Contacts of the helix formed by residues 38 - 52 (chain A) 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 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.2 25.8 - - - +
20A ILE* 3.5 1.4 - - - -
21A GLY 2.8 19.6 + - - -
22A GLY* 2.9 26.0 + - - -
36A ASP* 3.3 8.8 + - - +
37A GLY* 1.3 71.7 - - - +
39A VAL* 1.3 60.6 + - - +
40A ALA* 3.4 3.6 + - - +
41A LEU* 3.1 24.5 + - - +
42A HIS* 3.0 36.5 + - - -
73A SER* 3.4 20.4 - - - +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP* 3.5 17.2 - - - +
9A VAL* 3.6 6.3 - - - -
10A HIS* 3.4 33.9 - - + +
20A ILE* 3.7 18.4 - - + -
31A LEU* 4.1 5.4 - - + -
37A GLY 3.1 5.5 + - - -
38A ASP* 1.3 71.0 + - - +
40A ALA* 1.3 63.4 + - - +
43A ALA* 3.1 26.5 + - - +
98A ILE* 5.7 0.4 - - + -
146A ILE* 3.4 48.5 - - + +
148A CYS* 3.4 12.6 - - + +
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Residues in contact with ALA 40 (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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20A ILE* 3.7 15.5 - - + -
21A GLY* 3.6 17.9 - - - +
38A ASP* 3.2 10.9 + - - +
39A VAL* 1.3 81.4 - - - +
41A LEU* 1.3 59.3 - - + +
43A ALA* 3.8 2.3 - - - +
44A LEU* 3.0 27.8 + - - +
96A VAL* 4.4 13.1 - - + +
98A ILE* 4.6 4.9 - - + -
112A MET* 5.4 0.9 - - - -
116A ILE* 6.1 2.2 - - + -
129A VAL* 6.0 0.7 - - + -
148A CYS* 3.4 20.0 - - - -
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Residues in contact with LEU 41 (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 GLY* 3.8 11.9 - - - -
22A GLY* 3.7 5.4 - - - +
38A ASP* 3.1 31.8 + - - +
40A ALA* 1.3 78.8 - - - +
42A HIS* 1.3 54.3 + - - +
44A LEU* 3.6 14.2 - - + +
45A THR* 2.6 41.7 + - - +
73A SER* 3.9 23.6 - - - +
74A ARG* 3.6 34.5 - - + +
77A LEU* 4.0 10.3 - - + +
115A PHE* 6.4 0.2 - - + -
116A ILE* 3.8 31.4 - - + -
119A ASP* 5.5 0.7 - - - +
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Residues in contact with HIS 42 (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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8A ASP* 3.0 20.1 + - - +
10A HIS* 3.2 9.9 + - - -
34A HIS* 3.6 15.3 - + - -
35A SER* 4.2 6.8 - - - -
37A GLY* 4.1 5.2 - - - -
38A ASP 3.0 26.5 + - - +
41A LEU* 1.3 72.3 - - - +
43A ALA* 1.3 59.2 + - - +
45A THR* 3.3 7.0 + - - -
46A ASP* 2.8 35.5 + - - +
57A ILE* 3.6 31.0 - - + +
73A SER* 2.7 32.9 + - - -
76A LEU* 4.3 3.0 - - + +
1900A ZN 2.4 30.8 - - - -
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Residues in contact with ALA 43 (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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6A GLY* 3.1 22.3 - - - +
7A PHE 4.2 2.0 - - - +
8A ASP* 3.9 10.2 - - - +
39A VAL 3.1 20.0 + - - +
40A ALA 3.8 3.4 - - - +
42A HIS* 1.3 72.7 - - - +
44A LEU* 1.3 60.6 + - - +
46A ASP* 3.3 1.1 + - - -
47A ALA* 2.9 26.2 + - - +
148A CYS* 3.3 33.7 - - - +
150A ALA* 3.6 5.4 - - + -
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Residues in contact with LEU 44 (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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40A ALA 3.0 18.8 + - - +
41A LEU* 3.6 14.1 - - + +
43A ALA* 1.3 75.9 - - - +
45A THR* 1.3 60.4 + - - +
47A ALA* 3.3 3.9 + - + +
48A LEU* 3.0 38.7 + - + +
77A LEU* 3.8 24.7 - - + -
94A VAL* 3.8 40.4 - - + -
96A VAL* 4.0 15.9 - - + -
116A ILE* 3.7 29.4 - - + -
120A LEU* 4.7 2.0 - - + -
150A ALA* 3.7 10.3 - - + +
151A VAL 5.4 1.3 - - - +
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Residues in contact with THR 45 (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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41A LEU 2.6 28.7 + - - -
42A HIS* 3.4 9.2 - - - -
44A LEU* 1.3 72.7 - - - +
46A ASP* 1.3 56.5 + - - +
48A LEU* 3.3 5.3 + - - +
49A LEU* 2.9 50.4 + - + +
57A ILE* 3.9 23.5 - - + +
