Contacts of the helix formed by residues 39 - 47 (chain F) in PDB entry 6I5J
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 39 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F ALA 3.2 9.6 + - - +
37F LEU 3.1 8.7 - - - +
38F THR* 1.3 78.0 - - - +
40F GLY* 1.3 62.1 + - - +
42F ILE* 3.1 22.3 + - - +
43F LYS* 3.4 14.7 + - - +
77F PHE* 3.8 25.0 - - - -
110F LEU* 2.7 35.0 + - - +
111F ASP 3.8 3.4 - - - -
112F CYS* 4.0 3.6 - - - -
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Residues in contact with GLY 40 (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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37F LEU 4.9 1.3 - - - -
38F THR 3.5 2.8 + - - -
39F SER* 1.3 70.7 - - - +
41F THR* 1.3 64.2 + - - +
43F LYS* 3.4 13.2 + - - +
44F ALA* 3.3 19.4 + - - +
110F LEU 4.1 0.2 - - - -
111F ASP* 3.2 25.9 + - - -
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Residues in contact with THR 41 (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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40F GLY* 1.3 75.2 - - - +
42F ILE* 1.3 65.5 + - - +
44F ALA* 3.2 9.3 + - + +
45F MET* 3.1 39.0 + - + +
109F PHE* 2.8 43.0 + - + +
110F LEU* 3.1 21.2 + - + -
111F ASP* 4.0 5.8 + - - +
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Residues in contact with ILE 42 (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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21F LEU* 3.9 34.8 - - + -
36F ALA* 3.6 32.3 - - + +
37F LEU* 4.9 0.2 - - + -
39F SER* 3.1 22.4 + - - +
41F THR* 1.3 76.1 - - - +
43F LYS* 1.3 63.7 + - - +
45F MET* 3.2 8.3 + - - +
46F LEU* 3.0 45.8 + - + +
60F VAL* 4.4 7.4 - - + -
62F PHE* 3.8 24.2 - - + -
70F LEU* 6.1 0.4 - - + -
77F PHE* 4.2 8.7 - - + -
110F LEU* 4.2 7.2 - - + -
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Residues in contact with LYS 43 (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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16C MET* 6.1 3.4 - - - +
17C MET 6.4 0.4 - - - +
37F LEU* 3.8 31.6 - - + +
39F SER 3.4 10.2 + - - +
40F GLY* 3.6 13.5 - - - +
41F THR 3.2 0.6 - - - -
42F ILE* 1.3 79.6 - - - +
44F ALA* 1.3 58.7 + - + +
46F LEU* 4.6 1.3 - - - +
47F SER* 2.9 38.0 + - - +
48F GLY 3.3 25.5 + - - -
49F PRO* 4.8 1.0 - - - +
50F GLY 3.1 29.0 + - - +
51F GLN* 4.9 5.7 - - - +
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Residues in contact with ALA 44 (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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40F GLY 3.3 8.9 + - - +
41F THR* 3.2 12.6 + - + +
43F LYS* 1.3 82.0 - - + +
45F MET* 1.3 61.2 + - + +
48F GLY* 3.2 34.1 + - - +
49F PRO* 5.1 2.3 - - + +
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Residues in contact with MET 45 (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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41F THR* 3.1 34.4 + - + +
42F ILE* 3.2 7.1 + - - +
44F ALA* 1.3 79.8 - - + +
46F LEU* 1.3 62.2 + - - +
57F THR* 3.8 9.7 + - - -
59F GLU 5.6 0.3 - - - +
60F VAL* 3.7 35.7 - - + -
61F ASN 4.8 8.5 - - - +
62F PHE* 4.3 13.9 - - + -
109F PHE* 5.4 6.7 - - + -
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Residues in contact with LEU 46 (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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19F VAL* 4.2 16.2 - - + -
33F ARG* 3.8 27.6 - - + +
36F ALA* 5.2 0.9 - - + -
37F LEU* 4.4 11.0 - - + -
42F ILE* 3.0 37.1 + - + +
43F LYS* 4.1 2.2 - - - +
45F MET* 1.3 80.7 - - - +
47F SER* 1.3 62.2 + - - +
55F ASN 4.4 0.3 - - - +
56F GLU* 3.4 6.8 - - - -
57F THR* 3.3 50.1 + - - +
58F ASN* 4.3 0.9 - - - -
59F GLU 3.9 12.6 - - - +
60F VAL* 3.5 24.9 - - + -
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Residues in contact with SER 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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16C MET* 3.5 39.4 + - - -
33F ARG* 3.5 12.8 + - - -
37F LEU* 5.3 2.6 - - - +
43F LYS* 2.9 25.4 + - - +
44F ALA 4.3 0.2 - - - -
46F LEU* 1.3 75.6 - - - +
48F GLY* 1.3 60.0 + - - +
50F GLY 6.0 0.4 - - - -
53F ALA* 3.3 24.8 - - - +
55F ASN 4.0 4.2 - - - +
56F GLU* 4.4 7.6 - - - -
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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