Contacts of the helix formed by residues 69 - 80 (chain E) in PDB entry 1S89
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 GLY 69 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ALA* 5.2 0.2 - - - -
79B SER* 4.2 4.9 + - - -
107B ARG* 5.1 0.9 - - - -
108B LEU* 3.6 24.8 - - - +
64E LEU* 4.4 1.1 - - - -
66E GLY 2.9 6.5 + - - -
67E PRO 3.3 2.4 + - - -
68E MET* 1.3 80.7 - - - +
70E GLY* 1.3 64.9 + - - +
71E ASP* 3.2 3.4 - - - -
72E GLN* 3.2 8.3 + - - +
73E GLN* 3.1 28.3 + - - +
101E ASP* 5.3 0.7 - - - -
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Residues in contact with GLY 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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45E THR* 4.0 7.9 - - - -
63E MET* 4.6 1.1 - - - +
64E LEU* 3.0 27.3 + - - +
65E SER 2.8 11.8 + - - -
66E GLY* 3.4 0.6 + - - -
68E MET 3.8 0.4 - - - -
69E GLY* 1.3 77.0 - - - +
71E ASP* 1.3 63.1 + - - +
73E GLN* 3.1 14.0 + - - +
74E VAL* 3.0 26.9 + - - +
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Residues in contact with ASP 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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72B GLN* 4.0 1.4 - - - +
17E VAL* 4.2 5.2 - - - +
45E THR* 3.9 9.1 - - - +
66E GLY* 3.8 9.1 + - - +
69E GLY 3.2 0.6 - - - -
70E GLY* 1.3 75.5 - - - +
72E GLN* 1.3 57.8 + - + +
74E VAL* 3.3 5.9 + - - +
75E GLY* 3.0 22.0 + - - -
88E PHE* 4.5 1.5 - - - -
98E ASN* 2.7 30.8 + - - -
101E ASP* 3.5 34.9 - - + +
102E VAL* 4.4 5.3 - - - +
105E LEU* 3.7 22.3 - - + +
205E PGA 2.9 21.0 - - - +
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Residues in contact with GLN 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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71B ASP 4.0 2.6 - - - +
72B GLN* 3.5 43.3 - - + +
75B GLY* 3.3 19.4 - - - -
76B ALA* 4.4 4.3 - - - +
101B ASP 5.2 0.3 - - - +
104B ALA* 3.0 32.1 + - + +
105B LEU* 4.1 7.8 + - - +
108B LEU* 2.9 30.9 - - + +
69E GLY 3.2 8.7 + - - +
71E ASP* 1.3 75.2 - - - +
73E GLN* 1.3 60.3 + - - +
75E GLY* 3.6 0.6 - - - -
76E ALA* 2.9 29.1 + - - +
101E ASP* 3.1 26.0 + - + +
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Residues in contact with GLN 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 4.0 16.8 - - + -
79B SER* 4.3 3.8 - - - +
80B GLU* 2.9 36.3 + - - +
63E MET* 3.2 25.3 - - + +
64E LEU* 2.7 53.0 + - - +
69E GLY 3.1 13.0 + - - +
70E GLY* 3.1 9.5 + - - +
72E GLN* 1.3 77.3 - - - +
74E VAL* 1.3 63.3 + - - +
76E ALA* 3.3 4.2 + - - +
77E LEU* 3.1 28.2 + - - +
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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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15E ALA* 3.9 27.6 - - + -
17E VAL* 4.7 8.7 - - + -
43E TYR* 5.9 2.0 - - + -
44E ALA* 5.3 2.9 - - - +
45E THR* 4.7 14.6 - - + +
63E MET* 4.6 15.7 - - + -
70E GLY 3.0 14.4 + - - +
71E ASP* 3.6 7.9 - - - +
73E GLN* 1.3 74.7 - - - +
75E GLY* 1.3 65.8 + - - +
77E LEU* 3.2 11.2 + - + +
78E ILE* 3.0 31.4 + - + +
83E ILE* 4.8 3.1 - - + -
86E LEU* 4.5 6.1 - - + -
105E LEU* 3.9 17.5 - - + -
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Residues in contact with GLY 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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72B GLN* 3.2 22.4 - - - -
71E ASP 3.0 10.5 + - - -
72E GLN 3.3 0.4 + - - -
73E GLN 3.3 0.2 - - - -
74E VAL* 1.3 77.9 - - - +
76E ALA* 1.3 55.6 + - - +
78E ILE* 3.2 5.9 + - - +
79E SER 3.0 22.9 + - - -
105E LEU* 3.6 13.9 - - - +
108E LEU* 3.3 20.5 - - - +
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Residues in contact with ALA 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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69B GLY 5.2 0.2 - - - -
72B GLN* 4.2 2.8 - - - +
73B GLN* 3.9 28.5 - - + +
76B ALA* 4.4 7.6 - - + -
72E GLN 2.9 17.4 + - - +
73E GLN 3.6 5.2 - - - +
74E VAL 3.2 0.2 - - - -
75E GLY* 1.3 73.5 - - - +
77E LEU* 1.3 65.1 + - + +
79E SER* 2.7 23.8 + - - -
80E GLU* 3.0 28.8 + - - +
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Residues in contact with LEU 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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43E TYR* 4.3 17.3 - - + -
63E MET* 4.0 26.2 - - + -
73E GLN 3.1 18.8 + - - +
74E VAL* 3.2 11.6 + - + +
76E ALA* 1.3 75.8 - - + +
78E ILE* 1.3 62.6 + - - +
80E GLU* 3.2 10.4 + - - +
82E LYS* 2.8 56.5 + - + +
83E ILE* 3.5 29.2 - - + -
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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
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6E ARG* 5.7 0.2 + - - -
74E VAL* 3.0 25.3 + - + +
75E GLY* 3.2 8.0 + - - +
77E LEU* 1.3 77.5 - - - +
79E SER* 1.3 57.5 + - - +
81E GLY* 2.9 19.8 + - - -
83E ILE* 3.6 30.3 - - + +
86E LEU* 4.5 11.7 - - + -
105E LEU* 3.9 23.8 - - + +
108E LEU* 4.2 12.8 - - + +
109E ALA* 4.5 6.3 - - + +
112E TRP* 4.0 28.8 - - + +
114E ILE* 3.9 29.4 - - + +
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Residues in contact with SER 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.5 34.0 - - - +
68B MET 3.5 15.0 - - - -
69B GLY* 4.1 8.5 - - - -
73B GLN* 4.1 5.4 - - - +
75E GLY 3.0 10.7 + - - -
76E ALA* 2.7 26.5 + - - -
78E ILE* 1.3 77.7 - - - +
80E GLU* 1.3 59.0 + - - +
81E GLY 3.2 1.2 + - - -
108E LEU* 4.3 1.3 - - - -
112E TRP* 3.6 31.2 - - - +
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Residues in contact with GLU 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 5.1 1.3 - - + -
73B GLN* 3.7 27.5 + - - +
76E ALA* 3.0 33.8 + - - +
77E LEU* 3.6 11.0 + - - +
78E ILE 3.0 0.6 - - - -
79E SER* 1.3 78.4 - - - +
81E GLY* 1.3 62.1 + - - +
82E LYS* 2.9 38.1 + - + +
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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