Contacts of the helix formed by residues 72 - 87 (chain B) in PDB entry 2AMT
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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ILE* 6.1 2.2 - - + -
35B SER 4.2 2.5 - - - -
36B ASP* 3.5 16.2 - - + +
70B GLY 3.8 2.0 + - - -
71B ALA* 1.3 75.8 - - - +
73B SER* 1.3 62.9 + - - +
74B ARG* 3.2 14.0 + - - +
75B GLU* 2.9 59.6 + - - +
76B LEU* 3.2 12.6 + - - +
78B ARG* 4.5 2.1 + - - -
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Residues in contact with SER 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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35B SER 3.8 1.6 + - - -
36B ASP* 2.6 30.8 + - - -
38B ASP* 3.3 21.2 - - - +
41B LEU* 3.9 13.3 - - - +
42B HIS* 2.7 31.1 + - - -
45B THR* 4.8 1.4 + - - -
72B ASP* 1.3 72.5 - - - +
74B ARG* 1.3 56.7 + - - +
76B LEU* 3.4 12.6 + - - +
77B LEU* 2.9 28.4 + - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 6.1 1.6 - - + -
22B GLY* 4.3 18.3 + - - -
41B LEU* 3.6 20.9 - - + -
72B ASP* 3.2 11.5 + - - +
73B SER* 1.3 74.4 - - - +
75B GLU* 1.3 61.5 + - - +
77B LEU* 3.3 5.1 + - - +
78B ARG* 2.9 50.2 + - - +
115B PHE* 3.2 51.3 + - + +
118B GLU* 3.5 21.2 + - - -
119B ASP* 2.8 39.2 + - - +
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Residues in contact with GLU 75 (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 PHE* 4.2 10.3 - - + -
71B ALA* 3.8 18.7 - - + +
72B ASP* 2.9 46.6 + - - +
74B ARG* 1.3 76.0 - - - +
76B LEU* 1.3 57.2 + - - +
78B ARG* 3.4 26.7 + - - +
79B GLU* 3.1 28.8 + - - +
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Residues in contact with LEU 76 (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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35B SER* 5.3 2.7 - - - +
42B HIS* 4.3 6.7 - - + +
45B THR* 4.8 6.1 - - + +
57B ILE* 5.9 0.4 - - + -
61B PHE* 3.3 41.0 - - + -
68B PHE* 3.7 39.7 - - + +
71B ALA* 4.2 9.0 - - + +
72B ASP 3.2 15.4 + - - +
73B SER* 3.5 16.6 - - - +
75B GLU* 1.3 73.4 - - - +
77B LEU* 1.3 60.7 + - - +
80B ALA* 2.9 27.5 + - - +
2901C 1AA 3.6 33.7 - - + -
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Residues in contact with LEU 77 (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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41B LEU* 3.8 27.6 - - + +
44B LEU* 4.4 13.2 - - + -
45B THR* 3.7 25.5 + - + +
48B LEU* 3.7 29.8 - - + -
73B SER 2.9 17.5 + - - +
74B ARG 3.3 4.5 + - - +
76B LEU* 1.3 73.7 - - - +
78B ARG* 1.3 59.9 + - - +
80B ALA* 3.3 3.9 + - - +
81B TRP* 2.8 30.7 + - - +
116B ILE* 4.9 4.7 - - - -
119B ASP* 3.7 31.4 - - + +
120B LEU* 4.0 12.3 - - + -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 4.5 1.6 + - - -
74B ARG* 2.9 38.8 + - - +
75B GLU* 3.4 36.2 - - - +
77B LEU* 1.3 75.4 - - - +
79B GLU* 1.3 57.1 + - - +
81B TRP* 3.4 7.7 + - - +
82B ARG* 2.9 28.1 + - - +
119B ASP* 3.1 53.5 + - + +
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Residues in contact with GLU 79 (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 PHE* 3.6 17.3 - - + -
68B PHE* 3.5 33.6 - - + -
75B GLU 3.1 18.3 + - - +
76B LEU 3.8 3.8 - - - +
78B ARG* 1.3 73.9 - - - +
80B ALA* 1.3 65.0 + - - +
82B ARG* 2.7 45.1 + - - +
83B ARG* 2.8 53.5 + - - +
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Residues in contact with ALA 80 (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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45B THR* 3.5 26.2 - - + +
