Contacts of the helix formed by residues 38 - 52 (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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.3 18.9 - - - +
20B ILE* 3.5 2.6 - - - -
21B GLY 2.7 21.7 + - - -
22B GLY* 2.8 29.1 + - - -
36B ASP* 2.9 9.4 + - - +
37B GLY* 1.3 71.8 - - - +
39B VAL* 1.3 65.3 - - - +
40B ALA 3.5 1.6 + - - -
41B LEU* 3.1 25.7 + - + +
42B HIS* 3.0 29.1 + - - -
73B SER* 3.3 22.2 - - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP* 3.2 46.7 - - + +
9B VAL* 3.8 2.9 - - - +
10B HIS* 3.9 10.5 - - + +
20B ILE* 3.9 17.1 - - + +
31B LEU* 4.0 9.0 - - + -
37B GLY 2.9 13.3 + - - +
38B ASP* 1.3 71.2 + - - +
40B ALA* 1.3 62.9 + - - +
43B ALA* 3.1 26.7 + - - +
98B ILE* 6.4 0.2 - - + -
146B ILE* 3.4 30.7 - - + +
147B ALA 3.9 0.2 - - - -
148B CYS* 3.7 15.0 - - + +
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Residues in contact with ALA 40 (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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20B ILE* 3.8 15.2 - - + +
21B GLY* 3.7 17.9 - - - +
38B ASP* 3.2 9.5 + - - +
39B VAL* 1.3 79.1 - - - +
41B LEU* 1.3 58.6 + - + +
43B ALA* 4.0 1.9 - - - +
44B LEU* 3.1 27.9 + - - +
96B VAL* 4.2 16.0 - - + +
98B ILE* 4.3 5.6 - - + -
112B MET* 5.5 0.9 - - - -
116B ILE* 6.0 3.1 - - + -
129B VAL* 5.9 0.7 - - + -
148B CYS* 3.5 19.4 - - - +
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Residues in contact with LEU 41 (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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21B GLY* 3.9 10.3 - - - -
22B GLY 3.7 5.8 - - - +
38B ASP* 3.1 32.9 + - - +
40B ALA* 1.3 76.9 - - - +
42B HIS* 1.3 56.9 + - - +
44B LEU* 3.7 6.7 - - + +
45B THR* 2.5 39.5 + - - +
73B SER* 3.9 13.9 - - - +
74B ARG* 3.6 41.7 - - + +
77B LEU* 3.8 19.0 - - + +
115B PHE* 6.4 0.4 - - + -
116B ILE* 3.8 32.1 - - + -
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Residues in contact with HIS 42 (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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8B ASP* 3.1 17.6 + - - +
10B HIS* 3.1 6.4 + - - -
35B SER* 3.3 29.3 - - - -
38B ASP 3.0 18.7 + - - +
41B LEU* 1.3 75.0 - - - +
43B ALA* 1.3 58.9 + - - +
45B THR* 3.3 7.5 + - - -
46B ASP* 3.0 34.6 + - - -
57B ILE* 4.1 9.8 - - + +
73B SER* 2.7 32.3 + - - -
76B LEU* 4.3 5.1 - - + +
2900B ZN 2.2 31.3 - - - -
2901C 1AA 3.5 27.2 - + - -
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Residues in contact with ALA 43 (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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6B GLY* 3.2 28.0 - - - +
7B PHE 4.3 1.3 - - - +
8B ASP* 4.0 8.7 - - - +
39B VAL 3.1 17.1 + - - +
40B ALA 4.0 2.9 - - - +
42B HIS* 1.3 77.6 - - - +
44B LEU* 1.3 58.8 + - - +
46B ASP* 3.4 2.3 + - - -
47B ALA* 2.9 24.9 + - - +
148B CYS* 3.6 28.5 - - - +
150B ALA* 3.7 9.6 - - + -
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Residues in contact with LEU 44 (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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40B ALA 3.1 19.3 + - - +
41B LEU* 3.7 13.0 - - + +
43B ALA* 1.3 73.9 - - - +
45B THR* 1.3 59.6 + - - +
47B ALA* 3.1 2.5 + - + +
48B LEU* 2.9 46.8 + - + +
77B LEU* 4.4 9.4 - - + -
94B VAL* 3.6 37.2 - - + -
96B VAL* 4.3 11.9 - - + -
116B ILE* 3.6 44.4 - - + -
120B LEU* 4.6 2.0 - - + -
150B ALA* 3.7 12.5 - - + +
151B VAL 4.9 0.7 - - - +
152B ALA* 4.9 3.6 - - + -
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Residues in contact with THR 45 (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 2.5 29.7 + - - -
42B HIS* 3.3 8.6 + - - -
44B LEU* 1.3 73.6 - - - +
46B ASP* 1.3 52.9 + - - +
