Contacts of the helix formed by residues 25 - 33 (chain X) in PDB entry 2BOD
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 ARG 25 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16X TRP* 4.1 9.3 - - + -
23X ASP* 2.8 36.5 + - - +
24X PRO* 1.3 83.7 - - + +
26X THR* 1.3 64.6 + - - +
27X PRO* 3.5 0.9 - - - -
28X VAL* 3.4 6.3 + - - +
29X ILE* 3.0 33.0 + - + +
276X PRO* 4.1 18.6 - - - +
277X GLN* 3.0 47.7 + - - +
280X TYR* 3.6 42.8 - - + -
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Residues in contact with THR 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X TRP* 3.3 19.5 - - - -
17X VAL* 3.9 30.3 - - + +
20X ASN 2.6 27.8 + - - +
21X PRO* 4.2 12.1 - - + +
23X ASP* 3.1 15.4 + - - +
25X ARG* 1.3 77.7 - - - +
27X PRO* 1.3 62.3 - - - +
29X ILE* 4.5 0.9 - - - +
30X ARG* 2.7 45.4 + - - +
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Residues in contact with PRO 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X PRO 5.7 1.1 - - - +
23X ASP 3.7 8.7 - - - +
24X PRO* 3.7 9.4 - - + +
25X ARG 3.6 3.6 - - - -
26X THR* 1.3 92.2 - - + +
28X VAL* 1.3 58.0 + - + +
30X ARG* 3.7 26.4 - - - +
31X ASP* 3.0 40.1 + - - +
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Residues in contact with VAL 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X ARG 3.4 2.3 + - - +
26X THR 3.2 0.4 - - - -
27X PRO* 1.3 77.6 - - + +
29X ILE* 1.3 62.5 + - - +
31X ASP* 5.0 0.7 - - - -
32X ARG* 2.8 60.1 + - - +
280X TYR* 3.7 37.2 - - + +
283X ALA* 3.6 28.9 - - + -
284X ILE* 4.0 11.0 - - + -
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Residues in contact with ILE 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X SER* 4.7 4.9 - - - +
16X TRP* 3.7 26.0 - - + -
17X VAL* 3.8 18.2 - - + -
25X ARG* 3.0 29.3 + - + +
26X THR 4.0 1.8 - - - +
28X VAL* 1.3 75.9 - - - +
30X ARG* 1.3 60.5 + - - +
33X ILE* 3.0 21.0 + - + +
34X ALA 2.8 25.7 + - - +
274X PHE* 4.0 19.5 - - + -
276X PRO* 3.6 29.8 - - + +
279X ALA* 4.4 5.8 - - + -
280X TYR* 4.2 19.1 - - + +
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Residues in contact with ARG 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X VAL* 4.0 29.4 - - + +
21X PRO 5.3 3.8 + - - -
26X THR* 2.7 31.0 + - - +
27X PRO* 3.7 33.1 - - - +
29X ILE* 1.3 73.9 - - - +
31X ASP* 1.3 84.7 + - - +
34X ALA* 3.8 5.2 - - + -
35X SER* 3.1 32.7 + - - -
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Residues in contact with ASP 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X PRO* 3.0 25.0 + - - +
28X VAL* 4.3 0.7 - - - +
30X ARG* 1.3 107.3 + - - +
32X ARG* 1.3 65.5 + - + +
35X SER* 2.8 20.8 + - - -
36X VAL* 5.0 1.0 - - - +
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Residues in contact with ARG 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X VAL* 2.8 49.9 + - + +
31X ASP* 1.3 78.7 - - + +
33X ILE* 1.3 55.9 + - - +
36X VAL* 3.3 18.8 - - - +
239X ILE* 3.8 10.9 - - + +
242X PRO* 5.6 1.0 - - - +
257X TRP* 3.4 12.0 - - - -
283X ALA* 3.1 39.0 + - + -
284X ILE* 4.0 12.2 + - - +
286X ALA* 3.9 16.7 + - - +
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Residues in contact with ILE 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X SER* 4.1 17.7 - - - +
29X ILE* 3.0 22.8 + - + +
32X ARG* 1.3 77.4 - - + +
34X ALA* 1.3 65.3 + - - +
35X SER 3.1 3.7 + - - -
36X VAL* 3.1 8.0 + - - +
38X GLN* 2.8 29.9 + - - +
239X ILE* 4.3 12.1 - - + -
257X TRP* 3.9 4.5 - - + -
261X PRO* 3.7 40.2 - - + +
274X PHE* 5.1 0.4 - - + -
279X ALA* 3.4 41.3 - - + +
282X MET* 5.1 0.2 - - + -
283X ALA* 4.0 13.9 - - + -
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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