Contacts of the helix formed by residues 44 - 52 (chain B) in PDB entry 3CJD
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 ALA 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ALA* 3.8 0.7 - - - -
43B CYS* 1.3 82.9 - - - +
45B VAL* 1.3 65.0 + - - +
46B GLY* 4.1 7.2 - - - +
47B ALA* 3.0 23.5 + - + +
48B ILE 4.0 0.7 + - - -
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Residues in contact with VAL 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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34B ALA* 3.5 29.2 - - + -
35B ARG* 3.8 27.8 - - + +
38B ALA* 3.7 13.4 - - + +
44B ALA* 1.3 71.6 - - - +
46B GLY* 1.3 61.0 + - - +
48B ILE* 3.2 19.4 + - - +
49B TYR* 3.6 19.1 - - + -
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Residues in contact with GLY 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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44B ALA* 3.1 6.7 - - - +
45B VAL* 1.3 75.6 - - - +
47B ALA* 1.3 53.1 + - - +
48B ILE 3.2 0.2 - - - -
49B TYR* 3.5 10.3 + - - +
50B THR* 2.8 37.0 + - - -
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Residues in contact with ALA 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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12B LEU* 3.8 25.4 - - + -
16B LEU* 4.3 2.4 - - - +
43B CYS* 3.9 10.3 - - + -
44B ALA* 3.0 20.4 + - + +
46B GLY* 1.3 73.1 - - - +
48B ILE* 1.3 62.7 + - - +
50B THR* 3.5 7.8 - - - -
51B HIS* 2.9 33.5 + - + +
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Residues in contact with ILE 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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16B LEU* 3.9 23.3 - - + -
34B ALA* 3.2 36.6 - - + +
37B LEU* 3.6 22.7 - - + -
38B ALA* 3.7 8.3 - - + +
43B CYS* 4.6 7.0 - - - -
45B VAL 3.2 11.1 + - - +
47B ALA* 1.3 77.9 - - - +
49B TYR* 1.3 67.0 - - + +
51B HIS 3.2 2.6 + - - -
52B PHE* 2.9 43.7 + - + +
54B ASP 5.9 0.7 - - - +
55B LEU* 4.4 18.4 - - + -
58B LEU* 4.5 7.2 - - + -
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Residues in contact with TYR 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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34B ALA* 3.2 21.7 - - + +
45B VAL* 3.6 38.5 + - + -
46B GLY* 3.5 10.3 + - - +
48B ILE* 1.3 79.5 - - + +
50B THR* 1.3 60.9 + - - +
51B HIS 3.4 0.2 - - - -
52B PHE 3.2 18.2 - - - +
53B GLN* 3.6 22.5 + - - +
54B ASP* 3.8 19.5 - - + -
55B LEU* 4.0 18.5 - - + +
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Residues in contact with THR 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 GLY 2.8 21.6 + - - -
47B ALA* 3.5 13.0 - - - +
48B ILE 3.2 0.2 - - - -
49B TYR* 1.3 78.8 - - - +
51B HIS* 1.3 70.6 + - + +
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Residues in contact with HIS 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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10B ALA 5.7 4.2 + - - -
12B LEU* 4.2 26.4 - - + +
13B ARG* 3.8 46.4 + - + +
16B LEU* 4.4 7.1 - - - +
47B ALA* 2.9 23.5 + - + +
48B ILE 3.2 3.2 + - - +
50B THR* 1.3 91.5 - - + +
52B PHE* 1.3 85.2 + - + +
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Residues in contact with PHE 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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13B ARG* 3.6 42.0 - - + -
16B LEU* 3.7 21.3 - - + -
17B ILE* 3.7 6.1 - - + -
48B ILE* 2.9 24.8 + - + +
49B TYR* 3.2 25.1 - - - -
50B THR 3.7 0.2 - - - -
51B HIS* 1.3 92.4 - - + +
53B GLN* 1.3 65.7 + - - +
54B ASP 3.2 15.9 + - - +
57B ALA* 4.2 5.2 - - + -
58B LEU* 3.5 47.6 - - + +
61B GLU* 3.9 20.9 - - + -
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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