Contacts of the helix formed by residues 41 - 49 (chain B) in PDB entry 1WKJ
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 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B GLN* 3.5 5.6 + - - -
40B ILE* 1.3 80.4 - - - +
42B GLN* 1.3 66.2 + - - +
43B GLU* 3.3 20.5 - - - +
44B LEU* 3.2 26.7 + - - +
45B ALA* 2.9 20.8 + - - +
66B THR* 4.1 0.7 - - - -
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Residues in contact with GLN 42 (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 ILE 5.4 0.2 - - - +
41B SER* 1.3 74.2 - - - +
43B GLU* 1.3 69.2 + - - +
45B ALA* 3.4 1.9 + - - +
46B GLU* 3.1 40.7 + - - +
62B VAL* 3.2 29.1 - - - +
63B ARG* 4.9 2.8 - - - +
66B THR* 3.6 22.6 + - - -
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Residues in contact with GLU 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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41B SER* 3.3 17.9 - - - +
42B GLN* 1.3 88.6 + - - +
44B LEU* 1.3 70.6 + - + +
46B GLU* 3.2 11.9 + - - +
47B ARG* 3.0 34.5 + - + +
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Residues in contact with LEU 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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38B MET* 4.2 16.4 - - + -
39B GLN 5.4 0.4 - - - +
40B ILE* 4.0 20.4 - - + -
41B SER* 3.2 20.5 + - - +
43B GLU* 1.3 81.1 - - + +
45B ALA* 1.3 63.7 + - - +
47B ARG* 3.2 19.8 + - - +
48B HIS* 3.0 20.8 + - - +
129B LEU* 3.7 42.8 - - + +
130B PHE* 4.1 21.5 - - + -
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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 ILE* 3.6 6.9 - - + +
41B SER 2.9 18.1 + - - +
42B GLN 3.7 4.0 - - - +
44B LEU* 1.3 75.4 - - - +
46B GLU* 1.3 62.2 + - - +
48B HIS* 3.1 9.7 + - - +
49B TYR* 3.0 28.3 + - - -
62B VAL* 4.0 11.4 - - + -
65B ILE* 3.6 31.2 - - + -
66B THR* 3.7 9.6 - - + -
130B PHE* 5.9 0.2 - - - -
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Residues in contact with GLU 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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42B GLN* 3.1 32.8 + - - +
43B GLU* 3.2 8.8 + - - +
45B ALA* 1.3 76.1 - - - +
47B ARG* 1.3 58.6 + - + +
49B TYR 3.4 2.3 - - - -
50B ALA* 3.0 27.5 + - - +
58B PHE* 3.7 35.7 - - + -
62B VAL* 4.0 14.3 - - + +
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Residues in contact with ARG 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 GLU* 3.0 26.2 + - + +
44B LEU* 3.2 20.6 + - - +
46B GLU* 1.3 73.9 - - + +
48B HIS* 1.3 67.3 + - - +
50B ALA* 3.0 23.8 - - - +
125B ARG* 5.3 1.0 + - - -
129B LEU* 3.3 35.1 - - + +
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Residues in contact with HIS 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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7B MET* 5.7 3.9 - - + +
44B LEU 3.0 11.7 + - - +
45B ALA* 3.3 11.2 - - - +
47B ARG* 1.3 79.8 - - - +
49B TYR* 1.3 95.9 + + - +
50B ALA 3.3 2.1 + - - -
51B GLU* 4.2 10.7 - - - +
65B ILE* 5.6 4.0 - - + -
115B HIS* 4.6 15.6 + + - -
125B ARG* 3.4 25.1 + - - +
126B GLU* 3.7 33.2 - - + -
129B LEU* 3.7 14.2 - - + +
130B PHE* 3.7 30.2 - + + -
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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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9B LYS* 5.1 8.1 + - - -
45B ALA* 3.0 23.7 + - + +
46B GLU 3.4 4.0 - - - -
48B HIS* 1.3 101.2 + + - +
50B ALA* 1.3 63.9 + - - +
51B GLU* 3.2 3.6 - - - -
52B HIS* 2.9 30.3 + + + -
58B PHE* 3.0 27.8 - - + -
61B LEU* 3.7 59.7 + - + +
62B VAL* 4.3 8.7 - - + -
65B ILE* 3.9 33.7 - - + +
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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