Contacts of the helix formed by residues 72 - 86 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F ILE* 6.1 1.9 - - + +
36F ASP* 3.6 20.6 - - + +
70F GLY 4.0 1.8 + - - -
71F ALA* 1.3 77.0 - - - +
73F SER* 1.3 63.3 + - - +
74F ARG* 3.4 26.9 + - - +
75F GLU* 3.1 37.5 + - - +
76F LEU* 3.2 19.2 + - - +
78F ARG* 4.9 1.2 + - - -
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Residues in contact with SER 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ASP* 2.5 35.9 + - - -
38F ASP* 3.4 16.6 - - - +
41F LEU* 4.0 13.8 - - - +
42F HIS* 2.7 31.5 + - - -
45F THR* 4.9 1.4 + - - -
72F ASP* 1.3 70.6 - - - +
74F ARG* 1.3 58.6 + - - +
76F LEU* 3.3 11.2 + - - +
77F LEU* 2.8 29.5 + - - +
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 6.1 1.8 - - + -
22F GLY* 4.0 19.7 - - - -
41F LEU* 3.6 19.5 - - + -
72F ASP* 3.3 14.8 + - - +
73F SER* 1.3 74.3 - - - +
75F GLU* 1.3 61.0 + - - +
77F LEU* 3.7 4.4 - - - +
78F ARG* 3.0 51.4 + - - +
115F PHE* 3.3 48.7 + - + +
118F GLU* 3.7 20.8 + - - +
119F ASP* 2.8 40.4 + - - +
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Residues in contact with GLU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PHE* 5.0 7.4 - - + -
71F ALA* 3.6 23.4 - - + +
72F ASP* 3.1 28.8 + - - +
73F SER 3.3 0.2 - - - -
74F ARG* 1.3 75.4 - - - +
76F LEU* 1.3 60.7 + - - +
78F ARG* 3.4 23.8 + - - +
79F GLU* 2.9 31.5 + - - +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6901D 1AA 3.6 29.4 - - + -
35F SER* 5.0 3.8 - - - -
42F HIS* 4.5 5.6 - - - +
45F THR* 4.8 1.6 - - - +
57F ILE* 4.4 11.9 - - + -
61F PHE* 3.7 49.6 - - + -
68F PHE* 3.9 25.1 - - + +
71F ALA* 3.9 13.2 - - + +
72F ASP 3.2 16.7 + - - +
73F SER* 3.6 14.6 - - - +
74F ARG 3.3 0.2 - - - -
75F GLU* 1.3 77.8 - - - +
77F LEU* 1.3 55.6 - - - +
79F GLU* 4.4 0.7 - - - -
80F ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 3.9 27.6 - - + +
44F LEU* 4.2 13.5 - - + -
45F THR* 3.4 30.4 + - + +
48F LEU* 3.7 28.9 - - + -
73F SER 2.8 17.2 + - - +
74F ARG* 3.7 4.5 - - - +
75F GLU 3.3 0.2 - - - -
76F LEU* 1.3 76.6 - - - +
78F ARG* 1.3 56.6 + - - +
80F ALA* 3.4 4.1 + - + +
81F TRP* 2.9 30.9 + - - +
116F ILE* 4.9 3.6 - - - -
119F ASP* 3.8 28.5 - - + +
120F LEU* 4.2 11.2 - - + -
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Residues in contact with ARG 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ASP* 4.9 1.6 + - - -
74F ARG* 3.0 41.4 + - - +
75F GLU* 3.5 35.8 + - - +
77F LEU* 1.3 74.8 - - - +
79F GLU* 1.3 57.3 + - - +
81F TRP* 3.5 8.2 + - - +
82F ARG* 3.1 28.2 + - - +
118F GLU 5.4 0.9 - - - -
119F ASP* 2.8 55.4 + - + +
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Residues in contact with GLU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F PHE* 3.6 17.7 - - + -
68F PHE* 3.5 36.8 - - + -
75F GLU 2.9 18.4 + - - +
76F LEU 3.8 3.4 - - - +
78F ARG* 1.3 75.6 - - - +
80F ALA* 1.3 63.5 + - - +
82F ARG* 2.7 57.6 + - - +
83F ARG* 3.2 32.0 + - - +
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Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F THR* 3.7 26.0 - - + -
48F LEU* 6.2 0.7 - - + -
49F LEU* 3.9 15.9 - - + +
60F LEU* 3.8 17.3 - - + -
61F PHE* 4.3 0.4 - - + -
76F LEU 2.9 18.5 + - - +
77F LEU* 3.7 4.3 - - + +
79F GLU* 1.3 76.4 - - - +
81F TRP* 1.3 57.4 + - - +
83F ARG* 3.3 3.9 + - - +
84F ILE* 2.8 36.9 + - + +
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Residues in contact with TRP 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.0 10.7 - - + +
77F LEU 2.9 18.8 + - - +
78F ARG* 3.7 7.4 - - - +
79F GLU 3.3 0.2 - - - -
80F ALA* 1.3 78.2 - - - +
82F ARG* 1.3 57.8 + - + +
84F ILE* 3.3 24.3 + - + +
85F GLN* 2.8 67.7 + - + +
89F TYR 4.6 0.2 - - - -
90F THR* 3.8 6.7 - - - -
91F LEU* 3.6 41.3 - - + -
119F ASP 3.6 19.1 - - - -
120F LEU* 2.8 46.6 + - + -
154F LEU* 3.6 20.6 - - + -
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Residues in contact with ARG 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ARG 3.1 17.4 + - - +
79F GLU* 2.7 59.5 + - - +
81F TRP* 1.3 76.9 - - + +
83F ARG* 1.3 74.8 + - - +
85F GLN* 3.7 9.5 - - - +
86F ALA* 2.9 28.9 + - - +
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Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F LEU* 3.8 18.3 - - + +
60F LEU* 3.8 52.2 + - + +
61F PHE* 4.6 7.1 - - - -
68F PHE* 5.0 5.9 - - - -
79F GLU* 3.2 34.1 + - - +
80F ALA* 3.8 5.8 - - - +
82F ARG* 1.3 95.6 - - - +
84F ILE* 1.3 62.9 + - - +
86F ALA* 3.9 8.0 - - + +
87F LYS* 3.5 14.6 + - - +
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Residues in contact with ILE 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 3.6 38.1 - - + -
49F LEU* 3.7 10.8 - - + +
52F ALA* 3.9 9.2 - - + -
54F LEU* 3.8 21.1 - - + -
80F ALA* 2.8 27.8 + - + +
81F TRP* 3.4 24.0 - - + +
82F ARG 3.2 0.2 - - - -
83F ARG* 1.3 75.2 - - - +
85F GLN* 1.3 61.1 + - - +
87F LYS* 3.0 23.2 + - - +
88F GLY 3.5 4.0 + - - -
89F TYR* 3.5 14.4 + - + -
154F LEU* 3.7 25.8 - - + -
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Residues in contact with GLN 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F TRP* 2.8 62.2 + - + +
82F ARG* 3.4 9.5 + - - +
84F ILE* 1.3 76.1 - - - +
86F ALA* 1.3 56.2 - - - +
88F GLY* 3.1 18.5 + - - -
89F TYR 3.3 22.7 + - - +
90F THR* 4.5 12.7 - - - +
120F LEU 5.1 1.0 + - - -
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ARG* 2.9 25.3 + - - +
83F ARG* 3.9 11.2 - - + +
84F ILE 3.2 0.2 - - - -
85F GLN* 1.3 75.8 - - - +
87F LYS* 1.3 59.5 + - - +
88F GLY* 3.5 0.7 + - - -
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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