Contacts of the helix formed by residues 88 - 99 (chain E) in PDB entry 5ISO
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 ILE 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E PHE* 5.8 0.2 - - - -
64E LEU* 5.0 3.8 - - + -
70E ARG* 3.6 41.8 + - + +
87E THR* 1.3 74.0 - - - +
89E THR* 1.3 64.5 + - - +
91E PHE* 3.0 13.0 + - + +
92E ILE* 2.9 28.2 + - + +
243E LYS* 3.2 25.6 - - + +
244E PHE* 3.9 21.8 - - + +
246E VAL* 4.4 7.9 - - + -
247E ILE* 3.8 40.4 - - + +
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Residues in contact with THR 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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87E THR* 3.0 12.1 + - - -
88E ILE* 1.3 79.5 - - - +
90E ASP* 1.3 57.1 + - - +
92E ILE* 3.2 12.5 + - + +
93E ASN* 2.8 49.1 + - - +
121E TYR* 4.8 5.8 - - + +
243E LYS* 3.0 36.7 + - - +
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Residues in contact with ASP 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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61E PHE* 4.0 5.8 - - + -
85E MET 3.8 6.5 - - - +
86E LEU* 3.5 27.8 - - + +
87E THR* 3.1 34.1 + - - +
88E ILE 3.2 0.4 - - - -
89E THR* 1.3 79.2 - - - +
91E PHE* 1.3 56.4 + - - +
93E ASN* 3.1 8.1 + - - +
94E ILE* 2.8 35.0 + - - +
117E TRP* 3.2 23.1 + - - +
118E ARG* 5.6 2.9 - - - +
121E TYR* 3.9 16.7 - - - -
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Residues in contact with PHE 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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61E PHE* 3.4 49.3 - + + -
62E PHE* 6.5 0.4 - + - -
87E THR 3.7 0.4 + - - -
88E ILE* 3.0 17.5 + - + +
90E ASP* 1.3 78.0 - - - +
92E ILE* 1.3 61.4 + - - +
94E ILE* 3.3 1.5 + - - -
95E LEU* 3.0 62.0 + - + +
109E LEU* 4.5 13.0 - - + -
246E VAL* 3.7 34.8 - - + -
247E ILE* 4.4 10.1 - - + -
249E LEU* 4.1 1.3 - - + -
250E ALA* 4.0 27.1 - - + -
255E TYR* 4.1 16.2 - + + -
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Residues in contact with ILE 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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88E ILE* 2.9 17.4 + - + +
89E THR* 3.6 12.3 - - + +
91E PHE* 1.3 75.0 - - - +
93E ASN* 1.3 58.1 + - - +
95E LEU* 4.0 4.9 - - - +
96E HIS* 3.0 28.4 + - - +
217E LEU* 3.9 32.9 - - + +
220E PHE* 4.0 15.3 - - + -
221E VAL* 4.2 7.2 - - + -
243E LYS* 3.7 42.4 - - + -
246E VAL* 3.6 38.8 - - + -
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Residues in contact with ASN 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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89E THR* 2.8 36.0 + - - +
90E ASP 3.1 5.1 + - - +
92E ILE* 1.3 77.2 - - - +
94E ILE* 1.3 62.5 + - - +
96E HIS* 4.1 0.3 - - - +
97E ARG* 3.2 34.7 + - - +
117E TRP* 3.8 19.3 - - + -
121E TYR* 3.2 35.7 + - + -
221E VAL* 3.4 35.8 - - - +
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Residues in contact with ILE 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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57E VAL* 3.9 28.3 - - + -
61E PHE* 4.3 5.8 - - + -
90E ASP 2.8 22.2 + - - +
91E PHE* 3.9 4.3 - - - +
93E ASN* 1.3 73.1 - - - +
95E LEU* 1.3 63.6 + - + +
98E TYR* 3.1 41.8 + - + +
106E ILE* 5.1 0.7 - - + +
108E GLU 5.1 0.4 - - - -
109E LEU* 3.6 33.9 - - + +
112E HIS* 5.2 2.5 - - + -
117E TRP* 3.3 51.8 - - + +
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Residues in contact with LEU 95 (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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91E PHE* 3.0 63.9 + - + +
92E ILE 4.0 0.9 - - - +
94E ILE* 1.3 78.8 - - + +
96E HIS* 1.3 64.6 + - - +
99E TYR* 3.1 31.9 + - - +
106E ILE* 4.2 21.8 - - + -
109E LEU* 4.3 16.2 - - + -
214E TYR* 4.0 0.2 - - - -
217E LEU* 3.8 24.5 - - + -
246E VAL* 4.7 2.2 - - + -
249E LEU* 4.2 14.1 - - + -
255E TYR* 4.5 12.3 - - + +
258E LEU* 4.1 8.7 - - + -
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Residues in contact with HIS 96 (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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92E ILE 3.0 19.7 + - - +
93E ASN 4.2 2.7 - - - +
94E ILE 3.4 0.2 - - - -
95E LEU* 1.3 78.2 - - - +
97E ARG* 1.3 68.8 + - + +
214E TYR* 2.9 64.8 + + - -
215E VAL* 6.1 0.2 - - - -
217E LEU* 4.3 9.4 - - + +
218E GLY* 3.4 34.8 + - - -
221E VAL* 4.2 24.7 - - + +
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Residues in contact with ARG 97 (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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93E ASN* 3.2 23.1 + - - +
94E ILE 4.1 1.8 - - - +
96E HIS* 1.3 90.2 - - + +
98E TYR* 1.3 82.9 + - + +
99E TYR 3.9 3.2 + - - +
117E TRP* 4.0 16.8 - - - -
120E VAL* 3.4 42.4 + - - +
121E TYR* 4.1 11.3 + - - +
221E VAL* 6.4 1.8 - - + -
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Residues in contact with TYR 98 (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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94E ILE* 3.1 29.8 + - + +
97E ARG* 1.3 95.3 + - + +
99E TYR* 1.3 64.4 + - - +
100E LYS* 3.5 16.7 + - - +
106E ILE* 3.5 29.2 - - + +
108E GLU* 3.4 54.7 - - + +
112E HIS* 3.5 16.6 + + - -
117E TRP* 3.9 21.9 - + - -
120E VAL* 3.5 28.6 - - - +
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Residues in contact with TYR 99 (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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95E LEU 3.1 20.7 + - - +
97E ARG 3.5 3.3 - - - +
98E TYR* 1.3 78.8 - - - +
100E LYS* 1.3 73.2 + - - +
101E SER* 3.7 16.1 - - - -
102E ALA* 3.4 12.0 + - - -
106E ILE* 3.5 30.6 - - + +
214E TYR* 3.4 40.4 + + + -
256E ASN 3.3 21.8 - - - -
257E ASN* 4.1 0.2 + - - -
258E LEU* 3.3 41.9 + - + -
259E ASP* 2.8 32.1 + - - -
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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