Contacts of the helix formed by residues 61 - 73 (chain B) in PDB entry 2AAO
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 LYS 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B ASN 4.2 0.6 + - - -
60B LEU* 1.3 75.4 - - - +
62B GLU* 1.3 66.8 + - - +
63B SER* 3.6 18.3 + - - +
64B GLU* 2.9 47.5 + - + +
65B ILE* 3.1 11.4 + - - +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.5 22.9 - - - -
50B LYS* 2.8 39.3 + - - +
60B LEU 4.0 0.2 + - - -
61B LYS* 1.3 71.3 - - - +
63B SER* 1.3 64.9 + - - +
65B ILE* 3.1 13.6 + - - +
66B LEU* 3.0 39.3 + - + +
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LYS* 3.3 25.8 + - - +
62B GLU* 1.3 78.4 - - - +
64B GLU* 1.3 61.4 + - - +
66B LEU* 3.4 13.2 + - - +
67B ASP* 3.0 37.3 + - - +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.4 18.6 - - + +
61B LYS* 2.9 45.9 + - + +
63B SER* 1.3 78.2 + - - +
65B ILE* 1.3 64.5 + - - +
67B ASP* 3.3 12.2 + - - +
68B LEU* 3.0 24.1 + - - +
94B LYS* 3.1 29.0 + - - -
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.7 24.0 - - + -
49B LEU* 4.0 23.7 - - + +
50B LYS* 4.1 33.7 - - + +
53B LEU* 3.9 11.9 - - + -
60B LEU* 3.6 32.1 - - + +
61B LYS 3.1 11.3 + - - +
62B GLU* 3.1 17.0 + - - +
64B GLU* 1.3 75.2 - - - +
66B LEU* 1.3 57.4 + - - +
68B LEU* 3.2 4.6 + - - +
69B MSE 2.9 28.1 + - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 3.4 31.4 - - + -
62B GLU* 3.0 34.0 + - + +
63B SER* 3.6 11.2 - - - +
64B GLU 3.2 0.2 - - - -
65B ILE* 1.3 76.8 - - - +
67B ASP* 1.3 59.1 + - - +
69B MSE 3.3 6.0 + - + +
70B GLN* 2.9 30.9 + - - +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER* 3.0 25.0 + - - +
64B GLU* 3.6 13.8 - - - +
66B LEU* 1.3 75.3 - - - +
68B LEU* 1.3 58.2 + - - +
70B GLN* 3.3 16.4 + - - +
71B ALA* 2.9 30.9 + - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.2 24.7 - - + -
53B LEU* 4.3 5.6 - - + -
60B LEU* 4.3 11.9 - - + -
64B GLU 3.0 17.5 + - - +
65B ILE* 3.5 5.4 - - - +
67B ASP* 1.3 74.3 - - - +
69B MSE 1.3 65.6 + - - +
71B ALA* 3.3 4.9 + - + -
72B ALA* 2.8 39.3 + - + +
80B ILE* 5.3 1.8 - - + -
88B ALA* 4.8 1.3 - - + -
93B ASN* 3.7 26.9 - - + +
95B ILE* 3.6 43.5 - - + -
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Residues in contact with MSE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE 4.2 1.8 - - - +
45B THR 3.9 5.4 - - - +
46B PHE* 3.6 47.6 - - + +
49B LEU* 3.9 12.3 - - + +
65B ILE 2.9 15.8 + - - +
66B LEU* 3.3 8.3 + - + +
68B LEU* 1.3 75.1 - - - +
70B GLN* 1.3 64.7 + - - +
73B ASP* 3.0 41.5 + - + +
78B GLY* 3.9 21.8 - - - +
80B ILE* 3.6 33.9 - - + -
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU 2.9 16.7 + - - +
67B ASP* 3.6 17.2 + - - +
68B LEU 3.2 0.2 - - - -
69B MSE 1.3 80.0 - - - +
71B ALA* 1.3 62.5 + - - +
73B ASP* 3.9 12.3 + - - +
76B ASN* 5.7 0.3 - - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ASP 2.9 17.0 + - - +
68B LEU* 4.0 6.3 - - + +
70B GLN* 1.3 76.7 - - - +
72B ALA* 1.3 64.5 + - - +
74B VAL* 4.0 14.2 + - - +
88B ALA* 5.7 0.7 - - - -
91B HIS* 6.4 2.0 - - + -
93B ASN* 5.9 3.4 - - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 2.8 22.4 + - + +
71B ALA* 1.3 79.7 - - - +
73B ASP* 1.3 55.7 + - - +
74B VAL* 2.8 15.5 + - - +
80B ILE* 3.8 29.6 - - + -
84B GLU* 3.5 21.5 - - - +
88B ALA* 3.8 28.9 - - + +
95B ILE* 6.0 0.4 - - + -
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B MSE 3.0 31.9 + - + +
70B GLN* 4.3 9.6 - - - +
71B ALA 3.4 0.6 - - - -
72B ALA* 1.3 72.0 - - - +
74B VAL* 1.3 61.9 + - - +
75B ASP* 2.9 10.2 - - - +
76B ASN* 3.0 18.7 + - - +
77B SER 3.0 7.5 + - - -
78B GLY* 2.6 31.5 + - - -
79B THR 3.6 7.2 - - - +
80B ILE* 4.8 0.7 - - - -
84B GLU* 4.0 4.5 - - - -
298B CA 2.3 31.3 - - - -
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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