Contacts of the helix formed by residues 72 - 85 (chain E) in PDB entry 2AAZ
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 PHE 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70E ARG* 4.0 2.4 + - - -
71E VAL* 1.3 72.6 - - - +
73E LEU* 1.3 66.2 + - - +
74E ARG* 3.7 34.1 - - + -
75E GLY* 3.0 36.7 + - - -
76E VAL* 3.1 14.7 + - - +
97E GLY 3.8 23.6 - - - -
98E VAL* 4.2 10.3 - - + -
100E ILE* 5.0 1.3 - - + -
226E PHE* 3.8 16.0 - + + -
2551E CB3 3.5 45.1 + - + +
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Residues in contact with LEU 73 (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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63E LEU* 4.5 7.6 - - + -
65E LEU* 4.2 30.3 - - + -
71E VAL 2.7 13.7 + - - +
72E PHE* 1.3 70.8 - - - +
74E ARG* 1.3 64.3 + - - +
76E VAL* 2.9 20.6 + - + +
77E ILE* 3.0 35.0 + - + +
233E LEU* 4.6 9.0 - - + -
300E PHE 5.9 0.4 - - - +
302E VAL* 3.6 40.2 - - + -
305E TYR* 5.4 6.3 - - + -
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Residues in contact with ARG 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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72E PHE* 3.3 28.3 - - + -
73E LEU* 1.3 81.2 - - - +
75E GLY* 1.3 57.4 + - - +
77E ILE* 3.8 9.2 - - - +
78E ALA* 2.9 31.1 + - + +
96E GLN* 2.8 31.4 + - - +
97E GLY* 4.3 7.9 + - - -
98E VAL* 4.0 11.8 - - + +
297E VAL* 4.4 20.8 - - + +
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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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72E PHE* 3.0 36.0 + - - -
74E ARG* 1.3 81.7 - - - +
76E VAL* 1.3 59.6 + - - +
78E ALA* 3.8 0.9 - - - +
79E GLU* 3.0 25.8 + - - +
98E VAL* 4.0 17.1 - - - +
226E PHE* 3.9 8.3 - - - -
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Residues in contact with VAL 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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65E LEU* 5.2 0.2 - - + -
71E VAL* 4.3 8.7 - - + -
72E PHE 3.1 15.7 + - - +
73E LEU* 2.9 12.6 + - + +
75E GLY* 1.3 77.5 - - - +
77E ILE* 1.3 63.2 + - - +
79E GLU* 3.3 5.2 + - - +
80E LEU* 3.0 22.6 + - + +
226E PHE* 3.5 40.4 - - + +
229E ALA* 4.0 9.4 - - + -
230E SER* 3.7 36.2 + - - +
233E LEU* 3.9 14.4 - - + -
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Residues in contact with ILE 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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73E LEU* 3.0 38.2 + - + +
74E ARG* 3.8 7.6 - - - +
76E VAL* 1.3 76.9 - - - +
78E ALA* 1.3 62.9 + - - +
80E LEU* 3.2 7.1 + - - +
81E LEU* 3.0 33.2 + - + +
233E LEU* 4.0 20.9 - - + -
297E VAL* 4.1 19.3 - - + +
300E PHE* 3.6 58.6 - - + +
302E VAL* 5.3 0.4 - - + -
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Residues in contact with ALA 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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74E ARG* 2.9 21.1 + - + +
75E GLY 3.8 3.6 - - - +
77E ILE* 1.3 78.4 - - - +
79E GLU* 1.3 62.1 + - - +
81E LEU* 3.5 3.6 + - - +
82E TRP* 3.0 23.7 + - - +
93E LEU* 3.6 6.9 - - + +
96E GLN* 3.8 30.3 - - - +
98E VAL* 3.9 17.3 - - + -
297E VAL* 4.7 8.7 - - + +
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Residues in contact with GLU 79 (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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75E GLY 3.0 17.7 + - - +
76E VAL* 3.7 4.3 - - - +
78E ALA* 1.3 75.8 - - - +
80E LEU* 1.3 57.3 + - - +
82E TRP* 3.1 15.7 - - + +