48B LEU* 3.3 4.7 + - - +
49B LEU* 2.8 39.1 + - + +
57B ILE* 3.6 23.3 - - + -
61B PHE* 5.0 2.2 - - + -
73B SER 4.8 1.2 + - - -
76B LEU* 4.3 9.1 - - + +
77B LEU* 3.7 26.4 + - + +
80B ALA* 3.5 29.3 - - + +
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Residues in contact with ASP 46 (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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5B HIS 3.9 2.0 - - - -
6B GLY* 3.9 7.6 - - - -
7B PHE 4.4 12.0 - - - +
8B ASP* 5.5 1.4 - - - +
42B HIS 3.0 20.4 + - - +
43B ALA* 3.6 5.6 - - - +
44B LEU 3.2 0.2 - - - -
45B THR* 1.3 74.3 - - - +
47B ALA* 1.3 55.7 + - - +
49B LEU* 4.1 3.3 - - - +
50B GLY* 2.8 32.1 + - - -
56B ASP* 3.4 5.0 - - - +
57B ILE* 2.8 47.9 + - - +
130C LYS* 3.5 29.0 - - + +
131C ALA 5.6 0.7 - - - +
132C THR* 5.3 6.2 + - - -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY* 3.2 19.5 - - - +
5B HIS 3.6 11.2 - - - -
6B GLY* 3.6 1.0 - - - +
43B ALA 2.9 15.1 + - - +
44B LEU* 3.1 8.9 + - + +
46B ASP* 1.3 75.4 - - - +
48B LEU* 1.3 57.1 + - - +
51B ALA* 3.0 24.8 + - - +
150B ALA* 3.5 30.7 - - + +
151B VAL 4.1 0.4 - - - -
152B ALA* 4.0 14.4 - - + +
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Residues in contact with LEU 48 (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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44B LEU* 2.9 31.8 + - + +
45B THR* 3.6 3.4 - - + +
47B ALA* 1.3 74.1 - - - +
49B LEU* 1.3 65.0 + - - +
51B ALA* 3.2 6.5 + - - +
52B ALA* 3.1 17.5 + - - +
77B LEU* 3.7 28.0 - - + -
80B ALA* 6.0 1.1 - - + -
81B TRP* 4.1 9.6 - - + +
84B ILE* 3.5 20.8 - - + +
91B LEU* 3.7 30.3 - - + -
94B VAL* 4.1 2.5 - - + -
120B LEU* 3.7 14.6 - - + -
152B ALA* 3.8 17.7 - - + -
154B LEU* 3.7 15.4 - - + +
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Residues in contact with LEU 49 (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* 2.8 37.6 + - + +
46B ASP* 4.1 2.9 - - - +
48B LEU* 1.3 72.2 - - - +
50B GLY* 1.3 56.1 + - - +
52B ALA 3.2 2.3 + - - -
53B ALA 3.1 7.1 + - - -
54B LEU* 2.8 58.9 + - + +
55B GLY 4.2 10.8 - - - +
56B ASP* 3.5 32.1 - - - +
57B ILE* 3.8 5.2 - - - +
60B LEU* 3.9 23.1 - - + -
80B ALA* 3.9 20.9 - - + +
83B ARG* 5.7 0.2 - - + -
84B ILE* 3.9 12.3 - - + -
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Residues in contact with GLY 50 (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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2B ARG* 4.8 0.2 + - - -
3B ILE 4.0 0.7 - - - +
46B ASP 2.8 18.8 + - - -
49B LEU* 1.3 71.0 - - - +
51B ALA* 1.3 62.5 + - - +
53B ALA* 3.4 2.6 + - - +
55B GLY 4.1 0.4 + - - -
93C ASN* 4.4 4.0 + - - -
95C ASP* 3.2 29.4 - - - +
128C ASN* 3.3 38.7 - - - +
130C LYS* 4.1 0.4 - - - -
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Residues in contact with ALA 51 (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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2B ARG* 2.7 49.0 + - - +
3B ILE 3.3 14.4 - - - +
4B GLY* 3.6 15.6 - - - +
47B ALA 3.0 19.2 + - - +
48B LEU* 3.2 6.7 + - - +
50B GLY* 1.3 76.5 - - - +
52B ALA* 1.3 53.4 + - - +
53B ALA 3.3 0.9 - - - -
152B ALA 4.1 3.6 - - - +
154B LEU* 3.7 19.6 - - + +
93C ASN* 4.4 0.2 - - - +
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Residues in contact with ALA 52 (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 3.1 12.0 + - - +
49B LEU 3.2 7.8 + - - +
51B ALA* 1.3 76.2 - - - +
53B ALA* 1.3 69.7 + - - +
54B LEU* 3.3 10.3 + - + +
84B ILE* 3.8 22.7 - - + -
87B LYS* 3.2 20.3 + - - +
89B TYR* 3.8 32.1 + - + -
154B LEU* 3.9 3.3 - - + +
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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