Contacts of the strand formed by residues 250 - 258 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C PRO 4.1 0.5 - - - +
130C SER* 3.5 25.1 - - - -
242C MET* 3.5 27.8 - - + +
243C VAL 3.3 9.9 - - - +
244C LYS* 4.2 22.3 - - + +
248C GLY 3.9 6.7 + - - +
249C SER* 1.3 83.2 - - - +
251C ILE* 1.3 65.5 + - - +
252C THR* 5.4 1.6 - - + -
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Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ALA* 4.4 11.4 - - + -
129C PRO 3.6 19.3 - - - +
130C SER 3.7 4.9 - - - +
132C VAL* 3.3 32.5 - - + -
135C LEU* 4.7 7.6 - - + -
160C LEU* 4.2 19.3 - - + -
162C VAL* 4.3 8.5 - - + -
228C LEU* 4.8 0.4 - - + -
242C MET* 3.3 3.6 - - - +
243C VAL* 2.9 44.2 + - + +
245C LEU* 4.1 34.1 - - + -
249C SER* 5.4 1.3 - - - -
250C GLN* 1.3 79.1 - - - +
252C THR* 1.3 68.1 + - - +
253C TYR* 4.7 0.5 - - - -
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Residues in contact with THR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C SER 2.9 18.7 + - - +
131C HIS* 3.0 22.2 + - - +
132C VAL* 3.0 27.9 + - - +
240C ASP 4.8 1.8 - - - +
241C ASN* 3.1 12.6 - - - +
242C MET* 3.6 35.9 - - + -
250C GLN* 5.4 1.3 - - + -
251C ILE* 1.3 80.6 - - - +
253C TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C HIS* 4.0 6.7 - - - -
132C VAL* 3.2 8.3 - - + +
135C LEU* 3.8 38.8 - - + -
236C LEU* 3.9 16.7 - - + +
238C VAL* 4.0 12.6 + - - -
241C ASN* 2.9 65.0 + - + +
242C MET* 3.3 14.0 + - - -
243C VAL* 4.2 9.4 - - + -
252C THR* 1.3 76.0 - - - +
254C GLU* 1.3 65.5 + - - +
255C LYS 3.9 9.4 - - - +
256C CYS* 3.6 30.2 - - + +
432C ASN* 4.2 11.9 - - + -
433C ILE* 4.5 9.7 - - - +
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Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C HIS* 3.2 30.6 + - + +
132C VAL 3.4 1.0 + - - -
133C PRO* 3.1 33.3 + - + +
134C PHE* 6.1 0.2 - - + -
241C ASN* 4.8 0.9 - - - +
253C TYR* 1.3 76.2 - - - +
255C LYS* 1.3 81.0 + - + +
432C ASN* 3.4 19.4 - - - +
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Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PRO 3.0 7.0 + - - +
134C PHE* 3.7 27.2 - - + -
135C LEU 3.1 23.9 + - - +
253C TYR* 3.9 4.5 - - - +
254C GLU* 1.3 89.0 - - + +
256C CYS* 1.3 60.9 + - - +
432C ASN* 3.5 23.3 - - - +
434C TRP* 4.0 21.9 - - + -
468C ASN 5.3 0.4 + - - -
469C MET* 2.9 41.8 + - + +
470C THR* 5.1 0.4 - - - +
471C GLY* 5.1 4.2 - - - +
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Residues in contact with CYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 3.2 14.6 - - - +
137C ILE* 4.1 21.5 - - - -
236C LEU* 5.4 3.6 - - - -
253C TYR* 3.6 36.1 - - + -
255C LYS* 1.3 76.6 - - - +
257C LEU* 1.3 73.3 + - - +
258C ILE* 4.6 7.0 - - - -
432C ASN 2.8 12.2 + - - +
433C ILE* 3.4 10.9 - - + -
434C TRP* 2.9 30.8 + - - -
469C MET* 3.6 4.3 - - - -
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU 2.9 9.5 + - - -
136C LEU* 4.0 17.5 - - + -
137C ILE* 2.7 34.3 + - - +
142C ALA 4.5 2.9 - - - +
143C ALA* 4.5 4.5 - - - -
146C ALA* 3.6 29.8 - - + -
256C CYS* 1.3 75.0 - - - +
258C ILE* 1.3 64.8 + - - +
259C ALA* 3.7 17.7 + - + -
434C TRP* 3.4 23.8 - - + +
436C ALA* 3.9 18.4 - - + +
465C ALA* 3.7 26.0 - - + -
469C MET* 3.8 13.2 - - - +
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Residues in contact with ILE 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ILE* 4.2 17.9 - - + -
236C LEU* 4.1 9.4 - - + -
256C CYS* 4.7 2.5 - - - -
257C LEU* 1.3 74.1 - - - +
259C ALA* 1.3 59.4 + - - +
260C THR* 3.6 32.3 - - + +
406C LEU* 4.9 4.3 - - + -
412C LEU* 3.8 18.2 - - + -
421C PHE* 3.9 25.1 - - + -
433C ILE* 3.6 32.5 - - + -
434C TRP 2.8 12.6 + - - +
435C VAL* 3.3 17.8 - - + +
436C ALA 3.1 24.8 + - - -
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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