Contacts of the helix formed by residues 38 - 52 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 3.3 24.6 - - - +
20E ILE* 3.4 2.4 - - - -
21E GLY 2.7 20.3 + - - -
22E GLY* 2.8 28.1 + - - -
36E ASP* 3.3 10.9 + - - +
37E GLY* 1.3 72.7 - - - +
39E VAL* 1.3 56.8 + - - +
40E ALA 3.5 1.7 + - - -
41E LEU* 3.2 24.5 + - - +
42E HIS* 3.1 34.4 + - - -
73E SER* 3.2 21.7 + - - +
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Residues in contact with VAL 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ASP* 3.2 48.0 - - + +
9E VAL* 3.7 4.0 - - - +
10E HIS* 4.0 4.5 - - + +
20E ILE* 3.8 16.2 - - + +
31E LEU* 5.6 0.2 - - + -
37E GLY 2.8 11.2 + - - +
38E ASP* 1.3 70.4 + - - +
40E ALA* 1.3 65.6 + - + +
43E ALA* 3.1 31.0 + - - +
98E ILE* 4.9 0.7 - - + -
146E ILE* 3.5 43.5 - - + +
148E CYS* 3.6 14.1 - - + +
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 3.8 13.7 - - + -
21E GLY* 3.8 24.2 - - - +
38E ASP* 3.3 1.0 + - - -
39E VAL* 1.3 81.8 - - - +
41E LEU* 1.3 58.7 + - + +
43E ALA* 3.8 1.9 - - - +
44E LEU* 2.9 29.6 + - - +
96E VAL* 4.1 14.4 - - + +
98E ILE* 4.4 5.6 - - + -
112E MET* 5.4 0.4 - - - -
116E ILE* 6.0 2.9 - - + -
129E VAL* 5.9 0.9 - - + -
148E CYS* 3.4 22.8 - - - -
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLY* 3.8 11.7 - - - +
22E GLY* 3.6 6.1 - - - +
38E ASP* 3.2 32.9 + - - +
40E ALA* 1.3 75.8 - - - +
42E HIS* 1.3 57.9 + - - +
44E LEU* 3.5 5.8 + - + +
45E THR* 2.5 39.5 + - - +
73E SER* 3.8 24.0 - - - +
74E ARG* 3.6 33.9 - - + +
77E LEU* 3.8 16.4 - - + +
115E PHE* 6.3 0.7 - - + -
116E ILE* 3.7 32.3 - - + -
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Residues in contact with HIS 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ASP* 3.2 18.4 - - - +
10E HIS* 3.3 3.3 + - - -
35E SER* 3.0 35.8 + - - -
38E ASP 3.1 25.1 + - - +
39E VAL 3.9 0.2 - - - +
41E LEU* 1.3 74.2 - - - +
43E ALA* 1.3 60.0 + - - +
45E THR* 3.3 2.6 + - - -
46E ASP* 3.0 34.4 + - - +
57E ILE* 4.0 26.4 - - + +
73E SER* 2.7 31.5 + - - -
76E LEU* 4.7 1.2 - - - +
5900E ZN 2.1 30.2 - - - -
5901E 1AA 3.2 17.1 + + - -
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLY* 3.2 26.1 - - - +
7E PHE 4.3 2.2 - - - +
8E ASP* 4.0 8.2 - - - +
39E VAL 3.1 19.0 + - - +
40E ALA 3.8 2.9 - - - +
42E HIS* 1.3 72.7 - - - +
44E LEU* 1.3 60.2 + - - +
46E ASP* 3.5 1.7 + - - -
47E ALA* 3.0 25.1 + - - +
148E CYS* 3.5 32.5 - - - +
150E ALA* 3.6 6.5 - - + +
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ALA 2.9 18.1 + - - +
41E LEU* 3.6 9.0 - - + +
43E ALA* 1.3 73.7 - - - +
45E THR* 1.3 59.4 + - - +
47E ALA* 3.2 4.5 + - + +
48E LEU* 3.0 43.8 + - + +
77E LEU* 3.9 16.8 - - + -
94E VAL* 3.6 36.6 - - + -
96E VAL* 4.0 15.9 - - + -
116E ILE* 3.7 44.2 - - + -
120E LEU* 4.5 2.2 - - + -
150E ALA* 3.7 10.7 - - + +
151E VAL 5.2 2.2 - - - +
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Residues in contact with THR 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU 2.5 30.3 + - - -
42E HIS 3.3 5.1 + - - -
44E LEU* 1.3 72.7 - - - +
46E ASP* 1.3 57.4 + - - +
48E LEU* 3.3 3.8 + - - +
49E LEU* 2.8 43.3 + - + +
57E ILE* 3.9 25.8 - - + +
61E PHE* 5.0 0.2 - - + -
73E SER 4.8 0.9 + - - -
76E LEU 4.4 5.4 - - - +
77E LEU* 3.4 26.7 + - - +
80E ALA* 3.6 29.4 - - + -
