Contacts of the strand formed by residues 250 - 258 (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 GLN 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D PRO 4.1 1.9 - - - +
130D SER* 3.6 24.3 - - - +
242D MET* 3.5 27.9 - - + +
243D VAL 3.7 11.0 - - - +
244D LYS* 4.0 17.6 - - + +
248D GLY 3.8 4.7 + - - +
249D SER* 1.3 80.6 - - - +
251D ILE* 1.3 64.4 + - - +
252D THR* 5.8 0.4 - - - -
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Residues in contact with ILE 251 (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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128D ALA* 5.8 2.0 - - + -
129D PRO* 4.0 15.9 - - + +
130D SER* 3.6 13.2 - - - +
131D HIS 4.6 0.4 - - - +
132D VAL* 3.5 21.8 - - + -
135D LEU* 4.6 5.4 - - + -
160D LEU* 3.9 22.2 - - + -
162D VAL* 4.5 10.3 - - + -
228D LEU* 5.0 4.3 - - + -
242D MET* 3.2 9.2 - - - +
243D VAL* 2.9 48.3 + - + -
245D LEU* 4.3 24.2 - - + -
249D SER* 5.4 1.8 - - - -
250D GLN* 1.3 79.9 - - - +
252D THR* 1.3 84.7 + - - +
253D TYR* 5.6 0.2 - - - -
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Residues in contact with THR 252 (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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130D SER 2.9 20.6 + - - +
131D HIS* 3.2 19.8 + - - +
132D VAL* 3.1 25.6 + - - +
240D ASP 4.4 2.2 - - - +
241D ASN* 3.2 11.4 - - - +
242D MET* 3.5 34.8 - - + -
250D GLN 5.8 0.7 - - - -
251D ILE* 1.3 84.2 - - - +
253D TYR* 1.3 63.2 + - - +
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Residues in contact with TYR 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D HIS* 4.3 5.3 - - - -
132D VAL 3.2 9.0 - - - +
135D LEU* 3.7 33.7 - - + -
236D LEU* 4.1 11.8 - - + +
237D ASP 3.9 7.4 + - - -
238D VAL* 4.2 9.0 + - - +
241D ASN* 3.0 59.5 + - + +
242D MET* 3.5 4.9 - - - -
243D VAL* 4.0 16.8 - - + -
252D THR* 1.3 76.6 - - - +
254D GLU* 1.3 62.1 + - - +
255D LYS 3.6 23.8 - - - +
256D CYS* 3.8 27.8 - - + -
432D ASN* 4.2 13.9 - - + -
433D ILE* 4.6 9.1 - - + +
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Residues in contact with GLU 254 (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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131D HIS* 3.8 22.9 + - + +
132D VAL 3.5 1.0 + - - -
133D PRO* 3.1 37.8 + - - +
241D ASN* 5.9 0.4 - - - -
253D TYR* 1.3 77.5 - - - +
255D LYS* 1.3 72.2 + - + +
432D ASN* 3.4 24.8 + - - +
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Residues in contact with LYS 255 (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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133D PRO 3.1 3.2 + - - +
134D PHE* 3.5 25.8 - - + -
135D LEU 2.9 25.6 + - - +
253D TYR* 3.5 6.0 - - - +
254D GLU* 1.3 85.7 - - + +
256D CYS* 1.3 60.5 + - - +
432D ASN* 3.5 28.5 - - - +
434D TRP* 3.6 26.9 - - + -
469D MET* 3.5 32.5 + - + +
471D GLY 5.8 1.2 - - - +
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Residues in contact with CYS 256 (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* 3.2 13.0 - - - +
137D ILE* 3.6 32.1 - - - -
236D LEU* 5.2 2.7 - - - -
253D TYR* 3.8 36.3 - - + -
255D LYS* 1.3 77.2 - - - +
257D LEU* 1.3 66.2 + - - +
258D ILE* 4.6 6.3 - - - -
432D ASN 2.8 10.1 + - - +
433D ILE* 3.2 11.2 - - + -
434D TRP* 2.9 27.9 + - - -
469D MET* 3.7 3.8 - - - +
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Residues in contact with LEU 257 (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 3.0 6.9 + - - -
136D LEU* 3.9 18.4 - - + -
137D ILE* 2.9 30.4 + - - +
142D ALA 4.5 1.3 - - - +
143D ALA* 4.4 6.1 - - - -
146D ALA* 3.7 27.6 - - + -
256D CYS* 1.3 76.5 - - - +
258D ILE* 1.3 63.7 + - - +
259D ALA* 4.1 16.2 - - + -
434D TRP* 3.2 16.6 - - + +
435D VAL 4.0 0.9 - - - -
436D ALA* 3.7 23.3 - - + +
465D ALA* 3.7 29.4 - - + -
469D MET* 3.7 18.1 - - + +
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Residues in contact with ILE 258 (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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137D ILE* 4.2 16.6 - - + -
236D LEU* 4.2 12.3 - - + -
256D CYS* 4.6 0.7 - - - -
257D LEU* 1.3 73.2 - - - +
259D ALA* 1.3 62.4 + - - +
260D THR* 3.7 28.7 - - + +
406D LEU* 4.9 9.0 - - + -
412D LEU* 3.9 17.0 - - + -
421D PHE* 4.0 23.8 - - + -
433D ILE* 3.4 33.7 - - + -
434D TRP 2.7 12.7 + - - +
435D VAL* 3.3 14.7 - - + +
436D ALA 3.0 24.4 + - - -
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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