Contacts of the helix formed by residues 21 - 29 (chain A) in PDB entry 2R2N
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PRO* 3.5 12.4 + - + +
19A ILE 3.9 4.2 + - - -
20A ARG* 1.3 74.6 - - - +
22A MET* 1.3 62.6 + - - +
24A ASP* 3.2 23.2 - - - +
25A ILE* 3.3 19.2 - - - +
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Residues in contact with MET 22 (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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19A ILE 3.1 13.6 + - - +
21A THR* 1.3 74.3 + - - +
23A THR* 1.3 59.5 + - + +
24A ASP 3.0 4.0 - - - -
25A ILE* 2.8 38.2 + - + +
26A LEU 3.5 2.6 + - - -
37A ALA* 4.3 7.4 - - + -
370B ILE* 3.6 31.6 - - + +
371B GLU* 4.1 10.8 - - + -
375B VAL* 3.7 22.0 - - + -
380B LEU* 3.7 40.4 - - + +
381B MET 3.7 6.5 - - - +
382B LEU* 4.1 22.4 - - + -
383B PRO* 4.7 6.3 - - + -
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Residues in contact with THR 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 ILE* 5.2 1.8 - - + -
20A ARG* 2.9 37.8 + - + +
22A MET* 1.3 75.8 - - + +
24A ASP* 1.3 60.8 + - - +
26A LEU* 3.5 26.6 - - - +
27A SER* 3.8 7.1 + - - -
35A SER* 4.9 3.1 - - - +
37A ALA* 4.1 8.7 - - + +
38A GLY* 3.4 37.7 - - - +
380B LEU* 4.9 2.5 - - - -
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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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20A ARG 3.2 18.7 + - - +
21A THR* 3.2 18.9 - - - +
23A THR* 1.3 76.7 + - - +
25A ILE* 1.3 64.3 + - - +
26A LEU 3.1 1.8 - - - -
27A SER* 3.0 26.3 + - - -
28A ARG* 3.7 28.9 + - - -
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Residues in contact with ILE 25 (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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21A THR 3.3 16.4 - - - +
22A MET* 2.8 26.6 + - + +
24A ASP* 1.3 71.5 - - - +
26A LEU* 1.3 61.9 + - - +
28A ARG* 3.5 29.7 + - + +
29A GLY* 3.2 18.6 + - - -
33A MET* 4.1 13.5 - - + +
371B GLU 5.4 1.6 - - - +
375B VAL* 4.1 40.4 - - + -
380B LEU* 4.7 4.0 - - + -
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Residues in contact with LEU 26 (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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22A MET 3.5 3.2 + - - -
23A THR* 3.5 18.4 - - - +
24A ASP 3.1 1.0 - - - -
25A ILE* 1.3 79.6 - - - +
27A SER* 1.3 61.9 + - - +
28A ARG 3.3 0.9 + - - -
29A GLY* 3.4 12.1 + - - +
30A PRO 5.1 2.2 - - - +
33A MET* 3.7 45.3 - - + +
35A SER* 3.9 25.1 - - - +
380B LEU* 4.0 10.6 - - + +
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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 THR 3.8 7.0 + - - -
24A ASP* 3.0 19.3 + - - -
26A LEU* 1.3 79.3 - - - +
28A ARG* 1.3 60.9 + - - +
29A GLY 4.8 1.7 - - - +
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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 ASP* 3.7 37.1 + - - -
25A ILE* 3.8 28.0 - - + +
26A LEU 3.3 0.2 - - - -
27A SER* 1.3 79.2 - - - +
29A GLY* 1.3 65.6 + - - +
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Residues in contact with GLY 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 ILE* 3.2 15.2 + - - -
26A LEU 3.4 9.4 + - - +
27A SER 4.8 1.4 - - - +
28A ARG* 1.3 83.4 - - - +
30A PRO* 1.4 78.6 - - - +
31A LYS* 3.8 1.7 + - - +
33A MET* 4.2 8.5 - - - -
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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