Contacts of the helix formed by residues 59 - 71 (chain E) in PDB entry 7JSL
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 ASP 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E GLY 4.5 4.5 - - - +
45E VAL* 3.2 17.8 + - + -
57E ILE* 3.7 2.7 - - - -
58E LYS* 1.3 77.3 - - - +
60E PRO* 1.4 67.3 - - - +
61E ASP* 3.1 8.7 + - - +
62E GLU* 3.1 35.6 + - + +
63E VAL* 3.3 12.8 + - - +
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Residues in contact with PRO 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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57E ILE* 3.4 19.2 - - + +
58E LYS 3.7 7.6 - - - +
59E ASP* 1.4 86.6 - - - +
61E ASP* 1.3 64.6 + - - +
63E VAL* 3.7 3.6 + - - +
64E ALA* 3.3 22.5 + - - +
78E TYR* 3.9 33.7 - - + +
102E PHE* 3.6 39.9 - - + -
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Residues in contact with ASP 61 (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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59E ASP* 3.3 7.4 + - - +
60E PRO* 1.3 79.2 - - - +
62E GLU* 1.3 59.5 + - - +
64E ALA* 3.6 5.7 - - - +
65E ARG* 3.0 27.4 + - - +
77E ASN* 4.8 6.8 - - - +
78E TYR* 4.3 16.5 + - - +
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Residues in contact with GLU 62 (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 TYR* 5.9 0.5 - - - -
45E VAL* 3.8 27.1 - - + +
59E ASP* 3.1 28.3 + - + +
61E ASP* 1.3 74.2 - - - +
63E VAL* 1.3 66.3 + - - +
65E ARG* 3.0 44.2 + - - +
66E LEU* 3.0 33.6 + - + +
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Residues in contact with VAL 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E PHE* 4.3 5.1 - - + -
33E ILE* 5.5 8.1 - - + -
36E LEU* 5.0 13.9 - - + -
45E VAL* 3.3 28.3 - - + +
46E ILE* 4.6 12.3 - - + -
57E ILE* 3.6 35.2 - - + -
59E ASP 3.3 1.2 + - - +
60E PRO 3.8 7.6 - - - +
62E GLU* 1.3 75.4 - - - +
64E ALA* 1.3 55.1 + - - +
66E LEU* 3.0 12.1 + - - +
67E TRP* 2.9 30.7 + - - +
78E TYR* 6.4 0.2 - - + -
81E LEU* 3.8 23.1 - - + -
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Residues in contact with ALA 64 (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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60E PRO 3.3 10.8 + - - +
61E ASP* 3.6 10.1 - - - +
63E VAL* 1.3 78.7 - - - +
65E ARG* 1.3 50.0 + - - +
67E TRP 3.1 2.3 + - - -
68E GLY* 2.7 32.7 + - - -
76E MET* 3.4 12.3 - - + +
77E ASN* 3.6 39.7 - - - +
78E TYR* 3.7 1.8 - - - +
81E LEU* 3.7 18.8 - - + +
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Residues in contact with ARG 65 (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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61E ASP 3.0 16.1 + - - +
62E GLU* 3.0 42.5 + - - +
64E ALA* 1.3 73.6 - - - +
66E LEU* 1.3 69.1 + - - +
68E GLY* 3.1 4.0 + - - -
69E VAL* 2.8 51.3 + - + +
76E MET* 4.9 5.3 + - - -
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Residues in contact with LEU 66 (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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32E PHE* 3.8 14.7 - - + -
36E LEU* 4.9 9.6 - - + -
42E TYR* 4.0 34.1 - - + +
45E VAL* 4.9 4.7 - - + -
62E GLU* 3.0 35.9 + - + +
63E VAL* 3.0 11.0 + - - +
65E ARG* 1.3 97.0 - - - +
67E TRP* 1.3 54.9 + - - +
68E GLY 3.2 0.2 - - - -
69E VAL* 3.1 14.1 + - + +
70E ARG* 2.8 34.3 + - - +
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Residues in contact with TRP 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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16D C 3.9 7.2 - - - -
17D T 3.1 26.4 + - - -
28E GLN* 3.4 23.6 - - - -
29E LEU* 3.5 42.9 - - + +
32E PHE* 3.6 42.0 - + + -
63E VAL 2.9 10.2 + - - +
64E ALA 3.6 5.4 - - - +
66E LEU* 1.3 74.6 - - - +
68E GLY* 1.3 55.8 + - - +
70E ARG* 3.9 7.5 - - + +
71E LYS* 3.0 68.5 + - + +
76E MET* 3.8 24.2 - - + -
81E LEU* 4.0 19.7 - - + +
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Residues in contact with GLY 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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64E ALA 2.7 17.7 + - - -
65E ARG* 3.1 6.3 + - - -
67E TRP* 1.3 71.4 - - - +
69E VAL* 1.3 57.7 + - - +
72E CYS* 3.1 5.5 + - - -
73E LYS* 2.7 51.7 + - - +
74E PRO* 4.6 3.7 - - - +
76E MET* 3.6 11.4 - - - +
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Residues in contact with VAL 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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65E ARG* 2.8 38.1 + - + +
66E LEU* 3.3 17.3 - - + +
68E GLY* 1.3 72.5 - - - +
70E ARG* 1.3 65.4 + - + +
72E CYS* 3.3 17.7 + - - +
72H CYS* 5.8 0.2 - - - +
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Residues in contact with ARG 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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32E PHE* 4.0 38.6 - - + +
35E GLU* 4.9 17.6 - - - +
36E LEU* 5.7 3.4 - - - +
66E LEU 2.8 19.3 + - - +
67E TRP* 4.1 12.3 - - + +
69E VAL* 1.3 78.2 - - + +
71E LYS* 1.3 60.9 + - + +
72E CYS* 3.4 6.6 + - - -
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Residues in contact with LYS 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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15D A 5.1 1.4 + - - -
16D C 3.3 30.4 + - - +
17D T 3.5 21.3 - - - +
28E GLN* 5.8 1.2 - - - +
67E TRP* 3.0 53.4 + - + +
69E VAL 3.3 0.2 - - - -
70E ARG* 1.3 77.7 - - + +
72E CYS* 1.3 68.1 + - - +
73E LYS* 3.0 26.7 + - + +
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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