Contacts of the helix formed by residues 38 - 52 (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 38 (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* 3.0 27.9 - - - +
20F ILE* 3.4 2.9 - - - -
21F GLY 2.9 18.3 + - - -
22F GLY 3.0 24.6 + - - -
36F ASP* 3.1 8.0 + - - +
37F GLY* 1.3 73.0 - - - +
39F VAL* 1.3 60.3 + - - +
40F ALA 3.4 1.6 + - - -
41F LEU* 3.1 25.3 + - - +
42F HIS* 2.9 34.2 + - - -
73F SER* 3.4 23.1 + - - +
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Residues in contact with VAL 39 (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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8F ASP* 3.6 15.5 - - - +
9F VAL* 3.8 6.3 - - - -
10F HIS* 3.3 33.0 - - + +
20F ILE* 3.7 20.0 - - + -
31F LEU* 4.8 1.6 - - + -
37F GLY 3.2 5.4 + - - +
38F ASP* 1.3 71.9 + - - +
40F ALA* 1.3 59.0 + - + +
43F ALA* 3.0 32.9 + - - +
98F ILE* 5.4 0.9 - - + -
146F ILE* 3.3 49.4 - - + +
148F CYS* 3.6 13.9 - - + +
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Residues in contact with ALA 40 (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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20F ILE* 3.8 15.5 - - + -
21F GLY* 3.7 17.9 - - - +
38F ASP* 3.2 9.9 + - - +
39F VAL* 1.3 83.2 - - - +
41F LEU* 1.3 59.0 + - + +
43F ALA* 3.9 2.1 - - - +
44F LEU* 3.0 29.6 + - - +
96F VAL* 4.3 13.5 - - + +
98F ILE* 4.7 4.3 - - + -
112F MET* 5.4 1.1 - - - -
116F ILE* 6.1 2.5 - - + -
129F VAL* 5.9 0.4 - - + -
148F CYS* 3.4 21.3 - - + +
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Residues in contact with LEU 41 (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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21F GLY* 3.8 11.7 - - - -
22F GLY* 3.5 11.7 - - - +
38F ASP* 3.1 35.2 + - - +
40F ALA* 1.3 74.7 - - - +
42F HIS* 1.3 56.7 + - - +
44F LEU* 3.7 6.6 - - + +
45F THR* 2.5 38.1 + - - -
73F SER* 4.0 21.8 - - - +
74F ARG* 3.6 28.7 - - + +
77F LEU* 3.9 19.2 - - + +
115F PHE* 6.3 0.7 - - + -
116F ILE* 3.8 32.3 - - + +
119F ASP* 5.4 0.4 - - - +
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Residues in contact with HIS 42 (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 4.6 9.1 - + - -
8F ASP* 3.0 20.3 + - - +
10F HIS* 3.2 6.6 + + - -
35F SER* 3.0 32.5 + - - -
38F ASP 2.9 18.0 + - - +
41F LEU* 1.3 76.2 - - - +
43F ALA* 1.3 57.4 + - - +
45F THR* 3.2 8.0 + - - -
46F ASP* 2.9 34.1 + - - +
57F ILE* 4.0 25.1 - - + +
73F SER* 2.7 35.4 + - - -
76F LEU* 4.5 2.4 - - - +
6900F ZN 2.2 31.7 - - - -
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Residues in contact with ALA 43 (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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6F GLY* 3.2 22.2 - - - -
7F PHE 4.2 1.3 - - - +
8F ASP* 3.9 11.8 - - - +
39F VAL 3.0 18.6 + - - +
40F ALA 3.9 2.7 - - - +
42F HIS* 1.3 76.5 - - - +
44F LEU* 1.3 57.3 + - - +
46F ASP* 3.4 1.7 + - - -
47F ALA 3.0 23.2 + - - -
148F CYS* 3.4 32.3 - - - +
150F ALA* 3.4 11.0 - - + +
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Residues in contact with LEU 44 (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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40F ALA 3.0 19.4 + - - +
41F LEU* 3.7 9.4 - - + +
43F ALA* 1.3 74.3 - - - +
45F THR* 1.3 63.1 + - - +
47F ALA* 3.3 5.6 + - + +
48F LEU* 3.0 37.4 + - + +
77F LEU* 4.2 16.4 - - + -
94F VAL* 3.7 36.6 - - + -
96F VAL* 4.0 15.9 - - + -
116F ILE* 3.6 45.1 - - + -
120F LEU* 4.8 1.8 - - + -
150F ALA* 3.7 10.0 - - + +
151F VAL 5.2 0.7 - - - +
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Residues in contact with THR 45 (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 2.5 26.2 + - - -
42F HIS* 3.4 6.4 - - - -
44F LEU* 1.3 76.0 - - - +
46F ASP* 1.3 57.0 + - - +
48F LEU* 3.2 6.1 + - - +
49F LEU* 2.8 50.2 + - + +
57F ILE* 4.0 24.2 - - + +
61F PHE* 5.1 0.4 - - + -
73F SER 4.9 1.2 + - - -
76F LEU 4.5 4.9 - - - +
