Contacts of the helix formed by residues 72 - 87 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 6.3 1.6 - - + -
35C SER* 6.2 0.4 - - - -
36C ASP* 3.6 17.3 - - + +
70C GLY 3.6 2.9 + - - +
71C ALA* 1.3 76.7 - - - +
73C SER* 1.3 62.4 + - - +
74C ARG* 3.0 13.4 + - - +
75C GLU* 2.7 46.0 + - - +
76C LEU* 3.2 20.8 + - - +
78C ARG* 5.2 1.0 + - - -
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C SER* 4.5 0.5 - - - -
36C ASP* 2.5 36.2 + - - -
38C ASP* 3.4 17.7 - - - +
41C LEU* 3.8 16.5 - - - +
42C HIS* 2.6 27.5 + - - -
45C THR* 4.8 1.6 + - - -
72C ASP* 1.3 72.3 - - - +
74C ARG* 1.3 53.2 + - - +
76C LEU* 3.7 11.0 - - - +
77C LEU* 2.8 34.1 + - - +
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Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLY* 4.0 22.1 + - - -
36C ASP* 4.8 0.6 + - - +
41C LEU* 3.5 21.1 - - + -
72C ASP* 3.0 11.3 + - - +
73C SER* 1.3 74.8 - - - +
75C GLU* 1.3 60.7 + - - +
77C LEU* 3.6 2.7 - - - +
78C ARG* 2.9 53.4 + - - +
115C PHE* 3.4 49.5 + - + +
118C GLU* 4.5 8.3 - - - +
119C ASP* 2.9 40.1 + - - +
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C PHE* 5.3 5.1 - - + -
70C GLY 4.7 0.7 - - - +
71C ALA* 3.4 15.6 - - + +
72C ASP* 2.7 50.2 + - - +
74C ARG* 1.3 71.2 - - - +
76C LEU* 1.3 59.5 + - - +
78C ARG* 3.4 25.5 + - - +
79C GLU* 3.0 29.8 + - - +
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 5.6 2.2 - - - -
42C HIS* 4.7 5.6 - - - +
45C THR* 4.8 1.8 - - - -
57C ILE* 3.8 24.9 - - + -
61C PHE* 3.4 47.2 - - + -
68C PHE* 4.0 21.1 - - + +
71C ALA* 4.0 16.8 - - + +
72C ASP 3.2 15.5 + - - +
73C SER* 3.7 13.2 - - - +
75C GLU* 1.3 74.4 - - - +
77C LEU* 1.3 58.8 + - - +
79C GLU* 3.5 0.8 + - - -
80C ALA* 2.9 30.5 + - - +
3901C 1AA 4.2 21.3 - - + -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.0 26.9 - - + +
44C LEU* 4.1 16.6 - - + -
45C THR* 3.5 27.0 + - + +
48C LEU* 3.9 28.0 - - + -
73C SER 2.8 21.5 + - - +
74C ARG 3.6 4.0 - - - +
76C LEU* 1.3 74.2 - - - +
78C ARG* 1.3 56.5 + - - +
80C ALA* 3.3 4.3 + - + +
81C TRP* 2.9 30.0 + - - +
116C ILE* 4.7 6.5 - - + -
119C ASP* 3.7 29.2 - - + +
120C LEU* 4.2 10.5 - - + -
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ASP* 4.8 1.2 + - - -
74C ARG* 2.9 41.8 + - - +
75C GLU* 3.4 34.4 + - - +
76C LEU 3.4 0.2 - - - -
77C LEU* 1.3 76.3 - - - +
79C GLU* 1.3 58.0 + - - +
81C TRP* 3.4 8.2 + - - +
82C ARG* 2.9 28.6 + - - +
118C GLU 5.6 0.4 - - - -
119C ASP* 2.7 63.5 + - - +
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 3.4 27.1 - - + -
68C PHE* 3.7 24.8 - - + -
75C GLU 3.0 19.5 + - - +
76C LEU 3.9 3.4 - - - +
78C ARG* 1.3 74.5 - - - +
80C ALA* 1.3 64.0 + - - +
82C ARG* 2.7 40.8 + - - +
83C ARG* 2.7 53.9 + - - +
