Contacts of the helix formed by residues 45 - 56 (chain F) in PDB entry 3X0X
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 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F ARG* 4.8 0.7 - - - -
43F GLY 3.9 0.6 + - - -
44F SER* 1.3 71.0 - - - +
46F THR* 1.3 52.8 + - - +
47F ALA 3.3 3.1 - - - -
48F GLU* 3.3 18.3 + - - +
49F ARG* 2.7 44.8 + - + +
90F LEU* 4.0 23.6 - - + -
212F GLN* 3.5 35.9 + - + +
214F ASP* 4.9 0.2 + - - -
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Residues in contact with THR 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F SER* 3.3 23.5 + - - -
45F ALA* 1.3 70.1 - - - +
47F ALA* 1.3 69.6 + - - +
48F GLU* 4.1 0.2 + - - -
49F ARG* 3.9 9.9 - - + +
50F GLU* 3.1 22.5 + - - +
166F LYS* 6.1 1.6 - - - +
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Residues in contact with ALA 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ALA 3.3 0.4 - - - -
46F THR* 1.3 81.7 - - - +
48F GLU* 1.3 76.7 + - + +
50F GLU* 3.1 12.4 + - - +
51F ASP* 3.3 18.0 + - - +
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Residues in contact with GLU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F TRP* 3.6 38.2 - - + +
34F THR* 3.5 6.8 + - - +
38F ARG* 3.0 42.9 + - - +
45F ALA* 3.5 24.4 - - - +
46F THR 4.1 0.2 + - - -
47F ALA* 1.3 84.1 - - - +
49F ARG* 1.3 64.2 + - - +
51F ASP* 3.3 5.8 + - - +
52F LEU* 3.1 23.6 + - - +
90F LEU* 3.6 25.1 - - + -
212F GLN* 5.7 0.2 + - - -
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Residues in contact with ARG 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F SER* 5.4 2.7 - - - -
45F ALA* 2.7 42.2 + - + +
46F THR* 3.9 10.2 - - + +
47F ALA 3.4 0.2 - - - -
48F GLU* 1.3 72.0 - - - +
50F GLU* 1.3 57.2 + - - +
52F LEU* 3.6 1.1 + - - -
53F ARG* 3.2 16.7 + - - +
90F LEU* 4.5 1.6 - - + -
93F LEU* 3.6 35.4 - - + +
126F TRP* 3.0 64.5 + - + +
164F GLY* 4.7 5.7 + - - -
166F LYS 3.0 22.9 + - - -
167F GLY* 2.8 35.2 + - - -
168F SER* 3.9 0.4 - - - +
212F GLN 5.8 0.2 - - - -
214F ASP* 3.3 18.4 + - - -
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F THR 3.1 13.4 + - - +
47F ALA* 3.4 9.9 - - - +
48F GLU 3.1 0.2 - - - -
49F ARG* 1.3 74.5 - - - +
51F ASP* 1.3 61.3 + - - +
52F LEU 3.3 1.1 - - - -
53F ARG* 3.2 39.2 + - - +
54F ALA* 2.9 32.8 + - + +
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Residues in contact with ASP 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LEU* 3.8 20.9 - - + +
30F LYS* 2.9 34.8 + - - -
31F TRP* 3.2 14.7 + - - +
47F ALA* 3.3 14.7 + - - +
48F GLU* 3.3 6.9 + - - +
50F GLU* 1.3 71.7 - - - +
52F LEU* 1.3 57.4 + - - +
54F ALA* 3.8 6.1 - - - +
55F SER* 2.7 36.2 + - - -
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F LEU* 3.9 17.7 - - + +
31F TRP* 4.0 24.5 - - + -
48F GLU 3.1 11.0 + - - +
49F ARG 3.6 9.2 - - - +
51F ASP* 1.3 76.7 - - - +
53F ARG* 1.3 61.2 + - - +
55F SER* 2.6 25.5 + - - +
56F GLY 3.5 2.6 + - - -
57F LEU* 4.0 13.8 + - + -
58F LEU* 4.2 7.8 - - + +
83F ILE* 4.3 11.7 - - + -
90F LEU* 5.0 12.3 - - + +
94F PHE* 4.0 32.5 - - + -
126F TRP* 3.9 28.3 - - + -
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Residues in contact with ARG 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ARG* 3.2 12.8 + - - +
50F GLU* 3.2 36.0 + - - +
52F LEU* 1.3 78.9 - - - +
54F ALA* 1.3 62.0 + - - +
56F GLY* 3.2 14.7 + - - -
58F LEU* 3.8 15.3 - - + +
123F ASN 4.8 4.2 + - - -
124F ASN* 3.2 52.6 + - + +
125F TRP* 4.4 0.8 - - - +
126F TRP* 3.6 21.6 - - - +
167F GLY 4.5 7.5 + - - -
169F ASP* 3.1 29.3 + - - -
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Residues in contact with ALA 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLU* 2.9 23.2 + - + +
51F ASP* 3.3 7.8 + - - +
53F ARG* 1.3 77.5 - - - +
55F SER* 1.3 61.0 + - - +
56F GLY* 3.2 1.9 + - - -
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Residues in contact with SER 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F VAL* 3.9 26.1 - - - +
27F LEU* 3.9 22.9 - - - -
51F ASP 2.7 19.4 + - - -
52F LEU* 2.6 17.3 + - - -
54F ALA* 1.3 72.1 - - - +
56F GLY* 1.3 54.9 + - - +
57F LEU* 3.0 22.2 + - - +
69F TRP* 4.0 7.6 - - - -
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Residues in contact with GLY 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU 3.5 0.2 + - - -
53F ARG 3.2 15.8 + - - -
54F ALA 3.2 2.3 + - - -
55F SER* 1.3 76.5 + - - +
57F LEU* 1.3 55.5 + - - +
58F LEU 2.9 12.5 + - - -
59F SER* 3.2 13.2 + - - -
69F TRP* 3.0 24.5 + - - -
124F ASN* 4.0 14.3 - - - +
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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