Contacts of the helix formed by residues 23 - 28 (chain A) in PDB entry 2OLM
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 LEU 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP* 3.6 17.9 + - - +
20A MET* 3.1 32.4 + - + +
22A GLY* 1.3 78.5 - - - +
24A PRO* 1.3 81.1 - - + +
25A HIS* 3.3 2.0 - - + +
26A ASN* 2.9 27.2 + - - +
27A ARG* 3.3 8.8 + - - +
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Residues in contact with PRO 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 GLY 3.6 0.4 - - - -
23A LEU* 1.3 90.8 - - + +
25A HIS* 1.3 75.9 + - + +
27A ARG* 3.2 49.6 + - - +
28A LYS* 4.4 4.3 + - - +
2002A SO4 3.7 21.8 - - - +
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Residues in contact with HIS 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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23A LEU* 3.3 2.2 - - + +
24A PRO* 1.3 91.9 - - + +
26A ASN* 1.3 59.6 + - - +
27A ARG 3.2 1.2 + - - -
28A LYS* 3.3 10.0 + - - +
86A ASN* 3.0 24.0 + - + +
87A GLU* 3.7 66.0 + - + +
90A LYS* 4.2 21.5 - - + +
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Residues in contact with ASN 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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20A MET* 2.9 36.8 + - - +
21A THR* 4.0 10.7 - - - +
23A LEU* 2.9 21.4 + - - +
25A HIS* 1.3 76.3 - - - +
27A ARG* 1.3 59.6 + - - +
28A LYS 3.3 2.9 - - - +
37A PRO* 3.1 26.5 - - - +
47A PHE* 3.4 31.0 - - + +
85A GLY* 4.5 5.1 - - - -
86A ASN* 2.8 36.0 + - - +
87A GLU 4.6 0.7 + - - -
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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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21A THR 3.9 12.6 - - - +
22A GLY* 2.8 26.1 + - - +
23A LEU 3.4 8.3 - - - +
24A PRO* 3.2 29.2 + - - +
26A ASN* 1.3 78.4 - - - +
28A LYS* 1.3 68.9 + - + +
36A GLY* 3.6 7.8 - - - -
37A PRO* 3.5 12.9 - - - +
2002A SO4 2.6 45.1 + - - -
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Residues in contact with LYS 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 PRO 5.2 3.1 - - - +
25A HIS 3.3 6.9 + - - +
26A ASN 4.1 0.7 - - - +
27A ARG* 1.3 87.2 - - + +
29A CYS* 1.3 65.7 + - - +
30A PHE* 4.2 0.2 - - - -
33A ASP* 3.4 39.3 - - - +
34A GLN 4.8 1.6 - - - -
35A ARG* 3.5 19.1 - - - +
36A GLY 4.8 0.2 - - - +
37A PRO* 4.0 4.7 - - - -
47A PHE 3.9 0.2 - - - +
86A ASN* 2.9 20.8 + - - -
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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