Contacts of the helix formed by residues 46 - 53 (chain B) in PDB entry 2ODE
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 SER 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B THR* 1.3 63.3 + - - +
48B GLU* 3.3 6.6 - - - +
49B GLU* 3.3 14.3 + - - +
50B ALA* 2.9 29.8 + - - +
175B SER* 3.9 7.6 - - - -
176B GLN* 3.3 36.0 + - - +
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Residues in contact with THR 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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46B SER* 1.3 73.5 - - - +
48B GLU* 1.3 62.5 + - - +
50B ALA* 4.1 2.2 - - - +
51B THR* 2.9 41.5 + - - +
172B LEU* 4.5 3.1 - - - +
175B SER* 2.4 51.8 - - - +
176B GLN* 3.5 26.9 + - + +
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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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46B SER 3.3 4.1 - - - +
47B THR* 1.3 80.0 + - - +
49B GLU* 1.3 57.4 + - - +
51B THR* 3.1 11.7 + - - -
52B ARG* 3.0 32.5 + - + +
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Residues in contact with GLU 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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46B SER* 3.3 17.3 + - - +
47B THR 3.2 0.4 - - - -
48B GLU* 1.3 77.0 - - - +
50B ALA* 1.3 65.5 + - - +
52B ARG* 3.1 15.9 + - - +
53B TRP* 3.1 47.2 + - - +
63B HIS* 3.4 38.8 - - + +
65B TYR* 3.5 29.8 + - - +
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Residues in contact with ALA 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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46B SER 2.9 19.8 + - - +
47B THR* 4.1 5.2 - - - +
49B GLU* 1.3 72.7 - - - +
51B THR* 1.3 56.1 + - - +
53B TRP* 3.4 33.6 + - + +
168B TYR* 2.7 33.0 + - + -
171B LEU* 5.0 2.9 - - + +
172B LEU* 4.2 22.4 - - + +
175B SER* 4.7 8.5 - - - -
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Residues in contact with THR 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 THR* 2.9 32.8 + - - +
48B GLU* 3.1 21.0 + - - -
50B ALA* 1.3 74.1 - - - +
52B ARG* 1.3 63.8 + - - +
54B ALA* 3.2 18.6 + - - +
55B ASP* 4.0 8.0 + - - +
168B TYR* 3.7 6.5 - - - -
172B LEU* 3.4 22.4 - - + -
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Residues in contact with ARG 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 22.6 + - - +
49B GLU* 3.1 14.8 + - - +
51B THR* 1.3 77.9 + - - +
53B TRP* 1.3 61.4 + - - +
55B ASP* 2.5 63.7 + - - +
59B VAL* 3.2 45.3 - - + +
63B HIS* 4.0 14.8 - - + +
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Residues in contact with TRP 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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49B GLU* 3.1 43.4 + - - -
50B ALA* 3.5 23.6 - - + +
51B THR 3.2 0.6 - - - -
52B ARG* 1.3 78.4 - - - +
54B ALA* 1.3 50.6 + - - +
55B ASP 3.3 0.2 - - - -
56B SER 3.3 10.2 - - - +
60B LEU* 3.6 22.4 - - + +
63B HIS* 3.9 15.8 - - + +
65B TYR* 3.5 20.6 - - + -
66B GLY* 3.3 32.6 - - - +
69B ALA* 3.7 20.4 - - + -
159B TYR* 2.7 30.7 + - - -
162B PHE* 4.1 9.2 - + + -
163B LEU* 4.4 1.8 - - - -
168B TYR* 3.6 29.6 - + + -
171B LEU* 4.1 19.5 - - + -
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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