Contacts of the helix formed by residues 66 - 75 (chain E) in PDB entry 7CR3
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 PHE 66 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E ILE* 3.8 11.7 - - + -
13E PHE 3.4 24.9 - - - -
14E LYS* 3.6 42.4 - - + -
17E PHE* 3.3 39.8 - + + -
26E GLY 4.4 2.1 + - - +
65E ASP* 1.3 73.9 - - - +
67E PRO* 1.3 67.7 - - + +
69E PHE* 4.1 5.4 - + - -
70E LEU* 2.9 70.6 + - + +
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Residues in contact with PRO 67 (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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65E ASP* 3.4 18.8 - - + +
66E PHE* 1.3 94.6 - - + +
68E GLU* 1.3 58.2 + - + +
70E LEU* 3.3 12.8 + - + +
71E THR* 2.9 35.8 + - + +
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Residues in contact with GLU 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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56E VAL* 3.5 30.7 - - + +
57E ASP* 2.9 28.0 - - - +
58E ALA* 3.1 33.1 + - + +
59E ASP* 3.6 11.6 + - - +
64E ILE* 4.3 0.7 - - - -
65E ASP* 2.8 45.8 + - - +
67E PRO* 1.3 70.6 - - + +
69E PHE* 1.3 58.5 + - - +
71E THR* 2.6 22.7 + - - +
72E MET* 3.0 17.0 + - - +
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Residues in contact with PHE 69 (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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538D VAL* 4.9 0.4 - - + -
542D ALA* 3.5 30.5 - - + -
546D MET* 4.9 5.4 - - + -
13E PHE* 3.2 39.0 - + + -
16E ALA* 3.6 24.0 - - + -
17E PHE* 4.0 13.2 - + + -
20E PHE* 5.0 8.5 - + - -
28E ILE* 6.0 0.9 - - + -
56E VAL* 3.9 8.2 - - + +
64E ILE* 4.0 11.7 - - + -
65E ASP 3.2 19.7 + - - +
66E PHE* 3.7 17.3 - + - +
68E GLU* 1.3 76.5 - - - +
70E LEU* 1.3 63.1 + - - +
72E MET* 3.3 11.7 + - + +
73E MET* 3.0 38.2 + - + +
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Residues in contact with LEU 70 (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 ILE* 3.6 32.5 - - + +
13E PHE* 3.8 23.2 - - + -
66E PHE* 2.9 65.6 + - + +
67E PRO* 3.5 10.3 - - + +
69E PHE* 1.3 78.1 - - - +
71E THR* 1.3 57.8 + - + +
73E MET* 3.2 5.9 + - - +
74E ALA* 2.8 31.8 + - - +
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Residues in contact with THR 71 (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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56E VAL 5.1 1.9 + - - -
67E PRO* 2.9 15.4 + - + +
68E GLU* 2.6 27.6 + - - +
70E LEU* 1.3 77.0 - - + +
72E MET* 1.3 61.6 + - - +
74E ALA* 3.3 14.4 + - - +
75E ARG* 3.6 42.1 + - - +
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Residues in contact with MET 72 (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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542D ALA* 3.7 7.2 - - - +
545D VAL* 3.6 31.3 - - + +
546D MET* 3.6 33.0 - - + -
549D LEU* 3.6 18.4 - - + -
56E VAL* 3.5 32.1 - - + -
68E GLU 3.0 17.2 + - - +
69E PHE* 3.6 11.9 - - + +
70E LEU 3.3 0.2 - - - -
71E THR* 1.3 79.0 + - - +
73E MET* 1.3 92.2 + - + +
75E ARG* 4.2 11.7 + - - +
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Residues in contact with MET 73 (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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346D PHE* 6.4 0.4 - - + -
538D VAL* 4.2 12.1 - - + -
541D ARG* 4.3 19.7 - - + -
542D ALA* 3.7 15.9 - - - -
545D VAL* 4.2 11.9 - - + -
13E PHE* 3.6 48.1 - - + -
69E PHE* 3.0 41.6 + - + +
70E LEU 3.2 2.2 + - - +
72E MET* 1.3 96.5 - - + +
74E ALA* 1.3 61.1 + - - +
75E ARG 3.5 4.1 + - - +
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Residues in contact with ALA 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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13E PHE* 5.3 3.8 - - + -
70E LEU 2.8 16.7 + - - +
71E THR* 3.3 10.4 + - - +
73E MET* 1.3 78.4 - - - +
75E ARG* 1.3 64.1 + - + +
76E LYS* 4.0 1.6 + - - +
79E ASP* 5.4 0.5 - - - +
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Residues in contact with ARG 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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346D PHE* 4.5 11.1 - - - -
71E THR* 3.6 32.1 + - - +
72E MET* 4.2 10.0 + - - +
73E MET 3.5 3.7 - - - +
74E ALA* 1.3 82.7 - - + +
76E LYS* 1.3 61.4 + - - +
79E ASP* 3.8 36.7 + - + +
80E THR* 5.5 3.0 - - + +
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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