Contacts of the helix formed by residues 67 - 78 (chain E) in PDB entry 2RCY
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 LYS 67 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A SER* 5.0 2.9 - - - -
226A PRO* 3.4 37.1 - - + +
155B LYS* 5.7 4.0 - - - +
157B LYS* 5.3 1.6 - - - +
188C GLY* 3.6 22.4 + - - -
189C LEU 5.6 0.2 - - - -
190C SER* 5.7 1.2 - - - +
66E VAL* 1.3 75.8 - - - +
68E PRO* 1.3 73.4 - - + +
69E ASP* 3.2 27.7 + - - +
70E ILE* 3.2 14.6 + - + +
71E ALA* 3.1 18.4 + - - +
264E NAP 3.5 45.3 - - - +
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Residues in contact with PRO 68 (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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225A SER* 5.9 2.2 - - - -
226A PRO 5.8 2.2 - - - +
227A GLY 6.5 0.2 - - - -
228A GLY* 6.2 2.9 - - - -
66E VAL 3.7 0.9 - - - +
67E LYS* 1.3 88.8 - - + +
69E ASP* 1.3 61.8 + - - +
70E ILE 3.3 0.6 + - - -
71E ALA* 3.6 11.6 + - + +
72E GLY 4.4 2.8 + - - -
91E CYS* 4.4 1.1 - - + -
92E GLY* 3.4 30.3 - - - +
94E LEU* 3.8 32.2 - - + +
102E MSE 4.8 2.6 - - - +
260E MSE 3.7 23.8 - - + -
264E NAP 3.3 22.4 - - - +
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Residues in contact with ASP 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PRO 5.9 0.2 - - - -
155B LYS* 4.6 2.6 + - - -
157B LYS* 3.1 38.1 + - + +
67E LYS* 3.2 35.7 + - - +
68E PRO* 1.3 79.2 - - - +
70E ILE* 1.3 78.1 + - - +
72E GLY* 5.0 1.6 + - - -
73E SER 5.8 0.2 + - - -
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Residues in contact with ILE 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LYS* 3.6 27.6 - - - +
157B LYS* 6.3 0.4 - - + -
66E VAL* 3.8 17.0 - - + -
67E LYS* 3.4 20.9 - - + +
69E ASP* 1.3 91.4 + - - +
71E ALA* 1.3 65.1 + - - +
72E GLY 3.2 3.1 - - - -
73E SER* 3.1 24.6 + - - +
74E VAL* 3.2 13.7 - - + +
264E NAP 3.4 47.8 - - + +
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Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E CYS* 4.4 5.4 - - - -
66E VAL* 3.8 20.2 - - + -
67E LYS 3.1 13.7 + - - +
68E PRO 3.6 2.6 + - - +
70E ILE* 1.3 77.8 - - - +
72E GLY* 1.3 54.6 + - - +
74E VAL* 4.3 0.4 - - - -
75E LEU* 2.8 43.7 + - + +
91E CYS* 3.9 10.3 - - - -
94E LEU* 3.8 27.6 - - + -
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Residues in contact with GLY 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E PRO 4.4 2.4 + - - -
69E ASP 5.0 1.6 + - - -
70E ILE* 3.2 1.4 - - - +
71E ALA* 1.3 78.4 - - - +
73E SER* 1.3 55.1 + - - +
75E LEU* 4.0 1.4 - - - +
76E ASN* 3.1 27.4 + - - +
102E MSE 3.8 35.3 - - - +
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Residues in contact with SER 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ILE* 3.1 19.9 + - - +
72E GLY* 1.3 73.3 - - - +
74E VAL* 1.3 67.7 + - - +
76E ASN* 3.4 7.2 + - - +
77E ASN* 3.2 33.1 + - - +
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Residues in contact with VAL 74 (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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10E MSE 3.2 28.0 - - + +
52E ASN* 3.6 14.9 - - - +
64E CYS* 5.3 1.3 - - - -
66E VAL* 4.4 14.8 - - + -
70E ILE* 3.2 26.8 + - + +
71E ALA* 3.9 6.1 - - - +
72E GLY 3.4 0.2 - - - -
73E SER* 1.3 81.5 - - - +
75E LEU* 1.3 60.2 + - - +
77E ASN* 3.5 18.9 + - - +
78E ILE* 3.6 14.0 + - - +
264E NAP 3.7 30.7 - - + +
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Residues in contact with LEU 75 (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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10E MSE 5.0 2.0 - - + -
64E CYS* 4.0 29.2 - - + -
71E ALA* 2.8 27.6 + - + +
74E VAL* 1.3 71.3 - - - +
76E ASN* 1.3 62.9 + - - +
78E ILE* 3.4 20.6 - - + +
79E LYS* 3.3 17.0 + - - +
87E LEU* 3.8 30.5 - - + -
89E SER* 6.2 0.2 - - - -
91E CYS* 5.7 0.2 - - - -
99E LEU* 4.0 19.3 - - + +
102E MSE 3.8 33.4 - - + -
103E VAL* 3.4 24.3 - - + +
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Residues in contact with ASN 76 (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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72E GLY 3.1 20.0 + - - +
73E SER* 3.5 10.3 - - - +
75E LEU* 1.3 77.9 - - - +
77E ASN* 1.3 64.7 + - - +
79E LYS* 3.3 27.0 - - - +
80E PRO* 4.4 2.3 - - - +
102E MSE 4.1 11.8 + - - +
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Residues in contact with ASN 77 (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 ASN* 5.9 1.3 - - + -
53E GLU* 3.4 28.5 + - - +
73E SER* 3.2 19.5 + - - +
74E VAL* 3.7 12.8 - - - +
75E LEU 3.3 0.4 - - - -
76E ASN* 1.3 84.8 - - - +
78E ILE* 1.3 58.8 + - + +
79E LYS 3.3 1.4 + - - -
80E PRO* 3.8 3.3 - - - +
81E TYR* 3.3 21.8 - - - -
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Residues in contact with ILE 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E MSE 3.8 34.8 - - + -
52E ASN* 3.4 37.7 - - + +
53E GLU* 3.9 5.2 - - + +
62E ILE* 4.5 4.5 - - + -
74E VAL 3.6 9.6 + - - +
75E LEU* 3.4 29.8 - - + +
77E ASN* 1.3 77.2 - - + +
79E LYS* 1.3 63.9 + - - +
80E PRO* 3.4 3.8 - - - -
81E TYR* 3.2 22.0 + - + -
82E LEU* 3.5 19.0 + - + +
87E LEU* 4.2 13.7 - - + -
103E VAL* 4.9 4.3 - - + -
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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