Contacts of the helix formed by residues 245 - 250 (chain E) in PDB entry 2OZB
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 PRO 245 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ASN* 3.3 35.9 - - + +
43D THR* 4.3 7.8 - - + -
44D LYS* 3.6 27.4 - - + -
47D ASN* 4.8 4.9 - - - +
243E LYS 4.3 2.9 - - - +
244E MET* 1.3 90.8 - - + +
246E ALA* 1.3 66.3 + - - +
247E CYS* 4.1 7.2 - - - -
248E ASN* 3.0 41.2 + - - +
249E ILE* 3.3 8.7 + - - +
300E THR* 4.5 0.9 - - - -
304E ARG* 4.9 0.2 - - - +
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ASN* 2.7 32.5 + - - +
244E MET 3.9 0.4 + - - -
245E PRO* 1.3 72.2 - - - +
247E CYS* 1.3 62.6 + - - +
248E ASN 3.2 0.2 + - - -
249E ILE* 3.3 2.8 + - - +
250E MET* 3.1 23.8 + - - +
296E ALA* 4.1 4.0 - - - +
297E ALA* 4.0 23.3 - - + +
300E THR* 3.3 24.1 + - - +
32F G 6.0 0.2 - - + -
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Residues in contact with CYS 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ASN* 5.2 0.2 - - - -
44D LYS* 3.5 16.4 - - - -
245E PRO* 3.1 12.0 + - - +
246E ALA* 1.3 78.0 - - - +
248E ASN* 1.3 72.7 + - - +
250E MET* 3.9 9.3 - - - +
251E LEU* 3.7 9.9 - - - +
35F G 4.8 0.7 - - - +
41F C 3.2 42.0 + - - +
42F C 3.6 19.1 - - - +
43F G 3.4 21.2 + - - +
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Residues in contact with ASN 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 5.5 2.8 - - - +
48D ARG* 6.0 0.2 - - - +
244E MET* 4.8 7.7 - - + +
245E PRO* 3.0 33.0 + - + +
247E CYS* 1.3 90.1 - - - +
249E ILE* 1.3 58.3 + - - +
250E MET 3.0 1.6 - - - -
251E LEU* 2.7 25.3 + - - +
252E LEU* 3.2 15.1 + - - +
40F U 3.3 51.3 + - + +
41F C 3.6 17.7 + - - +
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Residues in contact with ILE 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E ILE* 4.5 11.5 - - + +
241E LEU* 3.7 40.2 - - + +
244E MET* 3.7 22.4 - - + +
245E PRO 3.3 5.7 + - - +
246E ALA 3.8 6.5 - - - +
248E ASN* 1.3 77.6 - - - +
250E MET* 1.3 64.1 + - - +
251E LEU 3.0 1.4 + - - -
252E LEU* 3.2 28.3 + - + +
274E ILE* 3.8 26.3 + - + +
296E ALA* 4.6 5.6 - - + +
299E CYS* 5.0 4.3 - - + -
300E THR* 3.3 34.1 - - + +
303E ALA* 5.4 2.2 - - + -
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Residues in contact with MET 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ALA 3.1 13.1 + - - +
247E CYS* 3.9 7.6 - - - +
249E ILE* 1.3 78.2 - - - +
251E LEU* 1.3 68.1 + - + +
252E LEU 3.8 0.5 + - - +
270E HIS 5.0 5.4 - - - +
272E GLY* 3.8 18.2 + - - -
274E ILE* 4.3 12.9 + - + +
275E TYR 5.2 0.5 + - - -
289E ARG 5.6 0.4 - - - +
292E ALA* 4.1 14.1 - - + +
293E ARG* 3.9 36.8 - - + +
296E ALA* 3.6 23.8 - - + -
35F G 3.6 25.1 - - + +
39F A 4.2 13.5 - - + -
41F C 3.9 11.7 - - - +
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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