Contacts of the helix formed by residues 51 - 61 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50K THR* 1.3 72.4 - - - +
52K MET* 1.3 60.3 + - - +
53K LEU 3.3 0.2 - - - -
54K LEU* 3.6 8.6 - - + +
55K LYS* 2.9 27.5 + - - +
42L LEU* 4.5 17.6 - - + +
44L THR 3.1 24.9 + - - +
45L THR* 3.8 6.2 + - - +
47L ILE* 2.8 35.0 + - - +
49L LEU* 4.8 6.2 - - + +
66L PHE* 4.8 15.5 - - + -
67L CYS 4.2 13.7 - - - +
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Residues in contact with MET 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K TYR* 3.8 28.9 - - + +
50K THR* 3.3 7.1 + - - +
51K THR* 1.3 76.2 - - - +
53K LEU* 1.3 66.5 + - - +
55K LYS* 3.1 12.8 + - - +
56K ARG* 3.0 29.1 + - - +
45L THR* 3.1 47.1 + - - +
69L ASP* 3.8 20.9 - - - +
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Residues in contact with LEU 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K LEU* 3.6 27.1 - - + +
15K SER 3.8 15.7 - - - +
16K TYR* 3.8 24.6 - - + +
21K LEU* 3.3 40.4 - - + -
34K LEU* 4.9 3.4 - - + -
40K LEU* 5.3 0.2 - - + -
49K LEU* 4.6 10.3 - - + -
50K THR* 3.2 20.5 + - - +
52K MET* 1.3 79.4 - - - +
54K LEU* 1.3 58.0 + - + +
56K ARG* 3.2 2.6 + - - -
57K LEU* 2.8 53.8 + - + +
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Residues in contact with LEU 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K LEU* 3.7 28.3 - - + -
50K THR 3.2 14.4 + - - +
51K THR* 3.6 12.6 - - + +
53K LEU* 1.3 75.4 - - - +
55K LYS* 1.3 66.8 + - - +
57K LEU* 3.4 16.1 + - + +
58K ILE* 3.0 32.1 + - + +
64K VAL* 4.8 5.4 - - + -
66K PHE* 5.1 2.2 - - + -
77K ILE* 3.6 25.1 - - + -
49L LEU* 4.9 14.8 - - + -
54L LEU* 5.6 2.9 - - + -
66L PHE* 3.5 39.7 - - + -
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Residues in contact with LYS 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K THR* 2.9 14.8 + - - +
52K MET* 3.1 14.3 + - - +
54K LEU* 1.3 74.6 - - - +
56K ARG* 1.3 73.3 + - + +
58K ILE* 3.0 6.1 + - - +
59K ASP* 2.5 63.8 + - - +
45L THR* 4.6 1.6 - - + -
66L PHE* 6.2 0.6 - - - +
67L CYS 4.1 6.7 - - - +
68L ASP* 3.9 14.8 - - + +
69L ASP* 3.5 45.5 + - - +
74L ILE* 3.7 26.8 - - + +
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Residues in contact with ARG 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K TYR* 2.8 41.3 + - + -
19K ASN* 3.2 22.2 + - - +
34K LEU* 3.8 21.9 - - + +
52K MET* 3.0 24.4 + - - +
53K LEU 3.7 3.4 - - - +
55K LYS* 1.3 91.6 - - + +
57K LEU* 1.3 60.4 + - - +
59K ASP* 3.0 43.2 + - - +
60K GLU* 3.2 50.7 + - - +
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Residues in contact with LEU 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K LEU* 5.2 1.3 - - + -
34K LEU* 4.6 8.3 - - + -
37K ILE* 5.2 6.1 - - + -
40K LEU* 3.6 31.2 - - + -
49K LEU* 5.6 0.4 - - + -
53K LEU* 2.8 42.5 + - + +
54K LEU* 3.6 19.3 - - + +
55K LYS 3.3 0.2 - - - -
56K ARG* 1.3 76.6 - - - +
58K ILE* 1.3 63.4 + - + +
60K GLU 3.6 0.7 + - - -
61K LYS 3.2 3.3 + - - -
62K ILE* 3.2 65.6 + - + +
64K VAL* 3.9 20.0 - - + -
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Residues in contact with ILE 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K LEU 3.0 23.2 + - - +
55K LYS 3.4 6.7 - - - +
57K LEU* 1.3 76.7 - - - +
59K ASP* 1.3 61.1 + - - +
61K LYS* 2.8 40.5 + - - +
62K ILE 5.4 1.3 - - - -
64K VAL* 6.1 0.7 - - + -
77K ILE* 3.8 36.3 - - + -
79K PRO* 3.9 19.3 - - + -
66L PHE* 4.3 17.3 - - + -
74L ILE* 3.9 45.8 - - + +
75L GLY* 4.5 4.5 - - - -
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Residues in contact with ASP 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K LYS* 2.5 53.9 + - - +
56K ARG* 3.0 33.9 + - - +
58K ILE* 1.3 79.6 - - - +
60K GLU* 1.3 65.0 + - - +
61K LYS* 3.3 15.2 + - - +
68L ASP* 5.8 0.5 - - - +
74L ILE* 5.2 5.9 - - - +
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Residues in contact with GLU 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 3.6 22.4 + - + +
34K LEU* 4.0 27.8 - - + +
35K SER* 4.8 13.0 - - - -
56K ARG* 3.2 41.4 + - - +
57K LEU 4.0 0.2 - - - +
59K ASP* 1.3 81.2 - - - +
61K LYS* 1.3 68.9 + - - +
62K ILE* 3.4 20.1 + - + -
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Residues in contact with LYS 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 3.6 9.5 - - + +
57K LEU 3.2 1.2 + - - -
58K ILE* 2.8 42.5 + - - +
59K ASP* 3.8 11.0 + - - +
60K GLU* 1.3 80.2 - - - +
62K ILE* 1.3 62.6 + - - +
79K PRO* 3.9 23.2 - - + +
81K TYR* 3.8 15.4 - - - +
82K GLY* 3.5 32.9 - - - +
83K ARG 4.1 26.7 - - - +
84K HIS* 3.2 26.3 - - - +
74L ILE 5.4 0.6 + - - -
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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