Contacts of the helix formed by residues 64 - 74 (chain A) in PDB entry 1X5S
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 ILE 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASP* 3.3 43.2 - - + +
12A GLU* 3.9 18.8 - - - +
13A GLY* 4.6 6.5 - - - -
63A ASN* 1.3 72.4 - - - +
65A ASP* 1.3 76.9 + - - +
66A ASP 3.0 1.3 - - - -
67A ALA* 2.7 16.8 + - - +
68A LYS* 3.1 12.2 + - + -
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Residues in contact with ASP 65 (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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63A ASN* 4.9 5.7 - - - +
64A ILE* 1.3 82.4 + - - +
66A ASP* 1.3 57.7 + - - +
68A LYS* 3.4 24.1 + - + +
69A ASP* 2.7 37.6 + - - +
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Residues in contact with ASP 66 (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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37A GLY* 5.2 0.2 - - - -
38A GLN* 4.5 11.1 + - + +
61A PHE* 3.0 21.1 - - + -
62A GLU* 3.3 23.9 - - - +
63A ASN* 2.6 52.9 + - - +
64A ILE 2.9 0.4 + - - -
65A ASP* 1.3 80.2 - - - +
67A ALA* 1.3 61.6 + - - +
69A ASP* 3.4 16.3 - - - +
70A ALA 3.7 1.6 + - - -
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Residues in contact with ALA 67 (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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11A ASP* 6.2 0.9 - - + -
13A GLY* 3.0 35.4 - - - +
15A LEU* 4.1 12.9 - - + +
61A PHE* 3.2 25.1 - - + -
63A ASN 3.5 0.6 + - - -
64A ILE 2.7 13.6 + - - +
66A ASP* 1.3 70.9 - - - +
68A LYS* 1.3 55.1 + - - +
69A ASP 2.9 3.6 - - - -
70A ALA* 2.6 29.5 + - - +
71A MET* 2.9 10.6 + - - +
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Residues in contact with LYS 68 (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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11A ASP* 3.5 32.2 + - + +
15A LEU* 4.8 1.2 - - - +
64A ILE* 3.1 7.5 + - + +
65A ASP* 3.4 29.8 + - - +
67A ALA* 1.3 77.8 - - - +
69A ASP* 1.3 70.5 + - - +
71A MET* 3.5 13.6 - - - +
72A MET* 3.2 34.9 + - + +
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Residues in contact with ASP 69 (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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36A TYR* 3.4 22.5 - - - +
37A GLY* 4.0 7.3 - - - -
65A ASP* 2.7 21.5 + - + +
66A ASP* 3.4 11.7 - - - +
67A ALA 2.8 0.2 + - - -
68A LYS* 1.3 85.5 - - + +
70A ALA* 1.3 58.2 + - - +
72A MET* 3.0 35.5 - - - +
73A ALA* 4.3 3.5 + - - +
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Residues in contact with ALA 70 (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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15A LEU* 4.9 1.3 - - + -
33A PHE* 4.5 10.3 - - + +
36A TYR* 3.9 24.9 - - + -
37A GLY 4.7 1.6 - - - +
61A PHE* 3.8 29.6 - - + -
66A ASP 3.7 0.4 + - - -
67A ALA 2.6 14.2 + - - +
69A ASP* 1.3 78.4 + - - +
71A MET* 1.3 56.5 + - - +
72A MET 3.3 0.9 - - - -
73A ALA* 2.9 7.3 + - - +
74A MET* 2.9 29.9 + - - +
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Residues in contact with MET 71 (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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11A ASP* 3.9 7.0 - - - +
15A LEU* 4.2 19.2 - - + +
67A ALA 2.9 9.7 + - - +
68A LYS* 3.2 13.7 + - - +
70A ALA* 1.3 72.8 - - - +
72A MET* 1.3 61.7 + - + +
73A ALA 2.8 5.2 + - - -
75A ASN* 2.7 45.3 + - + +
86A VAL* 3.9 20.2 - - + +
87A ASP* 3.4 15.7 - - - +
88A GLN* 2.9 51.8 - - - +
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Residues in contact with MET 72 (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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68A LYS* 3.2 22.2 + - + +
69A ASP* 3.0 34.3 - - - +
71A MET* 1.3 83.5 - - + +
73A ALA* 1.3 58.1 + - + +
75A ASN* 4.6 9.3 + - - +
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Residues in contact with ALA 73 (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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36A TYR* 3.2 40.2 - - + -
69A ASP 4.5 4.0 - - - +
70A ALA* 3.2 12.3 - - - +
71A MET 2.8 2.6 + - - -
72A MET* 1.3 84.6 - - + +
74A MET* 1.3 55.6 + - - +
75A ASN 4.4 2.8 - - - +
77A LYS* 2.6 37.2 - - - +
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Residues in contact with MET 74 (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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29A LEU* 5.3 1.8 - - + -
32A VAL* 4.0 17.5 - - + -
33A PHE* 3.1 48.7 - - + -
36A TYR* 3.5 31.2 - - + -
70A ALA 2.9 15.0 + - - +
73A ALA* 1.3 71.6 - - - +
75A ASN* 1.3 54.1 + - - +
76A GLY 2.5 21.0 + - - -
77A LYS* 2.5 31.7 + - + +
78A SER 6.5 0.2 - - - -
79A VAL* 4.7 10.3 - - + -
84A ILE* 4.2 23.2 - - + +
86A VAL* 3.3 26.9 - - + +
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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