Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 2YSX
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 1.3 78.9 - - - +
19A ARG* 1.3 78.4 + - - +
20A SER* 3.7 12.4 + - - +
21A LYS* 3.1 35.0 - - + +
22A ALA* 3.2 4.3 + - - +
38A ARG* 4.7 1.1 - - - -
41A GLU* 4.3 11.9 + - - -
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Residues in contact with ARG 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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18A THR* 1.3 74.9 + - - +
20A SER* 1.3 67.9 + - - +
22A ALA* 2.6 30.7 + - + +
23A GLU* 3.4 20.6 + - + +
38A ARG* 4.8 15.3 - - - +
41A GLU* 3.9 13.0 + - - +
59A THR* 5.8 4.5 - - + +
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Residues in contact with SER 20 (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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18A THR* 3.5 11.7 + - - -
19A ARG* 1.3 77.0 - - - +
21A LYS* 1.3 57.9 + - - +
23A GLU* 3.6 10.6 + - - +
24A GLU* 2.8 35.9 + - - +
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Residues in contact with LYS 21 (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 ILE* 3.9 25.1 - - + -
18A THR* 3.1 26.4 + - + +
19A ARG 2.6 4.6 + - - -
20A SER* 1.3 73.5 + - - +
22A ALA* 1.3 67.6 + - - +
24A GLU* 2.9 46.4 + - - +
25A LEU* 2.9 24.9 + - + +
111A GLU* 3.4 34.6 + - - -
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Residues in contact with ALA 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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17A ILE* 3.8 9.5 - - - +
18A THR 3.2 4.4 + - - +
19A ARG* 2.6 19.7 + - + +
21A LYS* 1.3 76.7 - - - +
23A GLU* 1.3 64.7 + - + +
25A LEU* 3.7 0.4 + - - -
26A LEU* 3.5 9.8 + - - +
36A LEU* 3.3 31.2 - - + +
38A ARG* 4.4 13.7 - - - +
50A CYS* 3.6 29.2 - - - -
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Residues in contact with GLU 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 ARG* 3.4 21.8 + - + +
20A SER* 4.0 12.5 - - - +
21A LYS 3.2 0.6 - - - -
22A ALA* 1.3 74.2 - - + +
24A GLU* 1.3 69.6 + - - +
26A LEU* 2.9 22.8 + - - +
27A SER* 2.9 13.9 + - - -
57A VAL* 3.4 40.1 - - + +
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Residues in contact with GLU 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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20A SER* 2.8 27.4 + - - +
21A LYS* 2.9 47.4 + - - +
23A GLU* 1.3 72.7 - - - +
25A LEU* 1.3 68.8 + - - +
27A SER* 3.2 19.7 + - - -
28A ARG* 3.3 22.7 + - + +
111A GLU* 4.0 14.2 - - - +
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Residues in contact with LEU 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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14A HIS* 2.9 43.7 - - + +
17A ILE* 4.1 13.5 - - + -
21A LYS* 2.9 30.2 + - + +
22A ALA 3.8 2.7 - - - +
24A GLU* 1.3 75.9 - - - +
26A LEU* 1.3 66.3 + - - +
28A ARG* 2.9 32.5 + - - +
29A THR* 3.6 5.2 + - - -
36A LEU* 4.0 15.0 - - + -
108A VAL* 5.0 5.8 - - + -
109A PRO 4.7 3.1 - - - +
110A LEU 4.6 2.0 - - - -
111A GLU* 3.5 37.7 - - + +
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Residues in contact with LEU 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 ALA 3.5 16.8 - - - +
23A GLU* 2.9 9.6 + - - +
25A LEU* 1.3 74.8 - - - +
27A SER* 1.3 64.7 + - - +
29A THR* 3.0 10.2 + - - -
30A GLY 3.0 18.9 + - - -
34A SER* 3.8 27.4 - - - +
35A PHE* 4.0 5.2 - - - +
36A LEU* 3.7 14.8 - - + -
50A CYS* 4.0 12.6 - - + +
52A LEU* 3.7 42.9 - - + +
57A VAL* 3.6 37.5 - - + -
108A VAL* 4.2 4.9 - - + -
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Residues in contact with SER 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 GLU 2.9 11.2 + - - -
24A GLU* 3.2 15.3 - - - -
26A LEU* 1.3 76.2 - - - +
28A ARG* 1.3 68.5 + - - +
30A GLY* 3.2 13.2 + - - +
52A LEU* 4.8 5.9 - - - +
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Residues in contact with ARG 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 GLU* 3.3 24.7 + - - +
25A LEU* 2.9 28.0 + - - +
27A SER* 1.3 73.7 - - - +
29A THR* 1.3 67.6 + - - +
30A GLY* 4.3 0.2 - - - -
111A GLU* 4.9 17.3 - - - +
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Residues in contact with THR 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 LEU 4.2 4.2 + - - -
26A LEU 3.0 6.5 + - - -
28A ARG* 1.3 80.3 - - - +
30A GLY* 1.3 63.8 + - - +
31A LYS* 3.4 45.4 + - + +
34A SER* 3.3 26.3 + - - +
106A TYR* 6.3 0.7 - - + -
108A VAL* 4.0 17.8 - - + +
109A PRO* 5.0 5.4 - - - +
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Residues in contact with GLY 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 LEU 3.0 10.8 + - - -
27A SER* 3.2 10.9 + - - -
29A THR* 1.3 80.0 - - - +
31A LYS* 1.3 61.9 + - - +
32A ASP* 4.3 5.4 - - - +
52A LEU* 4.1 10.3 - - - -
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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