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C THR* 3.7 24.7 - - + -
48C LEU* 6.2 0.9 - - + -
49C LEU* 3.9 16.4 - - + +
60C LEU* 3.9 16.4 - - + -
61C PHE* 4.0 0.9 - - + -
76C LEU 2.9 19.0 + - - +
77C LEU* 3.6 5.2 - - + +
79C GLU* 1.3 76.0 - - - +
81C TRP* 1.3 57.6 + - - +
83C ARG* 3.3 4.3 + - - +
84C ILE* 2.9 37.3 + - + +
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Residues in contact with TRP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.0 6.0 - - + +
77C LEU 2.9 18.3 + - - +
78C ARG* 3.6 6.5 - - - +
80C ALA* 1.3 75.4 - - - +
82C ARG* 1.3 60.8 + - - +
84C ILE* 3.7 22.4 - - + +
85C GLN* 2.9 71.3 + - + +
89C TYR 4.4 0.7 - - - -
90C THR* 3.7 8.3 - - - -
91C LEU* 3.5 46.0 - - + -
119C ASP 3.8 13.0 - - - +
120C LEU* 2.9 52.4 + - + -
154C LEU* 3.6 21.8 - - + -
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG 2.9 14.4 + - - +
79C GLU* 2.7 58.1 + - - +
81C TRP* 1.3 78.5 - - - +
83C ARG* 1.3 70.2 + - - +
85C GLN* 3.4 8.3 + - - +
86C ALA* 2.9 32.2 + - - +
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Residues in contact with ARG 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 3.9 14.1 - - + +
60C LEU* 3.5 54.0 + - + +
61C PHE* 4.3 0.8 - - - -
68C PHE* 3.9 22.8 - - - -
79C GLU* 2.7 37.9 + - - +
80C ALA* 3.7 7.2 - - - +
82C ARG* 1.3 84.5 - - - +
84C ILE* 1.3 64.0 + - - +
86C ALA* 3.4 10.2 - - - +
87C LYS* 3.3 23.7 + - - +
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Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 3.6 39.9 - - + -
49C LEU* 3.8 9.2 - - + +
52C ALA* 3.8 17.3 - - + -
54C LEU* 3.8 13.5 - - + -
80C ALA* 2.9 27.8 + - + +
81C TRP* 3.6 24.9 - - + +
83C ARG* 1.3 76.9 - - - +
85C GLN* 1.3 61.8 + - - +
87C LYS* 3.1 10.3 + - - +
89C TYR* 3.3 37.8 + - + -
154C LEU* 3.7 15.9 - - + -
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Residues in contact with GLN 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C TRP* 2.9 61.3 + - + +
82C ARG* 3.8 7.1 - - - +
84C ILE* 1.3 74.4 - - - +
86C ALA* 1.3 59.7 + - - +
88C GLY* 2.9 19.4 + - - -
89C TYR 3.4 20.1 + - - +
90C THR* 4.7 11.3 - - - +
120C LEU 5.0 0.8 + - - -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 2.9 22.0 + - - +
83C ARG* 3.4 15.5 - - - +
84C ILE 3.2 0.4 - - - -
85C GLN* 1.3 77.0 - - - +
87C LYS* 1.3 57.4 + - - +
88C GLY* 3.2 1.4 + - - -
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP* 2.8 33.9 + - - -
52C ALA 2.8 22.1 + - - +
53C ALA 4.4 5.7 + - - -
54C LEU* 3.7 32.6 - - + +
83C ARG 3.3 11.3 + - - +
84C ILE 3.1 11.7 + - - +
86C ALA* 1.3 75.8 - - + +
88C GLY* 1.3 58.9 + - - +
89C TYR* 3.5 20.2 + - + -
156C LYS* 4.8 12.3 - - - -
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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