Contacts of the strand formed by residues 158 - 163 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B VAL* 4.6 0.2 - - - +
133B PRO* 3.9 29.5 - - + +
134B PHE* 3.3 30.9 + - - +
156B GLY 4.1 10.4 + - - -
157B ALA* 1.3 76.8 - - - +
159B VAL* 1.3 60.7 + - - +
217B LEU* 3.5 32.0 + - + +
218B PRO* 3.5 26.7 + - + -
219B HIS 4.0 2.2 + - - -
220B ILE 2.8 28.9 + - - -
221B GLU* 5.5 0.6 - - - +
222B ASN 4.7 4.9 - - - +
223B GLY* 3.6 17.2 - - - +
224B GLY 3.7 4.0 - - - -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 3.6 8.1 - - + +
136B LEU* 3.6 40.6 - - + -
147B ALA* 4.2 12.1 - - + +
150B ILE* 4.1 31.0 - - + -
151B ARG* 4.5 16.4 - - + -
157B ALA* 4.6 0.7 - - + -
158B ARG* 1.3 77.9 - - - +
160B LEU* 1.3 63.6 + - - +
161B ILE* 4.7 0.4 - - + -
217B LEU* 3.7 4.8 - - - +
224B GLY 3.0 11.9 + - - +
225B VAL* 3.5 10.7 - - + +
226B ALA 3.0 26.0 + - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 4.4 17.0 - - + -
132B VAL* 3.7 23.8 - - + +
134B PHE 2.8 12.2 + - - +
135B LEU* 3.6 20.3 - - + +
136B LEU* 2.7 34.1 + - - +
158B ARG 4.2 0.2 - - - -
159B VAL* 1.3 74.5 - - - +
161B ILE* 1.3 69.5 + - - +
162B VAL* 4.2 10.3 - - + -
214B ALA* 4.0 15.5 - - + -
217B LEU* 3.9 5.1 - - + +
226B ALA* 3.6 29.4 - - + +
227B VAL 4.5 0.2 - - - +
228B LEU* 4.5 11.2 - - + +
251B ILE* 4.3 16.2 - - + -
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 3.4 32.5 - - + -
138B GLY 3.9 19.3 - - - +
139B GLY* 4.0 14.1 - - - -
143B ALA* 4.7 2.0 - - + -
144B PHE* 4.7 14.8 - - + +
147B ALA* 4.4 7.0 - - + -
159B VAL* 4.7 0.7 - - + -
160B LEU* 1.3 72.9 - - - +
162B VAL* 1.3 64.1 + - - +
163B SER* 4.4 0.2 - - - -
169B PRO* 4.9 7.6 - - + -
211B TYR* 5.1 1.6 - - + -
225B VAL* 4.0 24.5 - - + -
226B ALA 2.8 13.8 + - - +
227B VAL* 3.3 24.8 - - + +
228B LEU 2.8 27.9 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.7 27.1 - - + -
136B LEU 3.1 6.9 + - - +
137B ILE* 4.9 0.9 - - - -
138B GLY* 2.7 32.6 + - - -
160B LEU* 4.2 12.8 - - + -
161B ILE* 1.3 74.1 - - - +
163B SER* 1.3 58.9 + - - +
228B LEU* 3.9 8.7 - - + +
231B LYS* 3.6 25.1 - - + +
233B VAL* 3.8 31.6 - - + +
245B LEU* 4.1 13.7 - - + -
251B ILE* 4.6 10.8 - - + -
1612B FAD 3.6 4.2 - - + -
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLY* 3.7 26.5 + - - +
161B ILE* 4.4 7.4 - - - -
162B VAL* 1.3 75.8 - - - +
164B GLU* 1.3 56.7 + - - +
165B ASP* 3.0 25.6 + - - +
167B GLU 4.0 7.0 + - - -
227B VAL* 4.4 10.1 - - - -
228B LEU 3.1 12.4 + - - -
229B THR* 3.4 1.4 - - - -
230B GLY 2.9 26.9 + - - -
231B LYS 3.0 6.8 + - - -
1612B FAD 3.9 3.8 + - - -
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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