61A PHE* 5.0 0.2 - - + -
73A SER 4.8 1.2 + - - -
76A LEU 4.6 2.9 - - - +
77A LEU* 3.5 28.0 + - - +
80A ALA* 3.7 19.3 - - + -
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Residues in contact with ASP 46 (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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5A HIS 4.0 2.0 - - - -
6A GLY* 3.8 11.2 - - - -
7A PHE 4.1 13.7 - - - +
8A ASP* 5.2 3.1 - - - +
42A HIS* 2.8 24.8 + - - +
43A ALA* 3.6 6.2 - - - +
45A THR* 1.3 72.2 - - - +
47A ALA* 1.3 53.6 + - - +
49A LEU* 3.8 4.3 - - - +
50A GLY* 2.8 31.4 + - - -
55A GLY 4.4 0.2 - - - +
56A ASP* 3.3 13.5 - - - +
57A ILE* 2.8 43.8 + - - +
1901A 1AA 5.7 0.3 + - - -
130B LYS* 3.6 18.2 - - + +
132B THR* 5.6 3.3 + - - -
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Residues in contact with ALA 47 (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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4A GLY* 3.1 18.9 - - - +
5A HIS 3.5 4.7 - - - -
6A GLY* 3.3 23.5 - - - +
43A ALA 2.9 14.5 + - - +
44A LEU* 3.6 6.1 - - + +
46A ASP* 1.3 76.5 - - - +
48A LEU* 1.3 58.6 + - - +
50A GLY 3.4 0.2 + - - -
51A ALA* 3.0 23.7 + - - +
150A ALA* 3.5 19.3 - - + +
151A VAL 4.1 1.1 - - - -
152A ALA* 4.0 11.1 - - + +
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Residues in contact with LEU 48 (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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44A LEU* 3.0 30.8 + - + +
45A THR* 3.3 3.6 + - - +
47A ALA* 1.3 74.7 - - - +
49A LEU* 1.3 63.9 + - - +
51A ALA* 3.3 6.7 + - - +
52A ALA* 3.2 18.4 + - - +
77A LEU* 3.8 26.7 - - + -
81A TRP* 3.9 10.1 - - + -
84A ILE* 3.6 16.7 - - + +
91A LEU* 3.6 31.0 - - + -
94A VAL* 4.1 2.9 - - + -
120A LEU* 3.8 15.5 - - + -
152A ALA* 3.9 15.5 - - + -
154A LEU* 3.6 23.7 - - + +
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Residues in contact with LEU 49 (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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45A THR* 2.9 38.2 + - + +
46A ASP* 4.1 3.1 - - - +
48A LEU* 1.3 75.1 - - - +
50A GLY* 1.3 59.2 + - - +
52A ALA* 3.2 2.1 + - - +
53A ALA 3.0 8.0 + - - -
54A LEU* 2.8 46.9 + - + +
55A GLY 4.2 9.6 - - - +
56A ASP* 3.6 29.4 - - - +
57A ILE* 3.7 3.6 - - - +
60A LEU* 3.6 30.3 - - + -
80A ALA* 4.0 9.2 - - + +
84A ILE* 3.8 23.8 - - + -
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Residues in contact with GLY 50 (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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3A ILE 4.0 0.7 - - - +
46A ASP 2.8 23.2 + - - -
47A ALA 3.7 0.4 - - - -
49A LEU* 1.3 74.4 - - - +
51A ALA* 1.3 59.0 + - - +
53A ALA* 3.4 2.9 + - - +
55A GLY 4.0 0.4 + - - -
93B ASN* 4.5 3.3 + - - -
95B ASP* 3.4 21.8 - - - +
128B ASN* 3.2 41.7 - - - +
130B LYS* 4.1 0.2 - - - -
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Residues in contact with ALA 51 (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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2A ARG* 3.3 42.3 + - - +
3A ILE 3.4 13.7 - - - -
4A GLY* 3.5 19.5 - - - +
47A ALA 3.0 10.1 + - - +
48A LEU* 3.5 10.8 - - - +
49A LEU 3.2 0.2 - - - -
50A GLY* 1.3 75.5 - - - +
52A ALA* 1.3 57.2 + - - +
53A ALA 3.2 0.9 - - - -
152A ALA* 4.4 2.9 - - + +
154A LEU* 3.6 23.3 - - + +
93B ASN* 4.0 0.3 + - - -
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Residues in contact with ALA 52 (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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48A LEU 3.2 15.2 + - - +
49A LEU 3.2 4.6 + - - +
51A ALA* 1.3 75.4 - - - +
53A ALA* 1.3 59.0 + - - +
54A LEU* 3.2 21.4 + - + +
84A ILE* 4.0 11.0 - - + -
87A LYS* 2.7 33.1 + - - +
89A TYR* 3.8 34.8 + - + -
154A LEU* 4.1 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