83E PHE* 2.9 59.8 + - + -
93E LEU* 4.0 6.7 - - + +
100E ILE* 3.6 20.6 - - + +
101E TRP* 2.8 25.3 + - + +
188E HIS* 5.4 1.0 + - - -
226E PHE* 4.3 9.0 - - - +
230E SER* 4.7 8.7 + - - -
550E UMP 5.5 0.2 - - - +
2551E CB3 3.2 26.1 - - - +
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Residues in contact with LEU 80 (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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76E VAL 3.0 16.6 + - - +
77E ILE* 3.2 6.5 + - - +
79E GLU* 1.3 75.5 + - - +
81E LEU* 1.3 59.2 + - + +
83E PHE* 3.1 18.7 + - + +
84E VAL* 3.0 36.2 + - + +
131E TRP* 4.4 7.9 - - + -
230E SER* 3.6 35.7 - - - +
233E LEU* 3.7 18.8 - - + -
234E LEU* 3.7 26.7 - - + +
237E MET* 3.6 29.6 - - - -
300E PHE* 5.1 3.8 - - + -
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Residues in contact with LEU 81 (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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77E ILE* 3.0 23.2 + - + +
78E ALA* 4.0 3.8 - - - +
80E LEU* 1.3 76.1 - - + +
82E TRP* 1.3 57.1 + - - +
84E VAL* 3.6 6.9 + - + +
85E SER* 3.0 28.1 + - - -
237E MET* 3.8 30.1 - - + -
292E ILE 5.9 0.2 - - - +
295E PHE* 3.8 20.0 - - + +
296E LYS* 3.7 10.3 - - - -
297E VAL* 3.5 44.4 - - + +
300E PHE* 4.1 9.0 - - + -
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Residues in contact with TRP 82 (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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78E ALA 3.0 14.6 + - - +
79E GLU* 3.1 14.8 - - + +
81E LEU* 1.3 76.4 - - - +
83E PHE* 1.3 99.8 + + - +
85E SER* 2.6 22.2 + - - -
86E GLY 3.4 3.3 + - - -
87E CYS* 3.4 43.2 + - + +
88E THR* 3.8 23.6 - - - -
89E ASP 3.1 25.1 + - - -
90E ALA* 4.0 5.8 - - - -
92E MET* 4.0 12.5 - - + +
93E LEU* 3.7 24.4 - - + +
96E GLN* 5.8 0.7 - - - +
101E TRP* 3.7 22.4 - + - -
123E LEU* 3.6 24.2 - - + -
126E VAL* 4.7 7.9 - - + -
127E TYR* 5.4 0.2 - + - -
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Residues in contact with PHE 83 (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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79E GLU* 2.9 50.9 + - + -
80E LEU* 3.1 16.4 + - + +
82E TRP* 1.3 101.1 - + - +
84E VAL* 1.3 58.6 + - - +
86E GLY* 2.8 18.4 + - - -
87E CYS 5.7 0.4 - - - -
101E TRP* 4.7 0.4 - - - -
127E TYR* 3.5 44.0 - + + -
128E GLY* 3.1 23.6 - - - +
131E TRP* 3.5 35.1 - + + -
132E ARG* 4.4 0.9 - - - +
188E HIS* 3.7 21.5 - + - -
230E SER* 4.5 9.6 - - - -
231E TYR* 6.1 0.2 - + - -
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Residues in contact with VAL 84 (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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80E LEU* 3.0 27.7 + - + +
81E LEU* 3.8 8.3 - - + +
83E PHE* 1.3 80.5 - - - +
85E SER* 1.3 60.2 + - - +
86E GLY 3.1 1.2 + - - -
131E TRP* 4.7 4.5 - - + -
132E ARG* 2.6 44.8 + - - +
153E LEU* 3.8 23.1 - - + -
234E LEU* 4.6 7.2 - - + -
237E MET* 4.3 18.8 - - + -
292E ILE* 3.4 25.8 - - + +
293E ASP* 3.8 5.6 - - - +
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Residues in contact with SER 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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81E LEU 3.0 14.5 + - - -
82E TRP* 2.6 24.1 + - - -
84E VAL* 1.3 76.5 - - - +
86E GLY* 1.3 59.5 + - - +
87E CYS* 3.1 18.7 + - - +
132E ARG* 4.6 2.0 - - - -
133E HIS* 5.1 4.0 + - - -
293E ASP* 4.7 5.4 - - - -
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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