Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 1AII
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 PRO 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.7 37.2 - - + +
20A SER* 1.3 88.3 - - - +
22A SER* 1.3 57.4 + - - +
24A ASP* 3.4 2.2 + - + +
25A ALA* 2.9 30.8 + - - +
56A LEU* 4.0 25.8 - - + +
57A ILE* 4.7 3.5 - - + +
60A GLU* 3.7 14.3 - - + +
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Residues in contact with SER 22 (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 SER* 3.7 8.2 + - - -
21A PRO* 1.3 76.8 - - - +
23A VAL* 1.3 67.1 + - - +
25A ALA* 4.0 1.2 - - - +
26A GLU* 3.1 25.5 + - - +
60A GLU* 3.7 26.6 - - - +
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Residues in contact with VAL 23 (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 SER* 3.1 29.1 + - - +
22A SER* 1.3 80.9 + - - +
24A ASP* 1.3 68.4 + - - +
26A GLU* 3.4 9.0 + - - +
27A ALA* 3.1 23.9 + - + +
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Residues in contact with ASP 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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19A PHE* 3.2 17.3 - - - -
20A SER 3.0 17.3 + - - +
21A PRO 3.9 0.9 - - - +
23A VAL* 1.3 80.9 - - - +
25A ALA* 1.3 60.7 + - - +
27A ALA* 3.2 6.5 + - - +
28A ILE* 2.9 35.0 + - - +
45A ILE* 3.8 14.2 - - + +
49A ARG* 2.5 46.3 + - - -
57A ILE* 3.7 23.0 - - + +
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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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21A PRO 2.9 21.4 + - - +
22A SER 4.2 2.9 - - - +
24A ASP* 1.3 72.9 - - - +
26A GLU* 1.3 57.0 + - - +
28A ILE* 3.5 1.1 + - - -
29A GLN* 3.0 29.3 + - - +
57A ILE* 4.2 13.6 - - + +
60A GLU* 4.3 9.2 - - + +
61A TYR* 3.5 41.9 - - + +
64A ALA* 6.0 0.2 - - + -
65A TYR* 3.8 7.3 - - + -
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Residues in contact with GLU 26 (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 SER 3.1 19.0 + - - +
23A VAL* 3.7 7.3 - - - +
25A ALA* 1.3 73.3 - - - +
27A ALA* 1.3 65.9 + - - +
29A GLN* 3.4 2.4 + - - +
30A LYS* 3.0 56.9 + - - +
65A TYR* 3.5 20.6 + - - +
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Residues in contact with ALA 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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23A VAL* 3.1 19.1 + - + +
24A ASP* 3.2 1.3 + - - +
26A GLU* 1.3 77.6 - - - +
28A ILE* 1.3 60.5 + - - +
30A LYS* 3.4 7.9 + - - +
31A ALA* 3.1 23.2 + - - +
41A MET* 4.2 14.6 - - - +
45A ILE* 3.6 24.2 - - + -
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Residues in contact with ILE 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 ASP 2.9 18.3 + - - +
25A ALA 3.9 3.1 - - - +
27A ALA* 1.3 73.4 - - - +
29A GLN* 1.4 68.4 + - - +
31A ALA* 3.3 2.8 + - - +
32A ILE* 3.2 26.4 + - + +
42A LEU* 3.6 27.1 - - + -
45A ILE* 4.1 22.0 - - + -
46A LEU* 3.9 25.1 - - + -
57A ILE* 3.6 31.0 - - + -
61A TYR* 3.8 7.0 - - + +
69A LEU* 3.4 32.3 - - + -
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Residues in contact with GLN 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 3.0 18.5 + - - +
26A GLU 3.9 2.5 - - - +
28A ILE* 1.4 74.5 - - - +
30A LYS* 1.3 65.1 + - - +
32A ILE* 4.0 0.9 - - + +
33A ARG* 3.1 73.2 + - + +
61A TYR* 3.3 28.6 - - + +
65A TYR* 3.6 46.7 + - + +
67A LYS* 4.9 12.4 - - + +
72A ASP* 5.1 1.6 - - - +
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Residues in contact with LYS 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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26A GLU* 3.0 46.1 + - + +
27A ALA* 3.7 7.0 - - - +
28A ILE 3.2 0.2 - - - -
29A GLN* 1.3 78.8 + - - +
31A ALA* 1.3 61.8 + - - +
32A ILE 3.3 0.7 + - - -
33A ARG* 3.5 57.5 + - - +
65A TYR* 5.2 2.0 + - - -
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Residues in contact with ALA 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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27A ALA 3.1 16.4 + - - +
28A ILE 3.3 5.6 + - - +
30A LYS* 1.3 76.6 - - - +
32A ILE* 1.3 58.0 + - - +
33A ARG 4.8 0.6 - - - +
36A GLY 4.0 1.2 - - - +
37A THR* 3.4 6.9 - - - +
38A ASP* 3.0 57.4 + - + +
41A MET* 4.0 13.7 - - + -
42A LEU* 4.3 11.4 - - + -
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Residues in contact with ILE 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 ILE* 3.2 17.9 + - + +
29A GLN* 4.1 2.2 - - + +
31A ALA* 1.3 80.0 - - - +
33A ARG* 1.3 65.6 + - + +
34A GLY 3.7 0.3 + - - +
36A GLY 4.6 0.2 - - - -
37A THR* 4.6 0.2 - - + -
42A LEU* 3.7 33.0 - - + -
61A TYR* 3.8 17.5 - - - +
69A LEU* 5.9 0.2 - - + -
72A ASP* 3.2 42.8 - - + +
73A LEU* 4.9 6.7 - - + -
76A ASP* 3.3 26.0 - - + +
351A CA 2.7 25.3 - - - -
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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