77F LEU* 3.4 25.7 + - - +
80F ALA* 3.7 20.2 - - + -
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Residues in contact with ASP 46 (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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130D LYS* 3.7 16.2 - - + +
132D THR* 4.2 11.1 + - - +
6901D 1AA 5.7 0.5 + - - -
5F HIS 4.0 1.8 - - - -
6F GLY* 3.8 11.4 - - - -
7F PHE 4.2 13.3 + - - +
8F ASP* 5.5 2.1 - - - +
42F HIS* 2.9 19.8 + - - +
43F ALA* 3.7 5.8 - - - +
45F THR* 1.3 75.3 - - - +
47F ALA* 1.3 53.4 + - - +
49F LEU* 4.0 4.1 - - - +
50F GLY* 2.7 32.4 + - - -
56F ASP* 3.3 12.5 - - - +
57F ILE* 2.8 43.3 + - - +
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Residues in contact with ALA 47 (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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4F GLY* 3.1 18.4 - - - +
5F HIS 3.5 12.6 - - - +
6F GLY* 3.4 15.9 - - - +
43F ALA 3.0 14.7 + - - +
44F LEU* 3.5 6.5 - - + +
45F THR 3.3 0.2 - - - -
46F ASP* 1.3 74.7 - - - +
48F LEU* 1.3 57.5 + - - +
51F ALA* 3.0 24.8 + - - +
150F ALA* 3.5 19.5 - - + +
151F VAL 4.2 0.2 - - - -
152F ALA* 3.8 12.2 - - + +
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Residues in contact with LEU 48 (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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44F LEU* 3.0 30.6 + - + +
45F THR* 3.6 3.4 - - - +
47F ALA* 1.3 77.7 - - - +
49F LEU* 1.3 60.4 + - - +
51F ALA* 3.3 2.5 + - - -
52F ALA* 3.1 17.3 + - - +
77F LEU* 3.7 27.4 - - + -
80F ALA* 6.2 1.1 - - + -
81F TRP* 4.0 11.0 - - + -
84F ILE* 3.6 18.8 - - + +
91F LEU* 3.7 30.1 - - + -
94F VAL* 4.0 3.1 - - + -
120F LEU* 3.8 16.4 - - + -
152F ALA* 3.9 14.6 - - + -
154F LEU* 3.6 26.9 - - + +
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Residues in contact with LEU 49 (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* 2.8 38.1 + - + +
46F ASP 4.0 3.1 - - - +
48F LEU* 1.3 70.9 - - - +
50F GLY* 1.3 58.4 + - - +
52F ALA* 3.5 1.0 + - - -
53F ALA 3.1 5.5 + - - -
54F LEU* 2.8 54.0 + - + +
55F GLY 3.9 11.2 + - - +
56F ASP* 3.5 32.5 - - - +
57F ILE* 3.7 6.5 - - - +
60F LEU* 3.8 29.4 - - + -
80F ALA* 3.9 9.0 - - + +
84F ILE* 3.8 21.5 - - + -
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Residues in contact with GLY 50 (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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93D ASN* 4.5 2.9 + - - -
95D ASP* 3.4 19.1 - - - +
128D ASN* 3.2 36.7 - - - +
130D LYS* 4.2 0.2 - - - -
2F ARG* 4.6 0.3 + - - -
3F ILE 4.1 1.9 - - - +
4F GLY* 4.1 0.4 - - - -
46F ASP 2.7 22.6 + - - -
47F ALA 3.7 0.2 - - - -
49F LEU* 1.3 71.8 - - - +
51F ALA* 1.3 62.9 + - - +
53F ALA* 3.1 9.9 + - - +
55F GLY 4.2 0.2 + - - -
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Residues in contact with ALA 51 (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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2F ARG* 2.6 47.0 + - - +
3F ILE 3.3 14.4 - - - -
4F GLY* 3.5 19.2 - - - +
47F ALA 3.0 13.4 + - - +
48F LEU* 3.3 1.8 + - - +
50F GLY* 1.3 75.9 - - - +
52F ALA* 1.3 54.4 + - - +
53F ALA 3.2 0.2 - - - -
89F TYR* 4.6 0.3 - - - -
152F ALA* 4.2 3.6 - - + +
154F LEU* 3.6 28.9 - - + -
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Residues in contact with ALA 52 (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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2F ARG* 4.4 1.6 - - - -
48F LEU 3.1 15.6 + - - +
49F LEU 3.5 2.2 + - - +
50F GLY 3.2 0.2 - - - -
51F ALA* 1.3 75.4 - - - +
53F ALA* 1.3 55.6 + - - +
54F LEU* 3.4 12.0 + - + -
84F ILE* 3.9 21.3 - - + -
87F LYS* 2.6 34.8 + - - +
89F TYR* 3.7 32.6 + - + -
154F LEU* 4.2 0.4 - - + -
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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
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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