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Residues in contact with ASP 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E HIS 3.8 2.0 - - - -
6E GLY* 4.0 7.6 - - - -
7E PHE 4.3 12.2 - - - +
8E ASP* 5.7 1.2 - - - +
42E HIS* 3.0 19.0 + - - +
43E ALA* 3.8 5.2 - - - +
45E THR* 1.3 72.3 - - - +
47E ALA* 1.3 56.6 + - - +
49E LEU* 4.1 3.8 - - - +
50E GLY* 2.7 32.1 + - - -
56E ASP* 3.3 5.4 - - - +
57E ILE* 2.7 43.9 + - - +
5901E 1AA 5.3 0.9 + - - -
130F LYS* 3.4 31.4 - - + +
131F ALA 5.2 1.7 - - - +
132F THR* 4.3 8.3 + - - +
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Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLY* 3.3 13.7 - - - +
5E HIS 3.5 12.5 + - - +
6E GLY 3.6 1.3 - - - +
43E ALA 3.0 15.1 + - - +
44E LEU* 3.2 9.6 + - + +
46E ASP* 1.3 75.0 - - - +
48E LEU* 1.3 57.4 + - - +
50E GLY 3.4 0.5 + - - -
51E ALA* 2.9 24.6 + - - +
150E ALA* 3.6 29.8 - - + +
151E VAL 4.2 0.4 - - - -
152E ALA* 3.8 17.9 - - + +
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 3.0 31.3 + - + +
45E THR* 3.7 3.8 - - - +
47E ALA* 1.3 73.1 - - - +
49E LEU* 1.3 64.9 + - - +
51E ALA* 3.2 5.6 + - - +
52E ALA 3.1 17.3 + - - -
77E LEU* 3.8 17.9 - - + +
80E ALA* 6.3 1.1 - - + -
81E TRP* 4.3 6.3 - - + -
84E ILE* 3.6 17.9 - - + +
91E LEU* 3.6 29.8 - - + -
94E VAL* 4.0 3.8 - - + -
120E LEU* 3.7 26.0 - - + -
152E ALA* 3.8 20.2 - - + -
154E LEU* 3.6 19.3 - - + +
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E THR* 2.8 38.0 + - + +
46E ASP* 4.1 3.1 - - - +
48E LEU* 1.3 69.1 - - - +
50E GLY* 1.3 59.6 + - - +
52E ALA 3.3 1.5 + - - +
53E ALA 3.1 7.3 + - - -
54E LEU* 2.8 53.1 + - + -
55E GLY 3.9 10.7 + - - +
56E ASP* 3.5 30.7 - - - +
57E ILE* 3.8 2.7 - - - +
60E LEU* 3.7 31.2 - - + -
61E PHE* 5.2 0.2 - - + -
80E ALA* 3.8 15.7 - - + +
84E ILE* 3.8 13.9 - - + -
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Residues in contact with GLY 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ARG* 4.8 0.2 + - - -
3E ILE 4.2 0.7 - - - +
46E ASP 2.7 20.3 + - - -
49E LEU* 1.3 74.8 - - - +
51E ALA* 1.3 58.3 + - - +
53E ALA* 3.3 9.0 + - - +
55E GLY 4.1 0.6 + - - -
93F ASN* 4.6 2.9 + - - -
95F ASP* 3.3 28.4 - - - +
128F ASN* 3.3 32.9 - - - +
130F LYS* 4.1 0.7 - - - -
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Residues in contact with ALA 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ARG* 2.7 45.4 + - - +
3E ILE 3.3 14.6 - - - -
4E GLY* 3.5 16.1 - - - +
47E ALA 2.9 17.4 + - - +
48E LEU* 3.2 7.6 + - - +
50E GLY* 1.3 76.1 - - - +
52E ALA* 1.3 52.8 + - - +
53E ALA 3.2 0.7 - - - -
152E ALA* 4.2 3.6 - - + +
154E LEU* 3.6 22.3 - - + +
93F ASN* 4.2 0.3 + - - -
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Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ARG* 4.2 2.2 - - - -
48E LEU 3.1 14.3 + - - +
49E LEU 3.3 3.1 + - - +
50E GLY 3.3 0.2 - - - -
51E ALA* 1.3 74.7 - - - +
53E ALA* 1.3 66.0 + - - +
54E LEU* 3.2 10.2 + - + -
84E ILE* 3.8 19.5 - - + -
87E LYS* 3.1 26.7 + - - +
89E TYR* 3.6 32.2 - - + -
154E LEU* 4.0 3.4 - - + -
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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
------------------------------------------------------------
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