Contacts of the helix formed by residues 51 - 60 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.3 15.7 - - + +
44C THR 3.0 16.7 + - - +
45C THR* 3.0 31.4 - - - +
47C ILE* 2.9 32.7 + - + +
49C LEU* 4.3 18.2 - - + -
66C PHE* 4.9 4.0 - - + -
67C CYS 5.0 5.0 - - - +
50D THR* 1.3 72.6 - - - +
52D MET* 1.3 59.6 + - - +
54D LEU* 3.6 13.8 - - + +
55D LYS* 2.9 27.9 + - - +
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Residues in contact with MET 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C THR* 3.4 42.1 + - - +
69C ASP* 5.5 6.3 - - + +
16D TYR* 3.9 17.9 - - + -
50D THR* 3.2 0.4 + - - -
51D THR* 1.3 74.2 - - - +
53D LEU* 1.3 65.4 + - - +
55D LYS* 3.1 18.1 + - + +
56D ARG* 3.0 49.1 + - + +
24G G 6.2 0.4 - - - -
-20R C 3.8 5.8 - - + +
-19R G 3.5 48.9 - - + +
-18R T 5.8 2.2 - - - -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.6 29.6 - - + +
15D SER 3.8 16.2 - - - +
16D TYR* 3.8 25.1 - - + +
21D LEU* 3.4 39.3 - - + -
34D LEU* 4.8 3.4 - - + -
49D LEU* 4.6 7.0 - - + -
50D THR* 3.1 21.1 + - - +
52D MET* 1.3 79.4 - - - +
54D LEU* 1.3 57.2 + - + +
56D ARG* 3.1 2.6 + - - -
57D LEU* 2.8 53.3 + - + +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 5.0 4.7 - - + -
54C LEU* 5.7 0.9 - - + -
66C PHE* 3.6 39.0 - - + -
49D LEU* 3.6 31.2 - - + -
50D THR 3.2 10.8 + - - +
51D THR* 3.6 16.4 - - + +
52D MET 3.2 0.4 - - - -
53D LEU* 1.3 78.0 - - + +
55D LYS* 1.3 65.4 + - - +
57D LEU* 3.6 18.0 - - + +
58D ILE* 3.0 32.1 + - + +
64D VAL* 4.8 7.0 - - + -
66D PHE* 5.1 4.9 - - + -
77D ILE* 3.6 25.1 - - + -
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C THR* 4.8 2.9 - - + -
67C CYS 4.7 5.2 - - - +
68C ASP* 4.2 13.7 - - + +
69C ASP* 3.7 35.0 - - - +
74C ILE* 4.0 28.0 - - + +
51D THR 2.9 14.4 + - - +
52D MET* 3.1 23.1 + - + +
54D LEU* 1.3 74.5 - - - +
56D ARG* 1.3 74.5 + - + +
58D ILE* 3.0 6.2 + - - +
59D ASP* 2.5 64.1 + - - +
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D TYR* 2.8 42.3 + - + -
19D ASN* 3.2 22.6 + - - -
34D LEU* 3.8 18.1 - - + +
52D MET* 3.0 40.9 + - + +
53D LEU 3.7 3.4 - - - +
55D LYS* 1.3 81.7 - - + +
57D LEU* 1.3 64.4 + - - +
59D ASP* 3.0 42.4 + - - +
60D GLU* 3.1 48.9 + - - +
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 5.3 1.3 - - + -
34D LEU* 3.9 14.1 - - + -
37D ILE* 5.3 3.6 - - + -
40D LEU* 3.6 30.3 - - + -
53D LEU* 2.8 37.9 + - + +
54D LEU* 3.6 19.1 - - + +
56D ARG* 1.3 78.8 - - - +
58D ILE* 1.3 51.1 + - + +
60D GLU 2.4 25.1 - - - +
62D ILE* 3.2 53.9 + - + +
64D VAL* 3.9 20.2 - - + -
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 4.8 13.2 - - + -
74C ILE* 4.0 40.8 - - + +
75C GLY* 4.8 1.6 - - - -
54D LEU 3.0 21.5 + - - +
55D LYS* 3.0 6.9 + - - +
57D LEU* 1.3 71.8 - - - +
59D ASP* 1.3 63.2 + - - +
60D GLU 2.9 13.7 - - - +
61D LYS* 4.3 6.2 - - - +
62D ILE 5.2 2.0 - - - +
64D VAL* 6.1 0.7 - - + -
77D ILE* 3.7 37.2 - - + -
79D PRO* 4.0 29.5 - - + +
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Residues in contact with ASP 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ILE* 5.8 1.9 - - - +
55D LYS* 2.5 51.5 + - - +
56D ARG* 3.0 34.7 + - - +
58D ILE* 1.3 77.6 - - - +
60D GLU* 1.3 66.2 + - - +
61D LYS* 3.8 13.2 + - - +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.0 25.6 - - + +
35D SER* 4.3 20.3 + - - -
56D ARG* 3.1 38.0 + - - +
57D LEU 2.4 24.4 - - - +
58D ILE 2.9 3.1 - - - +
59D ASP* 1.3 83.7 - - - +
61D LYS* 1.3 60.6 + - - +
62D ILE* 3.2 18.8 - - + -
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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