Contacts of the helix formed by residues 91 - 100 (chain E) in PDB entry 2ONK
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 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70E SER* 4.3 0.6 + - - -
89E THR* 2.6 18.9 + - - +
90E ALA* 1.3 79.6 - - - +
92E TYR* 1.3 65.2 + - - +
93E THR* 2.8 32.5 + - - +
94E LEU* 3.2 17.2 + - + +
154E PRO* 3.9 10.8 - - + -
157E TYR* 2.5 35.6 + - - +
158E ARG* 3.5 18.4 + - - +
278E VAL* 4.0 5.9 - - - +
281E LYS* 5.2 4.0 + - - +
284E VAL 3.7 0.6 + - - -
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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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89E THR* 3.4 8.0 + - - -
91E ASP* 1.3 74.6 + - - +
93E THR* 1.3 73.5 + - + +
94E LEU 3.3 0.2 - - - -
95E ILE* 3.4 19.6 + - - +
96E GLN* 3.9 19.2 + - - +
107E THR* 3.8 15.1 + - + +
109E MET* 4.0 33.5 - - + +
281E LYS* 2.6 36.2 + - - -
282E PRO 5.4 1.1 - - - -
284E VAL* 3.0 46.0 + - + +
285E TYR 4.1 1.3 - - - -
286E GLY* 3.5 26.0 - - - +
327E ARG* 6.1 1.1 - - - -
329E ASP* 6.2 1.6 - - + -
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Residues in contact with THR 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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91E ASP* 2.8 24.5 + - - +
92E TYR* 1.3 94.9 - - + +
94E LEU* 1.3 67.1 + - - +
96E GLN* 2.9 17.4 + - - +
97E LYS* 2.9 45.1 + - - +
278E VAL* 5.0 1.9 - - - +
281E LYS* 3.0 36.8 - - + +
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Residues in contact with LEU 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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70E SER* 3.6 15.0 - - - -
71E ALA* 3.8 11.0 - - + +
74E ILE* 3.8 13.9 - - + -
91E ASP* 3.2 13.2 + - + +
93E THR* 1.3 80.4 + - - +
95E ILE* 1.3 64.4 + - - +
97E LYS* 4.5 8.1 - - + -
98E MET* 2.9 48.8 + - + +
154E PRO* 3.3 23.1 - - + -
157E TYR* 3.3 29.4 - - + +
272E LEU* 4.1 21.1 - - + -
276E LYS* 5.6 3.1 - - + -
278E VAL* 4.4 8.5 - - + -
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Residues in contact with ILE 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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74E ILE* 3.9 10.3 - - + +
87E ILE* 4.4 2.9 - - + +
89E THR* 3.7 26.7 - - + +
92E TYR 3.4 10.2 + - - +
93E THR 3.1 0.6 - - - -
94E LEU* 1.3 77.0 - - - +
96E GLN* 1.3 56.9 + - - +
99E MET* 2.6 54.4 + - + +
100E TYR* 3.6 12.6 - - + -
104E ALA* 5.2 0.9 - - + -
106E TRP 4.9 0.2 - - - +
107E THR* 3.4 33.4 - - + +
286E GLY 4.1 2.2 - - - -
287E ILE* 4.0 13.7 - - - +
288E THR* 3.3 33.4 - - + +
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Residues in contact with GLN 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 TYR* 4.1 20.7 - - - +
93E THR* 2.9 22.0 + - - +
95E ILE* 1.3 76.3 - - - +
97E LYS* 1.3 56.2 + - + +
98E MET 2.7 11.4 + - - -
99E MET 3.3 6.1 + - - -
100E TYR* 3.4 48.0 + - + +
107E THR* 3.9 8.3 - - - +
329E ASP* 3.0 33.1 + - - +
329J ASP 5.6 4.0 + - - -
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Residues in contact with LYS 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 THR* 2.9 42.0 + - - +
94E LEU* 4.1 7.4 - - + +
96E GLN* 1.3 75.0 - - + +
98E MET* 1.3 59.2 + - + +
276E LYS* 3.1 40.9 + - + +
277E GLU* 2.8 39.7 + - - +
278E VAL* 4.8 9.9 - - + +
279E THR* 5.7 1.1 + - - +
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Residues in contact with MET 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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71E ALA* 4.0 22.9 - - + +
74E ILE* 4.2 19.5 - - + -
75E ARG* 3.4 30.7 - - + +
78E THR* 3.7 18.4 - - + +
94E LEU* 2.9 39.3 + - + +
95E ILE 4.1 0.2 - - - +
96E GLN 2.7 5.7 + - - -
97E LYS* 1.3 82.0 - - + +
99E MET* 1.3 61.8 + - - +
100E TYR 3.9 1.1 - - - -
103E PHE* 4.8 1.6 - - - -
272E LEU* 5.8 0.2 - - - -
274E ASN* 3.0 28.7 - - + +
276E LYS* 4.2 10.8 - - + +
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Residues in contact with MET 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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74E ILE* 3.3 35.4 - - + -
77E VAL* 4.5 7.4 - - + -
78E THR* 4.1 4.5 - - + -
87E ILE* 4.4 18.6 - - + -
95E ILE* 2.6 43.3 + - - +
98E MET* 1.3 75.5 - - - +
100E TYR* 1.3 63.1 + - + +
102E GLU* 3.4 1.2 + - - -
103E PHE* 2.9 31.4 + - + +
104E ALA* 2.9 52.7 + - + +
288E THR* 4.6 4.0 - - + -
290E PRO* 4.2 13.2 - - + -
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Residues in contact with TYR 100 (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 ILE* 3.6 16.6 - - + -
96E GLN* 3.4 43.3 + - + +
98E MET 3.9 0.5 - - - -
99E MET* 1.3 81.7 - - - +
101E PRO* 1.3 66.2 - - + +
102E GLU* 3.4 2.5 - - - -
104E ALA* 3.9 7.9 - - + -
105E ASN* 3.7 18.6 - - - -
106E TRP* 3.0 15.0 - - - -
107E THR* 2.7 33.3 + - - -
329E ASP* 2.8 24.7 + - - -
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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