Contacts of the helix formed by residues 50 - 60 (chain E) in PDB entry 1RTA
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 SER 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E MET* 4.2 0.2 - - - -
15E SER* 3.1 15.5 + - - -
49E GLU* 1.3 79.6 + - - +
51E LEU* 1.3 59.1 + - - +
52E ALA* 3.3 18.9 + - - +
53E ASP* 3.2 20.7 + - - +
54E VAL* 3.0 27.0 + - - +
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Residues in contact with LEU 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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8E PHE* 6.0 3.1 - - + -
9E GLU* 3.2 46.0 - - + +
13E MET* 3.6 24.4 - - + +
15E SER* 4.2 1.0 + - - -
49E GLU 3.5 3.2 + - - -
50E SER* 1.3 69.4 + - - +
52E ALA* 1.4 61.7 + - - +
54E VAL* 2.7 28.2 + - + +
55E GLN* 2.8 47.7 + - - +
117E PRO* 6.1 0.7 - - + -
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Residues in contact with ALA 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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50E SER* 3.3 12.2 + - - +
51E LEU* 1.4 83.1 - - - +
53E ASP* 1.3 63.9 + - - +
55E GLN* 3.2 21.2 - - - +
56E ALA* 3.3 10.2 + - - +
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Residues in contact with ASP 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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49E GLU* 4.5 14.1 - - + -
50E SER* 3.2 23.3 + - - +
51E LEU 3.1 0.6 - - - -
52E ALA* 1.3 78.8 - - - +
54E VAL* 1.3 59.8 + - - +
56E ALA* 2.9 28.1 - - + +
57E VAL* 3.8 4.3 + - - +
60E GLN* 4.6 2.4 + - - -
79E MET* 4.9 6.1 - - - +
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Residues in contact with VAL 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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8E PHE* 4.2 19.1 - - + -
13E MET* 3.9 20.4 - - - -
47E VAL* 4.0 9.6 - - + -
49E GLU* 3.8 11.0 - - + -
50E SER 3.0 14.5 + - - +
51E LEU* 2.7 15.7 + - + +
53E ASP* 1.3 67.1 - - - +
55E GLN* 1.4 57.1 + - - +
56E ALA 3.0 4.5 - - - -
57E VAL* 2.4 38.8 + - + +
58E CYS 4.4 0.2 + - - -
79E MET* 3.6 23.8 - - + -
106E ILE* 5.2 1.1 - - + -
108E VAL* 5.3 3.6 - - + -
117E PRO* 3.7 21.5 - - + +
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Residues in contact with GLN 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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51E LEU* 2.8 56.4 + - - +
52E ALA* 3.2 20.4 - - - +
54E VAL* 1.4 68.0 - - - +
56E ALA* 1.4 64.4 + - - +
57E VAL 3.1 0.2 - - - -
58E CYS* 3.2 21.4 - - - +
59E SER* 4.3 2.6 + - - -
115E TYR 4.6 3.8 - - - +
116E VAL* 3.8 26.9 - - + +
117E PRO* 3.8 25.2 - - + +
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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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52E ALA 3.3 8.9 + - - +
53E ASP* 2.9 28.7 - - + +
54E VAL 3.0 0.4 - - - -
55E GLN* 1.4 77.7 - - - +
57E VAL* 1.3 59.6 + - - -
58E CYS 3.2 1.2 + - - -
59E SER* 3.2 16.3 + - - -
60E GLN* 3.1 26.9 + - - +
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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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53E ASP 4.0 2.7 - - - +
54E VAL* 2.4 47.1 + - + +
56E ALA* 1.3 69.9 - - - +
58E CYS* 1.3 53.7 - - - +
60E GLN* 3.0 31.3 + - - +
73E TYR* 2.9 32.0 - - - +
74E GLN 4.0 1.1 - - - -
75E SER* 3.2 47.3 - - - +
79E MET* 4.2 2.7 - - + -
106E ILE* 4.1 17.9 - - + +
108E VAL* 4.4 9.0 - - + -
110E CYS* 5.0 0.2 - - - -
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Residues in contact with CYS 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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55E GLN 3.2 16.6 - - - +
57E VAL* 1.3 75.3 - - - +
59E SER* 1.3 56.3 + - - +
60E GLN 3.3 0.9 - - - -
73E TYR* 3.3 26.9 + - - -
110E CYS* 2.0 54.0 - - - -
115E TYR* 3.4 25.0 - - + +
116E VAL* 3.4 26.0 - - - -
117E PRO* 3.8 4.7 - - - -
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Residues in contact with SER 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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55E GLN 4.3 3.8 + - - -
56E ALA* 3.2 15.3 + - - -
58E CYS* 1.3 78.0 - - - +
60E GLN* 1.3 65.5 + - - +
73E TYR* 4.9 0.4 - - - -
76E TYR* 4.6 5.4 + - - -
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Residues in contact with GLN 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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53E ASP 4.6 2.4 + - - -
56E ALA* 3.1 40.9 + - - +
57E VAL* 3.0 27.5 + - - +
58E CYS 3.3 0.2 - - - -
59E SER* 1.3 83.7 - - - +
61E LYS* 1.3 67.8 + - - +
62E ASN* 2.9 5.2 + - - +
73E TYR* 3.1 10.6 - - - -
74E GLN 3.5 6.1 - - - +
75E SER* 3.4 1.2 - - - -
76E TYR* 2.9 61.7 + - + +
77E SER 4.4 1.2 + - - -
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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