Contacts of the helix formed by residues 19 - 25 (chain B) in PDB entry 2NO5
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 VAL 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B TYR* 3.9 7.2 - - + -
14B GLY* 3.8 26.5 - - - +
17B LEU 3.2 1.2 + - - -
18B ASP* 1.3 72.9 + - - +
20B HIS* 1.3 72.4 + - + +
22B ALA* 2.8 24.1 + - - +
23B VAL 4.3 0.2 + - - -
38B SER* 5.4 1.1 + - - +
42B ARG* 4.1 30.5 - - + +
92B TYR* 3.9 26.0 - - + +
95B LEU* 3.6 21.1 - - + -
98B TYR* 4.9 0.2 + - - -
1014B CNR 4.3 14.6 - - + -
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Residues in contact with HIS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLY* 6.2 2.5 - - - -
18B ASP* 2.9 19.5 + - - +
19B VAL* 1.3 82.5 + - + +
21B SER* 1.3 57.3 + - - +
22B ALA 3.1 0.9 + - - -
23B VAL* 3.4 5.2 + - - +
24B MET* 3.0 49.0 + - + +
35B GLU* 5.5 0.7 - - - -
38B SER* 4.7 4.1 + - - +
98B TYR* 3.8 3.3 + - - -
1012B SO4 2.4 38.0 + - - -
1014B CNR 3.3 49.0 + - + +
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP* 2.8 30.1 + - - -
19B VAL 2.9 0.8 + - - -
20B HIS* 1.3 78.7 - - - +
22B ALA* 1.3 63.8 + - - +
24B MET* 3.7 11.7 - - - -
25B ARG* 2.9 39.9 + - - +
95B LEU* 3.9 4.2 - - - +
96B SER* 3.1 30.7 + - - -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 2.8 15.5 + - - +
21B SER* 1.3 83.5 + - - +
23B VAL* 1.3 61.3 + - + +
26B ASN* 3.5 20.3 + - - -
41B TRP* 4.0 23.1 - - + -
88B LEU* 3.6 8.8 - - - +
91B ALA* 3.8 12.4 - - + +
92B TYR* 4.1 15.3 - - + +
95B LEU* 3.9 16.4 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 4.3 0.2 + - - -
20B HIS 3.4 2.8 + - - +
22B ALA* 1.3 77.3 - - + +
24B MET* 1.3 60.4 + - - +
26B ASN 3.0 3.8 + - - -
27B ALA* 2.9 25.5 + - - -
30B VAL* 4.7 7.6 - - + -
34B ALA* 3.4 41.5 - - + +
37B LEU* 4.4 11.0 - - + -
38B SER* 3.9 25.1 - - - +
41B TRP* 3.7 32.1 - - + -
88B LEU* 4.1 12.8 - - + -
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Residues in contact with MET 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 6.0 0.9 - - - +
20B HIS* 3.0 39.3 + - + +
21B SER* 3.8 7.6 - - - -
22B ALA 3.4 0.2 - - - -
23B VAL* 1.3 74.8 - - - +
25B ARG* 1.3 55.5 + - - +
26B ASN 2.7 12.3 + - - -
27B ALA* 3.0 22.4 + - + +
35B GLU* 4.5 16.2 - - - +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 2.9 30.2 + - - +
22B ALA 4.3 0.2 - - - +
24B MET* 1.3 74.5 - - - +
26B ASN* 1.3 68.9 + - - +
27B ALA 3.8 0.2 - - - -
29B GLU* 4.7 2.6 - - - +
91B ALA* 2.8 45.5 + - - +
94B GLU* 3.2 21.7 + - - +
95B LEU* 4.1 2.6 - - - +
96B SER* 3.4 27.9 + - - +
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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