Contacts of the helix formed by residues 21 - 33 (chain A) in PDB entry 2CSH
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 HIS 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.7 11.4 - - - +
19A PHE* 3.6 10.4 - - - +
20A THR* 1.3 93.2 + - + +
22A LYS* 1.3 87.8 + - - +
23A SER* 4.0 3.8 - - - +
24A GLN* 3.0 33.2 - - + +
25A ARG 3.4 13.9 + - - -
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Residues in contact with LYS 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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11A TYR* 2.9 50.3 + - + +
21A HIS* 1.3 98.9 + - - +
23A SER* 1.3 63.4 + - - +
24A GLN 3.2 0.2 - - - -
25A ARG* 3.1 16.6 + - - +
26A ASP* 2.8 31.7 + - - +
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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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21A HIS* 4.0 3.6 - - - +
22A LYS* 1.3 83.7 - - - +
24A GLN* 1.3 92.8 + - - +
26A ASP* 3.9 6.3 - - - +
27A ARG* 3.2 25.6 + - - +
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Residues in contact with GLN 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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19A PHE* 3.4 40.0 - - + -
20A THR 5.8 0.2 - - - +
21A HIS* 3.0 32.9 + - + +
22A LYS 3.2 0.4 - - - -
23A SER* 1.3 105.4 + - - +
25A ARG* 1.3 59.0 + - - +
27A ARG* 3.1 34.5 + - - +
28A HIS 3.8 0.2 + - - -
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Residues in contact with ARG 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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11A TYR* 3.5 24.5 - - + +
12A PRO* 3.0 33.1 + - - +
13A CYS* 3.6 14.7 - - + +
19A PHE* 3.5 17.5 - - + -
21A HIS 3.4 10.8 + - - +
22A LYS* 3.1 31.4 + - - +
24A GLN* 1.3 77.0 - - - +
26A ASP* 1.3 81.6 + - - +
28A HIS* 3.3 5.9 + - - +
29A MET* 3.2 38.0 + - - +
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Residues in contact with ASP 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 LYS 2.8 16.7 + - - +
23A SER* 3.9 8.1 - - - +
25A ARG* 1.3 92.9 + - - +
27A ARG* 1.3 62.9 + - - +
28A HIS 3.0 1.8 - - - -
29A MET* 2.6 28.7 + - - +
30A SER* 3.0 18.0 + - - -
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Residues in contact with ARG 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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19A PHE* 4.3 16.4 - - - -
23A SER 3.2 12.7 + - - +
24A GLN* 3.1 37.6 + - - +
26A ASP* 1.3 80.1 + - - +
28A HIS* 1.3 73.7 + - - +
30A SER* 3.1 19.9 + - - -
31A MET* 3.4 14.6 + - - +
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Residues in contact with HIS 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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13A CYS* 3.5 1.9 - - - -
15A CYS* 3.5 12.4 - - - -
17A LYS* 3.7 26.6 + - + -
19A PHE* 3.6 27.0 - + + -
24A GLN 4.0 2.5 - - - +
25A ARG 3.3 10.5 + - - +
26A ASP 3.0 0.6 - - - -
27A ARG* 1.3 94.0 - - + +
29A MET* 1.3 58.8 + - - +
31A MET* 3.2 35.1 - - + +
32A HIS* 2.8 34.8 + + - -
200A ZN 2.0 33.2 - - - -
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Residues in contact with MET 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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12A PRO 5.5 0.2 - - - +
13A CYS* 3.7 20.0 - - - -
14A GLN* 3.8 42.2 + - + +
25A ARG* 3.2 32.3 + - - +
26A ASP* 2.6 20.0 + - - +
28A HIS* 1.3 70.5 - - - +
30A SER* 1.3 63.9 + - - +
31A MET 3.2 0.2 - - - -
32A HIS* 3.2 22.2 + - - +
33A LEU* 3.6 11.2 + - + +
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Residues in contact with SER 30 (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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26A ASP* 3.0 17.2 + - - -
27A ARG* 3.1 17.3 + - - -
29A MET* 1.3 76.4 - - - +
31A MET* 1.3 63.7 + - - +
32A HIS 3.4 0.3 + - - -
33A LEU* 3.5 29.4 + - - +
35A LEU* 3.6 11.5 - - - +
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Residues in contact with MET 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 ARG 3.4 10.5 + - - +
28A HIS* 3.2 36.6 - - + +
29A MET 3.2 0.6 - - - -
30A SER* 1.3 80.0 + - - +
32A HIS* 1.3 99.2 + - + +
33A LEU 2.9 9.5 - - - +
35A LEU* 4.3 7.5 - - - +
46A LYS* 5.7 2.8 + - - +
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Residues in contact with HIS 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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14A GLN* 3.4 34.8 - - + +
15A CYS* 3.2 18.7 - - + +
28A HIS* 2.8 20.8 + + - -
29A MET* 3.2 16.5 + - - +
31A MET* 1.3 103.6 - - + +
33A LEU* 1.3 72.1 + - - +
34A GLY* 4.5 0.2 - - - -
200A ZN 2.0 35.8 - - - -
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Residues in contact with LEU 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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14A GLN* 4.9 14.3 - - - +
29A MET* 3.9 7.9 - - + +
30A SER* 3.6 26.5 - - - +
31A MET 2.9 11.0 - - - +
32A HIS* 1.3 88.7 - - - +
34A GLY* 1.3 63.7 + - - +
35A LEU* 3.6 10.3 + - + +
46A LYS* 5.3 2.9 + - - -
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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