Contacts of the helix formed by residues 17 - 34 (chain A) in PDB entry 2RAE
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 THR 17 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO 4.0 9.0 - - - +
16A SER* 1.3 78.1 + - - +
18A THR* 1.3 60.1 + - - +
19A GLN* 3.4 9.4 + - - +
20A ASP* 3.0 32.0 + - + +
21A ARG* 2.9 30.9 + - - +
68A ASP* 5.6 1.6 + - - +
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Residues in contact with THR 18 (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 THR* 1.3 73.9 - - - +
19A GLN* 1.3 58.4 + - - +
21A ARG* 3.4 25.1 + - - +
22A ILE* 2.9 41.7 + - + +
49A ILE* 4.7 12.1 - - + -
53A THR* 5.3 1.8 - - + -
57A TYR* 3.9 31.3 + - + +
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Residues in contact with GLN 19 (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 THR* 3.3 7.6 + - - +
18A THR* 1.3 78.0 - - - +
20A ASP* 1.3 59.5 + - - +
22A ILE* 3.4 10.6 + - - -
23A SER* 3.1 22.3 + - - -
57A TYR* 3.5 51.6 + - + +
58A PHE* 3.4 19.0 - - + -
67A GLY 3.3 23.2 + - - -
68A ASP* 3.6 37.7 + - + +
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 5.3 4.9 - - - -
17A THR* 3.0 25.0 + - - +
19A GLN* 1.3 78.2 - - - +
21A ARG* 1.3 57.2 + - - +
23A SER* 3.6 4.5 + - - -
24A THR* 2.9 32.6 + - - -
67A GLY* 3.8 6.8 - - - -
68A ASP* 3.2 37.7 + - - +
71A ALA* 6.0 0.2 - - - +
114A ARG* 5.1 6.7 + - - -
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 4.2 18.5 - - - +
17A THR 2.9 21.3 + - - +
18A THR* 3.7 27.3 + - - +
20A ASP* 1.3 76.0 - - - +
22A ILE* 1.3 62.1 + - - +
24A THR* 4.0 6.3 - - - +
25A VAL* 2.8 43.4 + - + +
47A SER* 3.4 35.0 + - - +
49A ILE* 5.0 4.4 - - - +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 2.9 36.3 + - + +
19A GLN* 3.4 7.2 + - - +
21A ARG* 1.3 72.3 - - - +
23A SER* 1.3 68.6 + - - +
25A VAL* 3.4 2.4 + - - +
26A GLY* 2.9 22.2 + - - -
43A VAL* 4.0 5.9 - - + +
47A SER* 3.8 21.5 - - - +
49A ILE* 3.4 30.1 - - + -
54A LEU* 3.9 24.0 - - + -
57A TYR* 3.5 29.2 - - + -
58A PHE* 3.6 18.8 - - + -
64A ILE* 4.2 1.7 - - + +
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Residues in contact with SER 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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19A GLN 3.1 17.8 + - - -
20A ASP* 3.6 9.6 - - - -
22A ILE* 1.3 78.3 - - - +
24A THR* 1.3 57.6 + - - +
26A GLY* 3.5 0.9 - - - -
27A ILE* 2.8 35.1 + - - +
58A PHE* 4.1 2.2 - - - -
64A ILE* 2.7 32.1 + - - +
67A GLY* 3.4 13.2 - - - -
114A ARG* 3.1 24.8 + - - -
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP 2.9 19.9 + - - -
21A ARG* 4.0 7.6 - - - -
22A ILE 3.3 0.2 - - - -
23A SER* 1.3 75.5 - - - +
25A VAL* 1.3 64.5 + - + +
27A ILE* 3.4 10.6 + - - +
28A GLU* 3.1 23.5 + - + +
110A ASN* 4.1 28.2 - - + +
114A ARG* 4.4 10.2 + - - -
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Residues in contact with VAL 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 ARG* 2.8 42.7 + - + +
22A ILE 3.9 1.1 - - - +
24A THR* 1.3 77.0 - - + +
26A GLY* 1.3 60.7 + - - +
28A GLU* 3.3 7.1 + - - +
29A LEU* 2.9 29.8 + - - +
43A VAL* 4.0 9.2 - - + +
46A ALA* 4.0 25.8 - - + +
47A SER* 3.0 26.7 - - - +
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Residues in contact with GLY 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 ILE 2.9 15.5 + - - -
