Contacts of the strand formed by residues 25 - 29 (chain D) in PDB entry 5BZZ
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 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D TYR 3.7 2.7 + - - +
17D GLN 3.8 1.7 - - - -
18D GLU* 3.5 39.0 + - + +
23D LEU* 3.2 20.7 + - + -
24D ASP* 1.3 78.2 + - - +
26D THR* 1.3 70.7 + - - +
27D TYR* 3.9 18.4 - - + -
33D ILE* 3.5 23.6 - - + -
34D ALA 3.5 6.7 - - - -
35D MET* 4.1 16.4 - - + -
48D ASN* 5.5 0.9 - - - +
53D VAL* 5.5 3.8 - - + -
56D PHE* 3.9 45.5 - - + -
57D LEU* 5.3 2.7 - - + -
159D ARG* 3.9 0.8 - - - +
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Residues in contact with THR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG* 3.5 28.5 + - + +
16D TYR 3.1 8.1 + - - -
25D LEU* 1.3 78.8 + - - +
27D TYR* 1.3 69.7 + - - +
28D ILE* 3.1 6.8 + - + +
33D ILE* 3.3 4.1 - - - -
34D ALA 2.8 37.3 + - - -
158D VAL* 3.5 29.4 - - + +
159D ARG* 2.8 36.6 + - - -
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Residues in contact with TYR 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG* 2.9 43.5 + - - +
18D GLU* 5.1 8.3 - - + -
25D LEU* 3.9 13.2 - - + -
26D THR* 1.3 72.2 - - - +
28D ILE* 1.3 62.3 + - - +
29D TYR* 3.3 13.2 - - - +
30D PRO* 3.1 33.2 - - + -
32D ILE 3.5 4.0 - - - -
33D ILE* 3.8 19.7 - - + +
56D PHE* 3.3 29.8 - + - -
60D LYS* 4.4 5.9 - - + +
61D HIS* 2.6 33.7 + + - -
158D VAL* 3.9 1.0 - - - +
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG* 5.0 1.4 + - - -
26D THR* 3.1 22.8 + - + +
27D TYR* 1.3 73.7 - - - +
29D TYR* 1.3 80.4 + - + +
32D ILE* 2.9 11.4 + - + +
34D ALA* 3.3 36.1 - - + +
135D ILE* 4.1 12.6 - - + -
139D LEU* 3.9 15.7 - - + -
154D PHE* 3.6 30.1 - - + -
155D TYR* 3.9 26.7 - - + -
158D VAL* 4.0 17.1 - - + +
159D ARG* 4.4 5.4 - - + -
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Residues in contact with TYR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D TYR* 3.3 14.2 - - - +
28D ILE* 1.3 94.0 - - + +
30D PRO* 1.3 81.1 - - + +
31D ASN* 3.1 17.2 + - - +
32D ILE* 2.9 26.1 + - + +
139D LEU* 3.6 31.6 - - + -
144D LYS* 3.8 32.1 + - + +
145D PHE* 3.6 19.9 - + - -
154D PHE* 3.7 27.8 - + - -
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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