Contacts of the helix formed by residues 51 - 59 (chain A) in PDB entry 5FNA
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 ASP 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.1 28.3 - - + +
46A ASN* 2.5 26.7 + - - +
47A ALA* 3.6 4.7 - - - +
48A THR* 2.8 11.9 + - - -
50A MET* 1.3 77.3 - - - +
52A LYS* 1.3 52.6 + - - +
53A THR* 2.7 2.7 - - - -
54A ARG* 2.4 66.4 + - + +
37B GLU* 4.3 4.0 - - - +
41B LYS* 3.1 26.9 + - - -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 6.4 0.2 - - + -
21A ILE* 5.4 13.2 - - + -
22A ASN* 5.3 8.1 + - - +
25A LEU* 5.6 4.5 - - + -
42A VAL* 3.6 46.8 - - + +
43A LYS* 4.3 16.5 - - - +
45A GLU* 3.6 27.8 - - + -
49A VAL* 2.5 52.9 + - + +
50A MET 2.4 3.0 + - - -
51A ASP* 1.3 78.8 - - - +
53A THR* 1.3 55.4 + - - +
54A ARG 3.1 0.2 - - - -
55A ALA* 2.9 7.7 + - - +
56A LEU* 2.8 29.9 + - + +
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.3 39.6 + - - +
16A MET* 3.8 37.5 - - + +
21A ILE* 3.8 14.8 - - + -
50A MET* 2.6 20.9 + - + +
51A ASP* 3.6 2.9 + - - -
52A LYS* 1.3 79.2 - - - +
54A ARG* 1.3 61.9 + - - +
56A LEU* 3.2 11.9 + - + +
57A ILE* 3.1 26.5 + - - +
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.6 12.0 - - + +
45A GLU* 4.7 9.9 - - - +
51A ASP* 2.4 56.8 + - + +
53A THR* 1.3 76.3 + - - +
55A ALA* 1.3 58.9 + - - +
57A ILE* 3.3 15.1 + - + +
58A ASP* 3.1 27.4 + - - +
37B GLU* 3.3 22.4 + - - -
41B LYS* 4.6 2.8 - - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.2 21.8 - - + -
45A GLU* 3.8 16.9 + - - +
51A ASP 3.8 0.4 + - - -
52A LYS 2.9 12.4 + - - +
54A ARG* 1.3 75.5 - - - +
56A LEU* 1.3 59.8 + - + +
58A ASP* 3.1 14.0 + - - +
59A SER* 2.9 27.8 + - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 3.8 30.1 - - + -
21A ILE* 4.0 23.3 - - + -
24A LEU* 4.4 17.9 - - + -
25A LEU* 4.0 27.4 - - + -
28A LEU* 4.9 4.9 - - + -
34A LEU* 6.0 0.4 - - + -
52A LYS* 2.8 15.1 + - + +
53A THR* 3.2 18.4 + - - +
55A ALA* 1.3 73.0 - - + +
57A ILE* 1.3 65.9 + - + +
59A SER* 2.6 26.6 + - - +
60A VAL* 3.2 13.5 + - - +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 6.5 0.4 - - + -
10A LYS* 3.7 47.6 - - + +
13A ILE* 3.8 20.6 - - + -
53A THR 3.1 16.5 + - - +
54A ARG* 3.4 13.5 - - + +
55A ALA 3.2 0.2 - - - -
56A LEU* 1.3 76.6 - - + +
58A ASP* 1.3 68.9 + - - +
60A VAL* 2.9 30.0 + - + +
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG* 3.1 14.3 + - - +
55A ALA* 3.1 15.0 + - - +
57A ILE* 1.3 83.0 - - - +
59A SER* 1.3 58.0 + - - +
60A VAL 3.0 12.8 + - - +
61A ILE* 3.8 10.1 + - - +
62A PRO* 5.0 2.6 - - - +
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 5.1 3.2 - - - +
33A VAL* 5.4 5.2 - - - +
34A LEU* 4.2 31.6 - - - +
55A ALA 2.9 10.9 + - - -
56A LEU* 2.6 35.0 + - - +
58A ASP* 1.3 72.6 - - - +
60A VAL* 1.3 59.7 + - - +
61A ILE* 3.1 20.4 + - - +
64A GLY 5.6 0.9 - - - +
68A CYS* 4.5 6.1 - - - -
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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