23A SER 3.5 3.8 - - - -
25A VAL* 1.3 76.4 - - - +
27A ILE* 1.3 51.8 + - - +
29A LEU* 3.1 4.4 + - - +
30A PHE* 2.8 44.7 + - - -
43A VAL* 3.8 26.2 - - - -
64A ILE* 4.2 5.6 - - - -
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Residues in contact with ILE 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 SER* 2.8 24.6 + - - +
24A THR* 3.8 6.7 - - + +
26A GLY* 1.3 72.2 - - - +
28A GLU* 1.3 55.5 + - - +
30A PHE* 3.4 7.9 + - + +
31A THR* 2.7 38.1 + - - -
65A PRO* 3.9 17.9 - - + +
110A ASN* 4.4 4.9 - - + +
113A LYS* 3.5 33.4 - - + -
114A ARG* 3.5 60.3 - - + +
117A LEU* 4.0 12.1 - - + +
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Residues in contact with GLU 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 THR* 3.1 17.9 + - + +
25A VAL* 3.7 7.2 - - - +
27A ILE* 1.3 76.0 - - - +
29A LEU* 1.3 63.0 + - - +
31A THR* 3.4 3.0 + - - +
32A GLU* 3.0 44.0 + - + +
113A LYS* 2.4 39.8 + - + +
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Residues in contact with LEU 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 VAL 2.9 14.8 + - - +
26A GLY* 3.4 8.3 - - - +
28A GLU* 1.3 77.0 - - - +
30A PHE* 1.3 55.2 + - - +
32A GLU* 3.2 5.0 + - + -
33A GLN* 2.8 69.6 + - + +
38A THR* 3.7 26.7 - - + -
42A GLU* 3.7 31.9 - - + +
43A VAL* 3.9 6.1 - - - +
46A ALA* 4.0 15.0 - - + -
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Residues in contact with PHE 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 GLY 2.8 29.1 + - - +
27A ILE* 3.8 1.3 - - - +
29A LEU* 1.3 73.1 - - - +
31A THR* 1.3 58.1 + - - +
34A GLY* 2.8 35.7 + - - -
35A PHE* 3.4 39.1 + + - -
38A THR* 3.6 22.2 - - + -
43A VAL* 3.8 29.8 - - + -
61A LYS* 4.0 13.5 - - + -
64A ILE* 4.0 29.2 - - + -
65A PRO* 4.1 9.4 - - + -
117A LEU* 3.7 36.9 - - + +
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Residues in contact with THR 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 ILE* 2.7 25.8 + - - +
28A GLU* 3.7 4.9 - - - +
29A LEU 3.2 0.2 - - - -
30A PHE* 1.3 80.1 - - - +
32A GLU* 1.3 65.1 + - + +
34A GLY* 4.1 2.4 + - - -
113A LYS* 3.8 42.3 + - + +
117A LEU* 4.4 9.4 - - - +
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Residues in contact with GLU 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 GLU* 3.0 38.5 + - + +
29A LEU* 3.9 4.9 - - + +
31A THR* 1.3 81.9 - - + +
33A GLN* 1.3 64.0 + - + +
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Residues in contact with GLN 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 LEU* 2.8 41.4 + - + +
32A GLU* 1.3 78.1 - - + +
34A GLY* 1.3 58.7 + - - +
37A ALA* 3.2 23.7 - - + +
38A THR* 2.9 25.2 + - - +
42A GLU* 3.4 25.8 + - - +
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Residues in contact with GLY 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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30A PHE 2.8 17.0 + - - -
31A THR 4.1 2.9 + - - -
32A GLU 3.6 1.4 - - - -
33A GLN* 1.3 80.0 - - - +
35A PHE* 1.3 63.2 + - - -
36A ASP 3.5 2.7 - - - -
37A ALA* 4.0 2.5 - - - -
38A THR* 2.8 26.2 + - - -
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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