Contacts of the helix formed by residues 51 - 60 (chain I) in PDB entry 5XVO
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 THR 51 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50I THR* 1.3 71.1 - - - +
52I MET* 1.3 59.0 + - - +
54I LEU* 3.3 11.9 + - + +
55I LYS* 2.9 28.2 + - - +
42J LEU* 4.1 16.4 - - + -
44J THR 3.1 22.6 + - - +
45J THR* 3.1 8.5 - - - +
47J ILE* 2.7 51.8 + - + +
49J LEU* 4.0 22.2 - - + -
66J PHE* 5.1 3.6 - - + -
67J CYS 5.0 3.5 - - - +
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Residues in contact with MET 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I TYR* 3.8 29.6 - - + +
50I THR* 3.2 7.3 - - - +
51I THR* 1.3 74.7 - - - +
53I LEU* 1.3 65.8 + - - +
55I LYS* 3.1 14.6 + - + +
56I ARG* 3.0 49.5 + - + +
45J THR* 3.3 47.4 + - - +
69J ASP* 5.6 4.3 - - + +
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Residues in contact with LEU 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 3.6 28.9 - - + +
15I SER 3.8 16.2 - - - +
16I TYR* 3.8 25.5 - - + +
21I LEU* 3.3 39.9 - - + -
34I LEU* 4.9 3.4 - - + -
40I LEU* 5.3 0.7 - - + -
49I LEU* 4.6 7.9 - - + -
50I THR* 3.2 20.3 + - - +
52I MET* 1.3 80.2 - - - +
54I LEU* 1.3 58.5 + - + +
56I ARG* 3.1 2.3 + - - -
57I LEU* 2.8 52.6 + - + +
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Residues in contact with LEU 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LEU* 6.3 0.2 - - + -
49I LEU* 3.6 32.1 - - + -
50I THR 3.2 11.3 + - - +
51I THR* 3.6 16.2 - - + +
52I MET 3.2 0.2 - - - -
53I LEU* 1.3 81.2 - - + +
55I LYS* 1.3 62.3 + - - +
57I LEU* 3.3 18.0 + - + +
58I ILE* 3.0 32.1 + - + +
64I VAL* 4.8 6.1 - - + -
66I PHE* 5.1 4.0 - - + -
77I ILE* 3.6 24.7 - - + -
49J LEU* 4.8 4.9 - - + -
54J LEU* 5.6 2.2 - - + -
66J PHE* 3.5 40.2 - - + -
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Residues in contact with LYS 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I THR 2.9 13.7 + - - +
52I MET* 3.1 23.5 + - + +
54I LEU* 1.3 74.9 - - - +
56I ARG* 1.3 74.8 + - + +
58I ILE* 3.0 6.1 + - - +
59I ASP* 2.5 63.8 + - - +
45J THR* 4.5 6.7 - - + -
66J PHE* 6.2 0.6 - - - +
67J CYS 4.1 9.9 - - - +
68J ASP* 3.9 19.5 - - - +
69J ASP* 3.5 40.9 + - - +
74J ILE* 3.9 16.5 - - + +
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Residues in contact with ARG 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I TYR* 2.8 36.6 + - + -
19I ASN* 2.5 31.5 + - - +
34I LEU* 3.8 18.5 - - + +
52I MET* 3.0 41.4 + - + +
53I LEU 3.7 3.6 - - - +
55I LYS* 1.3 82.9 - - + +
57I LEU* 1.3 62.1 + - - +
59I ASP* 2.9 43.6 + - - +
60I GLU* 3.2 49.7 + - - +
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Residues in contact with LEU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I LEU* 5.2 2.0 - - + -
34I LEU* 4.5 9.4 - - + -
37I ILE* 5.2 5.2 - - + -
40I LEU* 3.6 30.3 - - + -
53I LEU* 2.8 42.5 + - + +
54I LEU* 3.6 19.5 - - + +
56I ARG* 1.3 79.1 - - - +
58I ILE* 1.3 60.5 + - + +
60I GLU 3.6 0.7 + - - -
61I LYS 3.3 2.8 + - - -
62I ILE* 3.2 65.4 + - + +
64I VAL* 3.9 20.4 - - + -
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Residues in contact with ILE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I LEU 3.0 20.4 + - - +
55I LYS 3.4 6.3 - - - +
57I LEU* 1.3 75.1 - - - +
59I ASP* 1.3 67.0 + - - +
61I LYS* 3.2 27.3 + - - +
62I ILE 5.4 1.3 - - - -
64I VAL* 6.1 0.7 - - + -
77I ILE* 3.7 35.7 - - + -
79I PRO* 3.9 25.4 - - + -
66J PHE* 4.2 19.7 - - + -
74J ILE* 3.9 41.3 - - + +
75J GLY* 4.6 4.5 - - - -
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Residues in contact with ASP 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LYS* 2.5 49.8 + - - +
56I ARG* 2.9 36.1 + - - +
58I ILE* 1.3 80.5 - - - +
60I GLU* 1.3 63.8 - - - +
61I LYS* 3.3 13.5 + - - +
68J ASP* 5.7 0.9 - - - +
74J ILE* 5.1 6.4 - - - +
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Residues in contact with GLU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 3.6 21.4 + - - +
19I ASN* 5.4 0.2 - - - -
34I LEU* 4.0 28.5 - - + +
35I SER* 4.8 13.4 + - - -
56I ARG* 3.2 43.3 + - - +
57I LEU 4.0 0.2 - - - +
59I ASP* 1.3 81.7 - - - +
61I LYS* 1.3 69.0 + - - +
62I ILE* 3.4 19.9 + - + -
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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