Contacts of the helix formed by residues 38 - 46 (chain O) in PDB entry 2I2R
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 GLY 38 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69L THR* 5.1 17.4 - - - +
73L PHE* 4.7 6.7 - - - -
39O LEU* 1.3 62.3 + - - -
41O GLN* 3.0 30.4 + - - +
42O LEU* 3.4 29.2 + - - +
109O GLU* 5.0 10.1 + - - -
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Residues in contact with LEU 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L THR* 5.5 1.2 + - - -
72L GLU* 4.2 37.7 - - + +
73L PHE* 3.5 38.7 - - + -
38O GLY* 1.3 71.7 - - - -
40O GLU* 1.3 58.8 + - - +
42O LEU* 3.3 4.3 + - - +
43O GLU* 3.1 23.2 + - - +
50O LYS* 3.9 38.6 - - + +
53O LEU* 3.8 24.0 - - + -
54O GLN* 4.4 12.8 - - + +
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Residues in contact with GLU 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O GLY 3.5 0.6 - - - -
39O LEU* 1.3 75.4 - - - +
41O GLN* 1.3 70.1 + - - +
43O GLU* 3.7 13.4 - - + +
44O ALA* 3.4 17.7 + - - +
50O LYS* 3.1 34.9 + - - +
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Residues in contact with GLN 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O GLY* 3.0 36.0 - - - +
40O GLU* 1.3 77.1 + - - +
42O LEU* 1.3 54.9 + - + +
44O ALA* 2.8 13.1 + - - +
45O GLN* 2.7 53.5 + - - +
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Residues in contact with LEU 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L PHE* 4.2 13.7 - - + -
38O GLY 3.4 19.7 + - - +
39O LEU 3.3 7.9 + - - +
41O GLN* 1.3 79.3 - - + +
43O GLU* 1.3 55.3 + - - +
45O GLN* 4.0 23.8 - - + +
46O THR* 2.6 43.5 + - + -
53O LEU* 3.7 20.9 - - + -
108O PHE* 3.6 33.0 - - + -
109O GLU* 4.3 17.3 - - + +
112O VAL* 3.9 19.1 - - + -
113O THR* 5.8 0.4 - - - +
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Residues in contact with GLU 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN* 3.5 27.1 + - + +
36B LYS 5.7 2.5 - - - -
37B ARG* 5.4 5.4 + - - -
39O LEU 3.1 12.8 + - - +
40O GLU* 3.7 17.9 - - + +
41O GLN 3.1 0.4 - - - -
42O LEU* 1.3 77.4 - - - +
44O ALA* 1.3 59.5 + - - +
46O THR 3.1 19.8 - - - +
48O PHE 3.7 6.1 - - - +
49O THR* 3.5 11.3 - - - +
50O LYS* 3.1 52.9 + - + +
53O LEU* 3.6 14.5 - - + +
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Residues in contact with ALA 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN 4.2 12.8 + - - +
40O GLU 3.4 9.3 + - - +
41O GLN* 2.8 14.4 + - - +
43O GLU* 1.3 80.9 - - + +
45O GLN* 1.3 57.9 + - + +
46O THR 3.2 8.6 + - - +
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Residues in contact with GLN 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O GLN* 2.7 41.2 + - - +
42O LEU* 4.0 20.3 - - - +
44O ALA* 1.3 72.2 - - + +
46O THR* 1.3 66.3 + - + +
109O GLU* 5.4 4.9 - - - +
113O THR* 5.2 9.6 + - - +
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Residues in contact with THR 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN 4.7 4.2 + - - -
42O LEU* 2.6 35.3 + - + +
43O GLU 3.1 17.3 - - - +
44O ALA 3.2 4.3 + - - +
45O GLN* 1.3 90.7 - - + +
47O ASN* 1.3 66.5 + - - +
48O PHE* 3.2 22.2 + - - +
53O LEU* 4.1 2.1 - - - +
112O VAL* 4.6 6.3 - - + +
113O THR* 4.6 17.5 - - + +
116O SER* 3.5 24.2 - - - -
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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