.3 57.8 + - - +
53A ASP* 2.9 20.9 + - - +
56A THR* 3.2 16.9 + - + -
264A TYR* 3.5 4.3 - - - +
266A GLY* 3.4 33.2 - - - +
269A ARG* 3.8 30.9 - - - +
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Residues in contact with LEU 51 (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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47A LEU* 3.4 13.5 - - + +
48A ALA* 3.1 13.4 + - - +
50A ALA* 1.3 78.8 - - - +
52A ASN* 1.3 55.1 + - - +
57A TYR* 2.4 33.9 + - - -
264A TYR* 3.5 26.9 - - + +
44B LEU* 4.4 15.6 - - + +
47B LEU* 3.7 27.6 - - + -
48B ALA* 3.6 41.5 - - + +
51B LEU* 4.0 15.7 - - + -
237B PHE* 4.0 6.1 - - + -
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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