Contacts of the helix formed by residues 22 - 33 (chain A) in PDB entry 2GAU
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 ASN 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU 4.1 0.8 + - - -
21A LEU* 1.3 75.3 - - - +
23A GLU* 1.3 61.4 + - - +
24A GLU* 3.2 11.8 + - - +
25A GLU* 2.9 48.1 + - - +
26A ARG* 2.9 29.8 + - - +
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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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22A ASN* 1.3 77.8 - - - +
24A GLU* 1.3 61.9 + - - +
26A ARG* 3.5 27.0 + - - +
27A GLU* 3.1 39.4 + - + +
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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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22A ASN* 3.2 11.4 + - - +
23A GLU* 1.3 78.3 - - - +
25A GLU* 1.3 60.3 + - + +
27A GLU* 3.4 16.2 + - - +
28A LEU* 3.1 26.3 + - - +
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Residues in contact with GLU 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 LEU* 3.4 12.2 - - + +
22A ASN* 2.9 45.5 + - - +
24A GLU* 1.3 75.9 - - + +
26A ARG* 1.3 61.2 + - - +
28A LEU* 3.3 7.5 + - + +
29A LEU* 2.9 28.9 + - - +
119A LEU* 3.6 28.8 - - + +
122A GLY* 4.0 12.1 - - - +
123A ASN* 3.0 41.9 + - - +
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Residues in contact with ARG 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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18A TRP* 3.0 82.1 + - + +
19A SER* 3.7 15.2 + - - +
21A LEU* 3.1 25.7 + - + -
22A ASN 2.9 20.9 + - - +
23A GLU* 3.7 26.4 + - - +
25A GLU* 1.3 73.8 - - - +
27A GLU* 1.3 58.5 + - - +
29A LEU 3.4 0.2 + - - -
30A ASP* 2.9 32.7 + - - +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.1 38.1 + - + +
24A GLU* 3.5 15.6 - - - +
26A ARG* 1.3 72.5 - - + +
28A LEU* 1.3 61.0 + - - +
30A ASP* 3.5 6.9 + - - +
31A LYS* 2.9 30.5 + - - +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLU 3.1 10.6 + - - +
25A GLU* 3.5 8.5 - - + +
27A GLU* 1.3 75.4 - - - +
29A LEU* 1.3 66.8 + - - +
31A LYS* 3.2 9.5 + - + +
32A GLU* 3.0 52.0 + - + +
115A ALA* 4.4 9.9 - - + +
118A ALA* 4.0 26.5 - - + -
119A LEU* 4.0 25.1 - - + -
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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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11A GLY* 3.9 17.5 - - - +
14A LEU* 4.4 13.9 - - + -
17A VAL* 4.7 6.3 - - + -
18A TRP* 3.7 26.7 - - + -
21A LEU* 3.8 17.7 - - + -
25A GLU 2.9 17.5 + - - +
26A ARG 3.7 4.0 - - - +
28A LEU* 1.3 76.0 - - - +
30A ASP* 1.3 64.3 + - - +
32A GLU* 3.1 2.3 + - + -
33A ILE* 2.9 34.4 + - + +
111A ILE* 3.8 38.4 - - + -
115A ALA* 5.9 1.1 - - + -
116A ILE* 5.7 0.9 - - + -
119A LEU* 4.3 14.6 - - + +
126A PHE* 6.2 0.7 - - + -
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Residues in contact with ASP 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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10A LEU 3.5 10.7 + - - +
11A GLY* 2.9 30.7 + - - -
12A HIS* 4.2 0.9 + - - -
18A TRP* 3.3 23.6 - - - -
26A ARG 2.9 16.3 + - - +
27A GLU* 3.8 7.2 - - - +
29A LEU* 1.3 73.6 - - - +
31A LYS* 1.3 61.4 + - - +
32A GLU 3.6 0.2 + - - -
33A ILE* 3.7 16.9 + - - +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLU 2.9 18.4 + - - +
28A LEU* 3.5 11.4 - - + +
29A LEU 3.1 0.4 - - - -
30A ASP* 1.3 77.5 - - - +
32A GLU* 1.3 79.1 + - - +
33A ILE 4.6 1.7 - - - +
34A GLN* 4.6 6.9 + - - -
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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 LEU* 3.0 31.9 + - + +
29A LEU* 4.3 2.2 - - - +
31A LYS* 1.3 103.5 + - + +
33A ILE* 1.3 67.5 + - - +
34A GLN* 3.6 11.1 + - - +
111A ILE* 5.3 0.7 - - + -
112A PRO* 3.3 33.3 - - + +
115A ALA* 3.7 31.0 - - + -
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Residues in contact with ILE 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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10A LEU* 4.0 31.8 - - + +
11A GLY* 4.1 13.2 - - - +
14A LEU* 3.6 32.5 - - + -
29A LEU* 2.9 28.3 + - + +
30A ASP 3.7 14.5 - - - +
31A LYS 4.6 1.2 - - - +
32A GLU* 1.3 77.7 - - - +
34A GLN* 1.3 68.5 + - - +
35A PRO* 4.5 2.4 - - - +
109A LEU* 3.8 23.3 - - + -
110A ALA 3.4 12.6 - - - +
111A ILE* 4.1 15.9 - - + +
112A PRO* 4.8 0.9 - - - -
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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