48B LEU* 6.0 1.1 - - + -
49B LEU* 3.9 16.4 - - + +
60B LEU* 3.7 17.7 - - + +
76B LEU 2.9 19.6 + - - +
77B LEU* 3.6 4.3 - - + +
79B GLU* 1.3 74.7 - - - +
81B TRP* 1.3 57.8 + - - +
83B ARG* 3.3 4.2 + - - +
84B ILE* 2.9 36.4 + - + +
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Residues in contact with TRP 81 (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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48B LEU* 4.1 9.6 - - + +
77B LEU* 2.8 17.7 + - + +
78B ARG* 3.6 7.2 - - - +
80B ALA* 1.3 76.6 - - - +
82B ARG* 1.3 52.2 + - - +
84B ILE* 3.3 23.0 + - + +
85B GLN* 2.8 78.2 + - + +
89B TYR 4.5 0.7 - - - -
90B THR* 3.7 6.5 - - - -
91B LEU* 3.5 40.8 - - + -
119B ASP 3.5 19.3 - - - +
120B LEU* 2.9 48.2 + - + -
154B LEU* 3.6 21.8 - - + -
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Residues in contact with ARG 82 (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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78B ARG 2.9 14.5 + - - +
79B GLU* 2.7 48.7 + - - +
81B TRP* 1.3 77.6 - - - +
83B ARG* 1.3 86.0 + - - +
85B GLN* 3.4 8.9 + - - +
86B ALA* 2.9 29.7 + - - +
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Residues in contact with ARG 83 (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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54B LEU* 3.9 13.4 - - + +
60B LEU* 3.5 50.8 + - + +
61B PHE* 5.0 0.2 - - - -
65B ASP* 5.4 3.4 + - - -
68B PHE* 4.7 8.7 - - - -
79B GLU* 2.8 42.4 + - - +
80B ALA 3.8 5.8 - - - +
82B ARG* 1.3 96.2 - - - +
84B ILE* 1.3 64.2 + - - +
86B ALA* 3.6 8.9 - - - +
87B LYS* 3.3 26.2 + - - +
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Residues in contact with ILE 84 (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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48B LEU* 3.5 40.8 - - + -
49B LEU* 3.7 8.7 - - + +
52B ALA* 3.8 8.5 - - + -
54B LEU* 3.7 22.0 - - + -
80B ALA* 2.9 28.9 + - + +
81B TRP* 3.3 22.9 + - + +
83B ARG* 1.3 76.4 - - - +
85B GLN* 1.3 61.8 + - - +
87B LYS* 3.2 10.7 + - - -
89B TYR* 3.3 38.6 + - + -
154B LEU* 3.7 15.7 - - + -
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Residues in contact with GLN 85 (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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81B TRP* 2.8 68.2 + - + +
82B ARG* 3.8 7.8 - - - +
84B ILE* 1.3 71.3 - - - +
86B ALA* 1.3 59.9 + - - +
88B GLY* 3.0 19.1 + - - -
89B TYR 3.7 19.6 + - - +
90B THR* 5.4 4.2 - - - +
120B LEU 4.9 1.0 + - - -
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Residues in contact with ALA 86 (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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82B ARG* 2.9 23.1 + - - +
83B ARG* 3.6 12.1 - - - +
84B ILE 3.3 0.2 - - - -
85B GLN* 1.3 76.4 - - - +
87B LYS* 1.3 60.6 + - + +
88B GLY* 3.2 1.4 + - - -
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Residues in contact with LYS 87 (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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52B ALA 3.2 18.7 + - - +
53B ALA 4.5 3.2 + - - -
54B LEU* 3.6 35.4 - - + +
83B ARG 3.3 12.5 + - - +
84B ILE 3.2 11.8 + - - +
85B GLN 3.1 0.8 - - - -
86B ALA* 1.3 76.6 - - + +
88B GLY* 1.3 57.0 + - - +
89B TYR* 3.6 16.7 - - + -
156B LYS* 3.1 30.4 + - - +
125C ASP* 3.1 27.8 + - - -
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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