Contacts of the helix formed by residues 20 - 30 (chain A) in PDB entry 2J2C
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 ASP 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASN* 3.1 19.0 + - - +
19A MET* 1.3 76.4 - - - +
21A LYS* 1.3 61.5 + - - +
22A HIS* 3.1 20.0 + - - +
23A ALA* 3.0 31.2 + - + +
24A LEU* 2.9 25.1 + - - +
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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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19A MET 3.9 10.0 + - - +
20A ASP* 1.3 74.4 + - - +
22A HIS* 1.3 62.9 + - + +
24A LEU* 3.5 12.6 + - + +
25A LYS* 3.2 26.2 + - - +
28A ARG* 5.0 1.7 + - - -
472A PRO* 6.2 3.8 - - + -
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Residues in contact with HIS 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 ASP* 3.1 13.8 + - - +
21A LYS* 1.3 80.7 - - + +
23A ALA* 1.3 65.3 + - - +
25A LYS* 3.4 11.8 + - + +
26A LYS* 3.2 23.7 + - - +
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Residues in contact with ALA 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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18A ASN* 3.4 39.7 - - + +
20A ASP* 3.0 19.4 + - - +
22A HIS* 1.3 75.9 - - - +
24A LEU* 1.3 58.6 + - - +
26A LYS* 3.4 6.2 + - - +
27A TYR* 3.0 30.4 + - - +
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Residues in contact with LEU 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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17A ALA* 6.3 0.2 - - + -
18A ASN 3.4 19.1 - - - +
19A MET* 3.6 45.8 - - + +
20A ASP 2.9 13.8 + - - +
21A LYS* 3.6 16.2 - - + +
22A HIS 3.2 0.2 - - - -
23A ALA* 1.3 75.2 - - - +
25A LYS* 1.3 64.7 + - - +
27A TYR* 3.3 4.8 + - + +
28A ARG* 3.1 30.4 + - - +
238A ARG* 5.8 1.6 - - - +
469A LEU 4.5 4.9 - - - +
470A TYR* 3.6 47.1 - - + +
471A TYR 6.0 2.2 - - - -
472A PRO 6.2 0.2 - - - -
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Residues in contact with LYS 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 LYS 3.2 14.2 + - - +
22A HIS* 3.9 12.8 - - + +
23A ALA 3.4 0.4 - - - -
24A LEU* 1.3 79.4 - - - +
26A LYS* 1.3 61.4 + - - +
28A ARG* 3.4 33.4 - - - +
29A ARG* 2.9 57.0 - - - +
1492A SO4 3.3 22.0 + - - -
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Residues in contact with LYS 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 HIS 3.2 15.3 + - - +
23A ALA* 3.8 6.3 - - - +
25A LYS* 1.3 80.4 - - - +
27A TYR* 1.3 62.0 + - - +
29A ARG* 3.3 21.3 + - - +
30A GLU* 3.9 12.5 + - - +
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Residues in contact with TYR 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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12A ALA* 4.5 5.9 + - - +
15A MET* 3.3 41.1 - - + +
23A ALA 3.0 18.8 + - - +
24A LEU* 3.3 6.9 + - + +
26A LYS* 1.3 77.9 - - - +
28A ARG* 1.3 56.8 + - - +
30A GLU* 3.1 39.4 + - - +
33A HIS* 3.1 62.0 + + + +
470A TYR* 3.7 41.9 + + + -
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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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21A LYS 5.0 1.8 + - - -
24A LEU* 3.1 13.1 + - - +
25A LYS* 3.4 47.0 + - - +
27A TYR* 1.3 73.9 - - - +
29A ARG* 1.3 63.5 + - + +
30A GLU 3.3 1.6 - - - -
33A HIS* 3.7 13.5 - - - +
34A ARG* 3.5 27.7 - - - +
470A TYR* 2.9 45.1 + - + +
471A TYR* 3.3 34.9 + - + +
472A PRO* 3.8 22.6 - - - +
475A TYR* 4.3 6.5 - - - -
1492A SO4 2.6 39.3 + - - +
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Residues in contact with ARG 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 LYS* 2.9 60.2 - - - +
26A LYS* 3.5 12.8 - - - +
27A TYR 3.2 0.6 - - - -
28A ARG* 1.3 76.0 - - - +
30A GLU* 1.3 64.8 + - + +
31A ALA 3.5 2.4 + - - -
34A ARG* 4.4 12.0 + - - +
1492A SO4 2.7 26.4 + - - -
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Residues in contact with GLU 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 LYS* 4.3 10.7 - - - +
27A TYR* 3.1 28.3 + - - +
28A ARG 4.3 0.4 - - - -
29A ARG* 1.3 79.4 - - + +
31A ALA* 1.3 66.3 - - - +
32A TYR* 4.1 18.5 - - + -
33A HIS* 2.9 40.8 + - - +
34A ARG* 3.2 8.8 + - - +
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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