Contacts of the helix formed by residues 23 - 41 (chain A) in PDB entry 1AST
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 SER 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY 4.1 1.2 + - - -
22A VAL* 1.3 78.1 - - - +
24A GLY* 1.3 59.7 + - - +
25A ALA* 3.8 6.6 + - - +
26A ASP* 3.1 32.7 + - - +
27A GLN* 2.8 26.7 + - - +
59A THR* 4.8 1.4 + - - -
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Residues in contact with GLY 24 (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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22A VAL 3.8 0.8 + - - -
23A SER* 1.3 72.7 - - - +
25A ALA* 1.3 51.9 + - - +
27A GLN* 3.4 11.9 + - - +
28A SER* 2.7 37.1 + - - -
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Residues in contact with ALA 25 (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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23A SER* 3.3 7.0 + - - +
24A GLY* 1.3 73.8 - - - +
26A ASP* 1.3 66.9 + - - +
28A SER* 3.3 8.4 + - - -
29A ALA* 3.1 21.5 + - - +
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.5 19.7 - - + -
23A SER* 3.1 20.6 + - - +
25A ALA* 1.3 81.1 - - - +
27A GLN* 1.3 60.6 + - - +
29A ALA* 3.2 3.6 + - - +
30A ILE* 3.0 28.5 + - + +
59A THR* 3.9 17.0 + - + +
81A ALA* 4.1 17.8 - - - +
85A VAL* 3.6 30.6 - - + +
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Residues in contact with GLN 27 (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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19A PHE* 3.4 51.3 - - + +
22A VAL* 3.1 32.1 + - + +
23A SER 2.8 21.7 + - - +
24A GLY* 3.6 9.3 - - - +
26A ASP* 1.3 72.4 - - - +
28A SER* 1.3 56.4 + - - +
30A ILE* 3.2 0.9 + - - +
31A LEU* 2.9 41.9 + - + +
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Residues in contact with SER 28 (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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24A GLY 2.7 22.2 + - - -
25A ALA* 3.6 9.6 - - - -
26A ASP 3.3 0.2 - - - -
27A GLN* 1.3 76.0 - - - +
29A ALA* 1.3 63.4 + - - +
31A LEU* 3.5 9.7 + - - +
32A SER* 3.1 26.2 + - - -
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Residues in contact with ALA 29 (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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25A ALA 3.1 12.3 + - - +
26A ASP 3.6 7.6 - - - +
28A SER* 1.3 77.4 - - - +
30A ILE* 1.3 63.0 + - - +
32A SER* 3.2 8.1 + - - -
33A GLY 3.0 18.4 + - - -
85A VAL* 3.7 24.9 - - + +
87A HIS* 5.0 1.7 + - - -
90A ILE* 3.7 13.8 - - + +
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Residues in contact with ILE 30 (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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19A PHE* 3.9 23.8 - - + -
22A VAL* 4.2 9.9 - - + -
26A ASP* 3.0 28.7 + - + +
27A GLN 3.8 4.0 - - - +
28A SER 3.2 0.2 - - - -
29A ALA* 1.3 76.5 - - - +
31A LEU* 1.3 63.1 + - - +
33A GLY* 3.0 4.5 + - - -
34A MET* 2.9 38.3 + - + +
57A ILE* 3.9 29.6 - - + -
59A THR* 4.8 6.7 - - + -
79A LEU* 4.0 18.8 - - + -
85A VAL* 4.9 4.9 - - + -
90A ILE* 4.0 23.2 - - + +
94A LEU* 5.0 1.8 - - + -
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Residues in contact with LEU 31 (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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17A TYR* 3.5 26.9 - - + +
19A PHE* 4.3 14.6 - - + -
27A GLN* 2.9 29.5 + - + +
28A SER* 3.9 7.6 - - - +
30A ILE* 1.3 76.8 - - - +
32A SER* 1.3 55.4 + - - +
34A MET* 3.2 22.5 + - + +
35A GLN* 2.8 28.1 + - - +
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Residues in contact with SER 32 (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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28A SER 3.1 15.6 + - - -
29A ALA* 3.2 11.3 + - - -
31A LEU* 1.3 72.1 - - - +
33A GLY* 1.3 65.1 + - - +
35A GLN* 3.3 20.8 + - - +
36A GLU 3.3 10.4 + - - -
87A HIS* 3.5 17.9 - - - -
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Residues in contact with GLY 33 (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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29A ALA 3.0 11.9 + - - -
