Contacts of the strand formed by residues 158 - 163 (chain D) in PDB entry 4BUR
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 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D VAL* 4.0 0.5 - - - +
133D PRO* 3.4 43.2 - - + +
134D PHE* 3.4 15.0 + - - +
156D GLY 3.6 9.1 + - - -
157D ALA* 1.3 70.4 - - - +
159D VAL* 1.3 61.0 + - - +
160D LEU 4.3 0.2 - - - -
217D LEU* 3.3 38.7 + - + +
218D PRO* 3.6 25.9 + - - -
219D HIS 4.2 1.8 + - - -
220D ILE 2.7 30.3 + - - -
221D GLU* 4.8 4.0 + - - +
222D ASN* 4.8 4.0 - - - +
223D GLY* 3.9 13.4 - - - +
224D GLY 4.0 2.5 - - - -
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Residues in contact with VAL 159 (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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134D PHE* 3.5 16.2 - - + +
136D LEU* 4.0 30.7 - - + -
147D ALA* 4.3 11.2 - - + +
150D ILE* 4.0 31.0 - - + -
151D ARG* 4.5 10.1 - - + -
157D ALA* 4.2 10.1 - - + +
158D ARG* 1.3 76.1 - - - +
160D LEU* 1.3 65.5 + - - +
217D LEU* 3.8 5.6 - - - +
224D GLY 3.1 12.1 + - - +
225D VAL* 3.3 11.1 - - + +
226D ALA 2.9 26.0 + - - +
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Residues in contact with LEU 160 (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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129D PRO* 4.8 15.7 - - + -
132D VAL* 3.9 27.6 - - + +
134D PHE 3.1 8.4 + - - +
135D LEU* 3.7 7.5 - - + +
136D LEU* 2.8 33.8 + - - +
159D VAL* 1.3 74.7 - - - +
161D ILE* 1.3 67.1 + - - +
162D VAL* 4.0 11.9 - - + -
214D ALA* 4.9 6.5 - - + -
217D LEU* 3.9 9.0 - - + -
226D ALA* 3.7 14.6 - - + -
228D LEU* 3.9 33.2 - - + +
251D ILE* 3.9 27.8 - - + -
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Residues in contact with ILE 161 (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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136D LEU* 3.4 24.9 - - + +
138D GLY 4.0 19.7 - - - +
139D GLY* 4.1 14.8 - - - -
143D ALA* 4.2 10.3 - - + +
144D PHE* 4.5 6.5 - - + +
147D ALA* 3.9 17.0 - - + -
159D VAL* 4.6 0.7 - - + -
160D LEU* 1.3 77.3 - - - +
162D VAL* 1.3 58.3 + - - +
163D SER 3.9 0.3 + - - -
169D PRO* 4.9 7.2 - - + -
211D TYR* 5.6 2.0 - - + -
225D VAL* 3.8 22.7 - - + -
226D ALA 2.8 16.5 + - - +
227D VAL* 3.2 21.4 - - + +
228D LEU 2.8 31.1 + - - +
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Residues in contact with VAL 162 (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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135D LEU* 3.4 27.4 - - + -
136D LEU 2.8 12.0 + - - +
137D ILE* 4.9 0.7 - - - -
138D GLY* 2.8 29.1 + - - -
160D LEU* 4.0 16.8 - - + -
161D ILE* 1.3 74.3 - - - +
163D SER* 1.3 60.2 + - - +
228D LEU* 3.6 11.9 - - + +
231D LYS* 3.6 20.9 - - + +
233D VAL* 4.0 26.9 - - + +
245D LEU* 4.0 12.8 - - + -
251D ILE* 4.5 9.4 - - + -
1612D FAD 3.6 4.6 - - + -
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Residues in contact with SER 163 (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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139D GLY* 3.8 26.9 + - - +
161D ILE* 3.9 0.4 + - - -
162D VAL* 1.3 73.8 - - - +
164D GLU* 1.3 63.2 + - - +
165D ASP* 3.0 28.5 + - - +
167D GLU 3.9 5.4 + - - -
169D PRO* 5.9 0.2 - - - -
227D VAL* 4.7 13.5 - - - -
228D LEU 2.9 13.4 + - - -
229D THR* 3.4 5.1 - - - -
230D GLY 3.0 21.3 + - - -
231D LYS 3.1 7.7 + - - +
1612D FAD 4.0 2.8 + - - -
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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