Contacts of the helix formed by residues 69 - 79 (chain A) in PDB entry 2AIN
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.9 6.5 - - - -
68A LEU* 1.3 78.5 - - - +
70A GLN* 1.3 57.1 + - - +
71A GLU* 4.2 8.7 - - - -
72A ARG* 2.9 15.3 + - - +
73A ALA* 2.7 34.1 + - - +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.1 36.8 - - + +
22A VAL* 3.1 3.7 - - - -
23A ALA* 2.7 46.2 + - + +
32A LEU* 5.1 0.6 - - - +
34A ILE* 3.4 26.2 - - - +
68A LEU 4.0 0.8 + - - -
69A SER* 1.3 72.1 - - - +
71A GLU* 1.3 55.4 + - + +
73A ALA* 4.1 4.3 - - - -
74A ALA* 2.7 38.7 + - - +
100B PHE* 2.7 28.9 + - + +
102B THR* 4.1 12.1 - - + +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A SER* 3.1 7.5 - - - -
70A GLN* 1.3 79.2 - - + +
72A ARG* 1.3 60.8 + - + +
74A ALA* 5.1 1.3 - - - -
75A GLU* 2.8 34.6 + - - +
102B THR* 5.4 3.5 + - - -
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.1 30.5 - - + +
69A SER* 2.9 19.7 + - - +
71A GLU* 1.3 77.2 - - + +
73A ALA* 1.3 61.7 + - - +
75A GLU* 4.1 3.3 - - - +
76A LEU* 3.0 40.4 + - + +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.2 43.1 - - + -
65A LEU* 4.1 13.4 - - + +
68A LEU* 4.6 10.4 - - + +
69A SER 2.7 17.4 + - - +
70A GLN* 3.7 2.0 - - - +
72A ARG* 1.3 71.3 - - - +
74A ALA* 1.3 61.0 + - - +
76A LEU* 3.7 2.9 - - - +
77A MET* 3.0 36.2 + - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.4 5.1 - - + +
70A GLN 2.7 18.2 + - - +
71A GLU* 4.5 1.3 - - - +
73A ALA* 1.3 72.9 - - - +
75A GLU* 1.3 62.6 + - - +
77A MET* 3.1 12.1 + - - -
78A THR* 3.0 21.6 + - - +
102B THR* 3.2 36.8 - - + +
103B GLU 5.2 1.1 - - - +
104B VAL* 3.2 19.1 - - + +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU 2.8 23.8 + - - +
72A ARG* 4.1 4.3 - - - +
74A ALA* 1.3 76.7 - - - +
76A LEU* 1.3 58.7 + - + +
78A THR* 3.0 14.5 - - - +
79A ARG* 2.8 47.7 + - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.0 49.7 + - - +
65A LEU* 5.6 0.7 - - + -
68A LEU* 4.2 21.5 - - + -
72A ARG* 3.0 27.6 + - + +
73A ALA* 3.7 3.8 - - - +
75A GLU* 1.3 77.4 - - + +
77A MET* 1.3 64.5 + - - +
79A ARG* 3.1 30.6 + - + +
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Residues in contact with MET 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 3.9 13.9 - - + +
19A LEU* 4.7 2.2 - - + -
21A ILE* 4.5 9.9 - - + -
34A ILE* 4.2 16.4 - - + -
57A LEU* 3.8 26.7 - - + -
60A VAL* 3.5 31.5 - - + +
63A ARG* 3.7 6.1 - - - +
65A LEU* 4.8 2.2 - - + -
73A ALA* 3.0 34.7 + - - +
74A ALA* 3.4 9.9 - - - +
76A LEU* 1.3 76.1 - - - +
78A THR* 1.3 57.2 + - - +
80A THR* 2.8 28.9 + - - +
84A VAL* 5.3 0.2 - - - +
86A LEU* 4.9 3.8 - - + -
104B VAL* 3.5 31.9 - - + -
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.8 16.2 - - - +
17A MET* 4.6 2.9 - - - -
74A ALA 3.0 13.8 + - - +
75A GLU* 3.0 34.1 - - - +
77A MET* 1.3 75.4 - - - +
79A ARG* 1.3 61.9 + - + +
80A THR* 3.0 8.2 + - - +
104B VAL* 3.1 32.0 + - + +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 5.5 1.4 + - - -
75A GLU* 2.8 44.8 + - + +
76A LEU* 3.1 24.0 + - + +
78A THR* 1.3 79.8 - - + +
80A THR* 1.3 59.4 + - - +
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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