30A ILE 3.0 4.2 + - - -
32A SER* 1.3 74.5 - - - +
34A MET* 1.3 62.5 + - - +
35A GLN 3.3 0.5 + - - -
36A GLU* 3.4 6.6 + - - +
37A LEU* 3.4 17.9 + - - +
87A HIS* 3.8 17.5 + - - -
90A ILE* 4.0 18.6 - - - -
91A ILE* 3.8 15.0 - - - +
94A LEU* 4.9 0.2 - - - -
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Residues in contact with MET 34 (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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17A TYR* 3.9 20.4 - - + -
19A PHE* 5.0 0.4 - - + -
30A ILE* 2.9 22.7 + - + +
31A LEU* 3.5 31.6 - - + +
33A GLY* 1.3 76.2 - - - +
35A GLN* 1.3 57.2 + - - +
37A LEU* 3.1 7.2 + - - +
38A GLU* 2.9 35.5 + - - +
45A PHE* 3.6 53.8 - - + -
57A ILE* 3.6 31.0 - - + -
94A LEU* 3.8 13.6 - - + +
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Residues in contact with GLN 35 (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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31A LEU 2.8 16.7 + - - +
32A SER* 3.5 13.5 + - - +
33A GLY 3.2 0.2 - - - -
34A MET* 1.3 73.0 - - - +
36A GLU* 1.3 67.7 + - - +
38A GLU* 3.1 9.7 + - + +
39A GLU* 2.9 51.8 + - + +
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Residues in contact with GLU 36 (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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32A SER 3.3 5.7 + - - +
33A GLY 3.8 8.3 - - - +
34A MET 3.4 0.4 - - - -
35A GLN* 1.3 78.0 - - - +
37A LEU* 1.3 63.7 + - - +
39A GLU* 3.3 12.8 + - - +
40A LYS* 3.0 54.5 + - + +
87A HIS* 2.8 31.0 + - + +
91A ILE* 3.8 17.7 - - + -
181A HIS* 2.9 21.1 + - - +
182A MET* 2.9 31.7 + - - +
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Residues in contact with LEU 37 (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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33A GLY 3.4 13.1 + - - +
34A MET 3.1 8.1 + - - +
36A GLU* 1.3 78.5 - - - +
38A GLU* 1.3 56.4 + - - +
41A THR* 2.8 43.7 + - + +
43A ILE* 4.7 1.8 - - + -
45A PHE* 4.1 22.4 - - + -
91A ILE* 4.3 20.6 - - + +
94A LEU* 4.0 31.6 - - + -
95A MET* 5.3 1.8 - - + -
98A ILE* 4.0 11.9 - - + -
182A MET* 3.8 30.5 - - + -
190A ILE* 3.9 17.0 - - + -
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Residues in contact with GLU 38 (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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34A MET* 2.9 23.5 + - - +
35A GLN* 3.1 7.9 + - + +
37A LEU* 1.3 74.4 - - - +
39A GLU* 1.3 64.5 + - + +
41A THR 3.1 6.2 - - - +
43A ILE 3.4 13.2 - - - +
44A ARG* 3.0 46.6 + - - +
45A PHE* 2.8 44.8 + - + +
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Residues in contact with GLU 39 (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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35A GLN* 2.9 50.9 + - + +
36A GLU* 3.3 13.3 + - - +
38A GLU* 1.3 80.2 - - + +
40A LYS* 1.3 63.1 + - + +
41A THR 4.7 0.4 - - - +
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Residues in contact with LYS 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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36A GLU* 3.0 38.1 + - + +
37A LEU 4.3 1.3 - - - +
39A GLU* 1.3 84.2 - - + +
41A THR* 1.3 61.1 + - + +
181A HIS* 4.1 7.2 - - - +
182A MET* 2.9 45.1 + - + -
183A LEU 4.8 3.5 - - - +
184A GLN* 5.1 11.9 + - - +
187A ALA* 3.8 22.1 - - + +
191A ASN* 3.2 18.2 + - - -
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Residues in contact with THR 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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37A LEU* 2.8 27.2 + - + +
38A GLU 3.1 6.4 - - - +
39A GLU 4.7 0.3 - - - -
40A LYS* 1.3 85.1 - - + +
42A CYS* 1.3 58.1 - - - +
43A ILE* 3.1 22.5 + - - +
44A ARG* 3.0 21.0 + - - -
182A MET* 4.8 0.7 - - + -
187A ALA* 4.0 16.4 - - + +
190A ILE* 3.8 39.7 - - + -
191A ASN* 3.2 12.6 - - - +
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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