Contacts of the helix formed by residues 84 - 94 (chain E) in PDB entry 1DSX
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 84 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E ASN* 2.7 28.3 + - - +
82E ARG 3.2 0.8 + - - -
83E PRO* 1.3 76.8 - - - +
85E PHE* 1.3 64.6 + - - +
86E ASP 3.4 0.7 - - - -
87E ALA* 3.2 17.1 + - - +
88E ILE* 3.2 13.7 + - - +
101E PRO* 4.7 0.9 - - - -
104E VAL* 3.5 18.0 - - - +
108E ILE* 4.1 1.4 - - - +
109E PHE* 3.6 21.4 - - - -
112E GLU* 3.5 25.9 - - - +
116E TYR* 6.0 0.4 - - - -
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Residues in contact with PHE 85 (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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37E ILE* 3.8 26.0 - - + -
39E ILE* 3.7 19.1 - - + -
44E PHE* 3.6 44.6 - + + -
59E LEU* 3.9 16.2 - - + -
81E ASN 3.8 5.9 + - - +
82E ARG 3.2 13.8 + - - +
83E PRO 3.4 0.2 - - - -
84E SER* 1.3 75.8 - - - +
86E ASP* 1.3 66.4 + - - +
88E ILE* 3.2 20.3 + - + -
89E LEU* 2.8 41.6 + - + +
116E TYR* 3.5 39.5 - + - -
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Residues in contact with ASP 86 (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 LEU* 5.8 1.7 - - - +
44E PHE* 3.5 14.5 - - - -
82E ARG 4.6 2.5 + - - +
83E PRO* 4.4 10.0 + - - +
84E SER 3.4 1.0 + - - -
85E PHE* 1.3 74.5 - - - +
87E ALA* 1.3 57.8 + - - +
89E LEU* 3.5 6.6 + - - +
90E TYR* 2.9 29.0 + - - +
93E GLN* 5.0 0.7 - - - +
101E PRO* 6.4 0.2 - - + -
81H ASN* 4.7 5.1 - - - +
82H ARG* 3.4 34.9 + - - +
83H PRO* 3.8 27.4 - - + +
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Residues in contact with ALA 87 (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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84E SER 3.2 6.5 + - - +
85E PHE 3.2 0.4 - - - -
86E ASP* 1.3 75.1 - - - +
88E ILE* 1.3 68.5 + - - +
90E TYR* 3.2 8.3 + - - +
91E TYR* 3.1 20.8 + - - +
97E ARG 4.9 1.4 - - - +
98E LEU* 4.3 4.7 - - - +
99E ARG 3.4 26.8 + - - +
101E PRO* 3.7 13.9 - - + +
109E PHE* 3.5 20.6 - - + -
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Residues in contact with ILE 88 (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 LEU* 4.7 0.9 - - + -
84E SER* 3.2 17.9 + - - +
85E PHE* 3.2 23.6 + - + +
87E ALA* 1.3 76.2 - - - +
89E LEU* 1.4 62.7 + - - +
91E TYR* 3.2 21.2 - - - +
92E TYR* 3.3 24.4 - - + -
109E PHE* 3.9 23.3 - - + -
112E GLU* 4.5 7.6 - - + -
113E ILE* 4.5 7.4 - - + +
116E TYR* 3.8 45.3 - - + -
118E LEU* 4.0 21.5 - - + -
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Residues in contact with LEU 89 (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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44E PHE* 3.9 30.3 - - + -
45E GLU 4.8 1.8 - - - +
46E VAL* 3.7 35.4 - - + -
51E LEU* 5.0 4.7 - - + -
85E PHE* 2.8 32.9 + - + +
86E ASP* 3.7 5.2 - - - +
88E ILE* 1.4 78.6 - - - +
90E TYR* 1.3 61.2 + - - +
92E TYR* 3.0 23.7 + - + +
93E GLN* 3.0 38.3 + - + +
40H SER* 4.0 14.1 - - - -
80H ARG 5.3 0.2 - - - +
82H ARG* 5.4 2.5 - - + -
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Residues in contact with TYR 90 (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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86E ASP 2.9 18.9 + - - +
87E ALA* 3.2 10.0 + - - +
89E LEU* 1.3 72.2 - - - +
91E TYR* 1.3 58.5 + - - +
93E GLN* 3.4 21.5 + - + +
94E SER* 2.7 62.1 + - - -
97E ARG* 4.1 26.7 + - + -
99E ARG* 5.9 3.8 - - + -
81H ASN* 4.1 28.3 - - + +
108H ILE* 3.7 51.0 + - + +
111H GLU* 5.1 7.4 - - - +
112H GLU* 4.9 7.8 + - - -
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Residues in contact with TYR 91 (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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54E PHE* 3.6 46.8 - + + -
57E THR* 5.0 2.1 - - + +
87E ALA 3.1 10.7 + - - +
88E ILE 3.2 12.3 - - - +
90E TYR* 1.3 75.8 - - - +
92E TYR* 1.3 69.7 + + - +
94E SER* 3.3 0.2 + - - -
96E GLY* 2.8 53.3 + - - -
97E ARG 3.4 11.1 + - - +
98E LEU* 3.6 37.9 - - + -
118E LEU* 4.0 46.3 + - + -
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Residues in contact with TYR 92 (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 THR* 3.6 30.5 - - + +
51E LEU* 3.7 33.7 - - + -
53E GLN* 2.8 21.6 - - - +
54E PHE* 3.8 22.8 - + + -
57E THR* 2.7 33.7 + - + -
59E LEU* 3.7 32.0 + - + +
60E GLY 4.6 1.6 - - - -
88E ILE* 3.3 22.2 - - + -
89E LEU* 3.0 11.7 + - + +
91E TYR* 1.3 80.7 - + - +
93E GLN* 1.3 62.6 + - - +
95E GLY* 3.2 8.7 + - - -
116E TYR* 4.6 1.4 + - - +
118E LEU* 3.7 21.5 - - + +
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Residues in contact with GLN 93 (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 THR* 3.9 17.0 - - + -
53E GLN* 5.5 2.6 + - - -
86E ASP 5.0 0.5 - - - +
89E LEU* 3.0 35.4 + - + +
90E TYR* 3.1 33.3 + - + +
92E TYR* 1.3 75.7 - - - +
94E SER* 1.3 58.5 + - - +
95E GLY 3.6 0.3 + - - -
40H SER* 3.1 26.3 + - - -
79H ASP* 3.7 18.6 + - - +
80H ARG* 3.3 19.8 + - - +
81H ASN* 3.7 9.6 + - - +
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Residues in contact with SER 94 (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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90E TYR* 2.7 51.6 + - - -
91E TYR 3.3 0.7 + - - -
93E GLN* 1.3 75.8 - - - +
95E GLY* 1.3 59.6 + - - +
96E GLY 3.7 0.2 + - - -
97E ARG* 3.0 44.9 + - - +
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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