Contacts of the helix formed by residues 42 - 55 (chain B) in PDB entry 2EBJ
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B PRO* 3.1 17.7 + - + +
41B VAL* 1.3 80.0 - - - +
43B ALA* 1.3 62.3 + - - +
44B GLU* 3.1 12.3 + - - +
45B ALA* 2.7 45.2 + - - +
46B LEU* 3.1 18.7 + - - +
89B ASP* 3.4 7.1 - - - +
91B ARG* 3.4 42.6 + - + +
138B LEU* 3.3 4.6 - - - +
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Residues in contact with ALA 43 (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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42B ASP* 1.3 72.2 - - - +
44B GLU* 1.3 63.8 + - - +
45B ALA 3.4 0.3 + - - -
46B LEU* 3.5 5.4 + - - +
47B GLY 4.3 1.7 + - - -
83B LEU* 5.4 0.4 - - + -
85B PHE* 3.7 24.7 - - + -
89B ASP* 3.0 13.9 + - - +
93B ARG* 5.0 2.0 - - - -
95B LEU* 3.7 18.6 - - + -
138B LEU* 3.5 4.2 - - - +
141B GLN* 3.2 41.6 + - - +
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Residues in contact with GLU 44 (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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42B ASP* 3.1 8.5 + - - +
43B ALA* 1.3 79.6 - - - +
45B ALA* 1.3 60.0 + - + +
47B GLY* 4.4 4.3 + - - -
48B GLU* 5.1 1.4 + - - +
89B ASP* 4.6 1.2 + - - +
91B ARG* 5.9 0.7 - - + -
93B ARG* 4.0 30.2 - - - +
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Residues in contact with ALA 45 (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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40B PRO* 4.7 5.2 - - + -
42B ASP* 2.7 32.8 + - - +
44B GLU* 1.3 71.4 - - - +
46B LEU* 1.3 63.6 + - - +
47B GLY 3.2 2.9 + - - -
48B GLU* 3.3 9.8 + - + +
49B ALA* 3.1 22.4 + - + +
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Residues in contact with LEU 46 (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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7B PHE* 4.5 1.8 - - + -
39B LEU* 4.1 31.6 - - + -
40B PRO* 4.4 11.4 - - + +
42B ASP* 3.1 17.0 + - - +
43B ALA 3.5 8.1 + - - +
45B ALA* 1.3 75.9 - - - +
47B GLY* 1.3 63.9 + - - +
49B ALA* 3.1 5.0 + - - +
50B LEU* 2.9 42.7 + - + +
138B LEU* 3.9 13.0 - - + +
141B GLN* 3.5 36.3 - - + +
142B ALA* 3.6 20.4 - - + +
145B LEU* 4.2 2.5 - - + -
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Residues in contact with GLY 47 (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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43B ALA 4.3 4.4 + - - -
44B GLU 4.4 3.4 + - - -
45B ALA* 3.2 1.2 - - - +
46B LEU* 1.3 79.0 - - - +
48B GLU* 1.3 56.8 + - - +
50B LEU* 3.5 2.6 + - - +
51B GLU* 3.1 28.6 + - - +
141B GLN* 4.8 1.2 - - - +
145B LEU* 4.1 18.7 - - - +
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Residues in contact with GLU 48 (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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44B GLU 5.1 1.0 + - - -
45B ALA* 3.3 11.3 + - + +
47B GLY* 1.3 72.2 - - - +
49B ALA* 1.3 66.0 + - - +
51B GLU* 2.8 47.1 - - + +
52B ASP* 3.0 20.4 + - - +
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Residues in contact with ALA 49 (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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39B LEU* 4.7 8.7 - - + -
40B PRO* 4.1 25.6 - - + -
45B ALA* 3.1 13.4 + - + +
46B LEU* 3.5 8.7 - - - +
48B GLU* 1.3 77.0 - - - +
50B LEU* 1.3 61.8 + - - +
52B ASP* 3.6 7.2 + - - +
53B LEU* 3.3 28.8 + - + +
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Residues in contact with LEU 50 (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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3B LEU* 5.4 0.4 - - + -
39B LEU* 3.9 23.8 - - + -
46B LEU* 2.9 24.7 + - + +
47B GLY* 3.9 4.0 - - - +
49B ALA* 1.3 76.3 - - - +
51B GLU* 1.3 54.4 + - - +
53B LEU* 3.1 8.8 + - + -
54B HIS* 2.6 58.7 + - + +
63B HIS* 3.9 23.1 - - + -
142B ALA* 3.8 24.7 - - - +
145B LEU* 3.7 35.9 - - + -
146B SER* 4.4 3.6 - - - +
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Residues in contact with GLU 51 (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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47B GLY 3.1 9.9 + - - +
48B GLU* 2.8 48.1 - - - +
50B LEU* 1.3 76.4 - - - +
52B ASP* 1.3 81.6 + - - +
54B HIS* 3.2 10.1 + - - +
55B ARG* 2.5 69.0 + - + +
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Residues in contact with ASP 52 (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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48B GLU* 3.0 28.8 + - - +
49B ALA* 3.7 7.4 - - - +
51B GLU* 1.3 90.8 + - - +
53B LEU* 1.3 63.4 + - + +
55B ARG* 2.5 50.3 + - - +
56B GLU* 3.5 19.0 + - - +
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Residues in contact with LEU 53 (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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1B MET* 5.1 0.5 - - - +
3B LEU* 4.1 25.4 - - + +
5B THR* 4.4 2.5 - - + -
35B ARG* 3.5 37.5 - - - +
37B ALA* 4.0 18.6 - - + -
39B LEU* 3.6 31.4 - - + -
49B ALA* 3.3 13.4 + - + +
50B LEU* 3.1 14.7 + - + +
52B ASP* 1.3 75.3 - - + +
54B HIS* 1.3 67.7 + - + +
56B GLU* 3.0 25.8 + - - +
58B PRO* 3.5 8.5 - - - +
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Residues in contact with HIS 54 (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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3B LEU* 4.9 12.1 - - + -
50B LEU* 2.6 45.5 + - + +
51B GLU* 3.6 9.3 - - - +
53B LEU* 1.3 75.8 - - + +
55B ARG* 1.3 56.7 + - + +
56B GLU 3.1 0.2 - - - -
57B GLY* 3.0 18.4 + - - -
58B PRO* 3.4 11.1 - - + +
145B LEU* 4.0 2.9 - - + -
146B SER* 2.9 45.9 + - - -
149B ARG* 3.6 27.4 - - + +
150B LEU* 3.7 30.6 - - + +
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Residues in contact with ARG 55 (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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51B GLU* 2.5 48.3 + - + +
52B ASP* 2.5 28.8 + - - +
53B LEU 3.2 0.4 - - - -
54B HIS* 1.3 72.9 - - + +
56B GLU* 1.3 60.9 + - - +
57B GLY* 2.9 7.1 + - - -
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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