Contacts of the helix formed by residues 55 - 67 (chain F) in PDB entry 5DNF
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 LYS 55 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F ALA 6.0 1.3 - - - -
52F ASN* 3.2 38.8 + - + +
54F GLU* 1.3 76.7 - - - +
56F LYS* 1.3 65.3 + - - +
57F TRP* 3.3 28.5 - - + +
58F VAL* 3.2 6.0 + - + +
59F ARG* 3.2 23.7 + - - +
102F SO4 3.5 29.7 + - - -
105F CL 3.8 11.1 - - + +
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Residues in contact with LYS 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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54F GLU 3.6 0.2 + - - -
55F LYS* 1.3 72.4 - - - +
57F TRP* 1.3 63.0 + - - +
58F VAL 3.3 0.2 + - - -
59F ARG* 3.3 27.5 + - - +
60F GLU* 3.0 55.4 + - + +
102F SO4 3.4 22.5 + - - +
105F CL 3.3 15.9 - - + +
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Residues in contact with TRP 57 (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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15F ILE* 4.0 29.1 + - + -
16F ALA 5.3 2.4 + - - -
18F PRO* 3.7 35.6 - - + +
19F LEU* 3.8 19.5 - - + -
41F PHE* 3.8 14.8 - + - -
51F ALA* 4.0 9.4 - - + -
52F ASN 5.5 0.4 - - - -
55F LYS* 3.7 28.7 - - + +
56F LYS* 1.3 78.9 - - - +
58F VAL* 1.3 72.7 + - + +
60F GLU* 3.9 10.9 - - - +
61F TYR* 3.0 76.3 + + + -
102F SO4 3.2 33.3 + - - +
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Residues in contact with VAL 58 (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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39F VAL* 3.9 25.4 - - + -
41F PHE* 3.7 19.1 - - + -
51F ALA* 3.8 9.9 - - + -
52F ASN 3.1 30.3 - - - +
53F PRO* 4.4 3.6 - - + +
55F LYS* 3.2 10.1 + - + +
56F LYS 3.2 0.4 - - - -
57F TRP* 1.3 110.0 - - + +
59F ARG* 1.3 65.7 + - - +
61F TYR* 3.3 2.9 + - - +
62F ILE* 3.0 25.9 + - + +
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Residues in contact with ARG 59 (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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17D ARG* 4.3 17.0 - - - +
23D HIS* 5.1 0.9 - - - -
53F PRO 3.4 19.3 - - - +
54F GLU* 2.5 32.9 + - - +
55F LYS 3.2 15.0 + - - +
56F LYS* 3.8 32.8 - - - +
58F VAL* 1.3 76.8 - - + +
60F GLU* 1.3 58.8 + - + +
62F ILE* 3.5 10.3 + - + +
63F ASN* 2.9 29.5 + - - +
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Residues in contact with GLU 60 (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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56F LYS* 3.0 56.7 + - + +
57F TRP* 3.9 10.2 - - - +
59F ARG* 1.3 77.3 - - + +
61F TYR* 1.3 64.5 + - + +
63F ASN* 3.4 6.5 + - - +
64F SER* 2.8 29.8 + - - -
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Residues in contact with TYR 61 (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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18F PRO* 4.9 4.0 - - - +
19F LEU* 2.6 29.6 + - + -
20F PRO* 4.4 0.2 - - - +
21F ARG* 3.3 44.2 + - + +
24F ILE* 4.1 20.0 - - + -
41F PHE* 3.7 16.2 - + + -
57F TRP* 3.0 59.3 + + + +
58F VAL 3.6 4.9 - - - +
60F GLU* 1.3 82.0 - - + +
62F ILE* 1.3 57.3 + - - +
64F SER* 3.2 7.6 + - - -
65F LEU* 2.8 36.3 + - + +
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Residues in contact with ILE 62 (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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17D ARG* 6.0 0.9 - - - +
20D PRO* 5.1 0.9 - - + -
23D HIS* 3.6 20.0 - - + +
27F TYR* 3.6 39.5 - - + +
29F TYR* 3.9 17.9 - - + +
39F VAL* 3.7 39.5 - - + -
41F PHE* 4.2 3.8 - - + -
53F PRO 6.1 0.2 - - - +
58F VAL* 3.0 20.2 + - + +
59F ARG* 3.7 8.3 - - + +
61F TYR* 1.3 76.5 - - - +
63F ASN* 1.3 57.5 + - - +
65F LEU* 3.0 10.8 + - - +
66F GLU* 2.9 27.9 + - - +
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Residues in contact with ASN 63 (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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20D PRO* 5.4 2.2 - - - +
22D ALA* 5.7 1.8 - - - +
23D HIS* 3.0 31.9 + - + +
59F ARG 2.9 18.3 + - - +
60F GLU* 3.7 7.6 - - - +
62F ILE* 1.3 76.1 - - - +
64F SER* 1.3 62.1 + - - +
67F MET* 3.0 39.2 + - - +
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Residues in contact with SER 64 (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 ARG* 3.0 31.3 + - - -
60F GLU 2.8 18.1 + - - -
61F TYR* 3.3 7.0 - - - -
63F ASN* 1.3 77.9 - - - +
65F LEU* 1.3 60.8 + - - +
67F MET 3.2 20.6 - - - +
68F SER* 3.8 7.3 - - - -
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Residues in contact with LEU 65 (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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45D LYS* 3.2 16.6 - - + +
21F ARG* 3.4 29.6 - - - +
24F ILE* 3.9 24.9 - - + +
25F LYS 4.6 12.8 - - - +
26F GLU* 4.1 1.1 - - - -
27F TYR* 3.7 46.9 - - + +
41F PHE* 4.4 5.2 - - + -
61F TYR* 2.8 17.5 + - + +
62F ILE 3.0 6.7 + - - +
64F SER* 1.3 77.7 - - - +
66F GLU* 1.3 57.3 + - - +
68F SER* 3.1 18.3 + - - -
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Residues in contact with GLU 66 (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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23D HIS* 3.4 39.0 - - + +
43D THR* 2.7 25.1 + - - -
44D ARG* 2.8 41.5 + - - +
45D LYS* 2.9 44.7 + - - +
47D ARG* 3.3 3.3 - - - +
27F TYR* 2.7 33.3 + - + +
62F ILE 2.9 14.7 + - - +
63F ASN 4.2 0.9 - - - +
65F LEU* 1.3 76.6 - - - +
67F MET* 1.3 57.6 + - - +
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Residues in contact with MET 67 (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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22D ALA* 3.2 36.8 - - + +
23D HIS* 3.4 21.8 - - + +
44D ARG* 3.6 26.9 - - - +
63F ASN* 3.0 32.9 + - - +
64F SER* 3.2 12.5 - - - +
66F GLU* 1.3 77.5 - - + +
68F SER* 1.3 61.8 + - - +
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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