Contacts of the helix formed by residues 50 - 60 (chain E) in PDB entry 1RBO
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 PRO 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E PRO* 4.7 5.4 - - + -
48E VAL 3.6 3.3 - - - +
49E PRO* 1.3 85.1 - - + +
51E GLU* 1.3 72.1 + - - +
53E ALA* 3.7 7.1 - - + +
54E GLY* 2.9 25.8 + - - -
87E ILE* 3.7 18.0 - - + +
95E ASN* 5.6 0.9 - - - +
97E TYR* 3.8 54.7 - - + +
99E CYS* 4.4 3.4 - - - -
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Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LYS* 4.0 16.7 - - + +
25E TYR* 3.6 46.7 + - + +
49E PRO* 3.6 17.7 - - - +
50E PRO* 1.3 91.0 - - - +
52E GLU* 1.3 58.1 + - - +
54E GLY* 4.2 0.2 - - - -
55E ALA* 3.1 28.1 + - - +
87E ILE* 3.7 13.3 - - + +
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Residues in contact with GLU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ASP* 3.5 16.3 - - - +
20E TYR* 2.9 35.6 + - + -
21E LYS* 2.9 42.2 + - - +
48E VAL* 4.5 10.1 - - + -
49E PRO* 3.0 28.0 + - + +
51E GLU* 1.3 79.0 - - - +
53E ALA* 1.3 59.8 + - - +
55E ALA* 3.3 1.7 + - - +
56E ALA* 2.8 31.7 + - + +
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 4.1 12.3 - - + -
44E PRO* 4.1 17.7 - - + -
48E VAL* 4.1 8.7 - - + +
49E PRO 3.0 11.9 + - - +
50E PRO 3.7 7.2 - - - +
52E GLU* 1.3 77.8 - - - +
54E GLY* 1.3 62.7 + - - +
56E ALA* 3.2 7.8 + - - +
57E VAL* 3.0 28.6 + - - +
129E ALA* 6.4 0.2 - - - -
130E LEU* 3.8 24.7 - - + +
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Residues in contact with GLY 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 5.3 0.7 - - - -
50E PRO 2.9 16.3 + - - -
53E ALA* 1.3 76.2 - - - +
55E ALA* 1.3 56.8 + - - +
57E VAL* 3.3 8.3 + - - +
58E ALA* 3.0 27.9 + - - +
84E CYS* 3.7 17.3 - - - +
99E CYS* 4.0 24.4 - - - -
101E VAL* 4.5 2.3 - - - +
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Residues in contact with ALA 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR* 3.6 7.2 - - - +
21E LYS* 3.5 32.3 - - - +
24E TYR* 3.5 20.0 - - + +
25E TYR* 4.0 6.1 - - + +
51E GLU 3.1 21.2 + - - +
52E GLU 3.6 3.4 - - - +
53E ALA 3.3 0.2 - - - -
54E GLY* 1.3 74.5 - - - +
56E ALA* 1.3 59.3 + - - +
58E ALA* 3.3 0.6 + - - -
59E ALA* 2.9 30.8 + - - +
84E CYS* 4.2 1.9 - - - +
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Residues in contact with ALA 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR* 3.6 31.8 - - + +
52E GLU* 2.8 19.1 + - + +
53E ALA* 3.2 8.3 + - - +
55E ALA* 1.3 75.4 - - - +
57E VAL* 1.3 64.5 + - + +
59E ALA* 3.8 0.2 - - - +
60E GLU* 3.0 30.0 + - - +
127E PHE* 3.6 18.5 - - + -
130E LEU* 6.0 1.8 - - + -
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Residues in contact with VAL 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PHE* 3.7 44.2 - - + -
42E VAL* 4.9 4.9 - - + -
53E ALA 3.0 19.6 + - - +
54E GLY* 3.6 10.5 - - - +
56E ALA* 1.3 76.1 - - - +
58E ALA* 1.3 56.2 + - - +
61E SER* 2.7 35.7 + - - +
99E CYS* 6.4 0.7 - - + -
101E VAL* 4.6 3.1 - - + -
124E VAL* 3.4 17.6 - - + +
127E PHE* 4.7 1.8 - - + -
130E LEU* 4.0 26.2 - - + -
133E LEU* 4.3 14.6 - - + -
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Residues in contact with ALA 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E TYR* 4.2 6.3 - - + +
54E GLY 3.0 16.3 + - - +
55E ALA 3.7 3.8 - - - +
56E ALA 3.3 0.2 - - - -
57E VAL* 1.3 77.6 - - - +
59E ALA* 1.3 53.0 + - - +
61E SER* 3.5 5.8 + - - -
62E SER* 2.7 35.0 + - - -
82E GLY* 3.9 12.1 - - - +
84E CYS 3.8 18.4 - - - +
101E VAL* 3.7 27.6 - - + -
103E TYR* 4.6 0.3 - - - -
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Residues in contact with ALA 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR* 3.4 30.5 - - + -
24E TYR* 3.5 32.7 - - + -
55E ALA 2.9 17.5 + - - +
56E ALA 3.8 0.7 - - - +
58E ALA* 1.3 76.1 - - - +
60E GLU* 1.3 62.5 + - - +
62E SER 3.1 10.0 + - - -
63E THR 3.2 1.2 + - - -
64E GLY* 2.9 25.4 + - - +
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E TYR* 5.1 3.5 + - + +
56E ALA 3.0 15.6 + - - +
59E ALA* 1.3 79.4 - - + +
61E SER* 1.3 57.3 + - - +
62E SER 3.3 2.2 + - - -
64E GLY 3.9 15.2 - - - +
65E THR* 4.7 8.0 + - - -
66E TRP 5.6 0.2 + - - -
123E ASN* 3.2 42.4 + - + +
124E VAL* 3.7 12.8 - - + +
127E PHE* 3.4 32.8 - - + -
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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