Contacts of the strand formed by residues 275 - 283 (chain E) in PDB entry 3ZXR
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 MET 275 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ALA* 4.4 7.6 - - + -
133E GLU 3.1 7.6 - - - +
134E ALA* 4.5 0.4 - - - -
242E MET* 3.9 37.5 - - + +
274E GLY* 1.3 72.8 - - - -
276E HIS* 1.3 65.2 + - - +
277E CYS* 3.4 24.1 + - - -
370E PRO* 2.9 40.3 + - + +
371E ASP* 3.5 30.6 - - - +
372E SER* 3.6 15.0 - - - +
376E PRO* 5.1 7.0 - - + -
379E ALA* 4.5 11.0 - - + -
380E PHE* 3.9 14.8 - - + -
383E MET* 4.4 4.7 - - + -
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Residues in contact with HIS 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLY 3.5 1.0 - - - +
132E ALA* 3.3 5.5 - - - -
133E GLU* 3.0 52.1 + - + +
135E GLU* 4.5 3.8 - - - -
274E GLY* 4.7 1.1 - - - -
275E MET* 1.3 73.3 - - - +
277E CYS* 1.3 59.5 + - - +
278E HIS 4.0 0.4 - - - -
329E ARG* 4.2 2.5 - - - -
366E GLU* 3.1 15.7 + - + +
367E PHE 3.5 5.8 - - - -
368E ARG* 3.4 43.5 + - + +
502E MG 4.3 1.6 - - - -
503E MG 2.4 20.8 - - - -
505E P3S 2.7 61.5 + - + -
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Residues in contact with CYS 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PHE* 4.6 5.8 - - + -
131E GLY 3.4 4.9 - - - +
132E ALA* 4.7 2.7 - - - -
275E MET* 3.4 22.4 - - - -
276E HIS* 1.3 74.2 - - - +
278E HIS* 1.3 61.6 + - - +
279E GLN* 3.3 27.2 + - + +
365E LEU 3.6 0.9 - - - +
366E GLU* 4.3 0.2 - - - -
367E PHE 2.9 37.6 + - - +
370E PRO* 4.3 0.7 - - - -
380E PHE* 3.6 30.7 - - - -
383E MET* 3.6 22.9 - - - -
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Residues in contact with HIS 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E TYR 3.4 2.1 - - - +
130E PHE* 3.4 2.4 - - - -
131E GLY 2.7 39.1 + - - +
133E GLU* 2.9 28.8 + - - -
276E HIS 4.5 1.3 - - - -
277E CYS* 1.3 71.5 - - - +
279E GLN* 1.3 60.0 + - - +
352E ARG* 4.5 1.6 - - - -
354E PRO* 4.1 10.5 - - + +
364E ARG* 3.1 36.8 + - + +
365E LEU 3.2 5.8 - - - -
366E GLU* 3.4 24.6 + - + +
501E IQ1 3.4 40.2 - - + +
506E PO4 3.2 24.7 + - - -
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Residues in contact with GLN 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E TYR 3.3 4.5 - - - +
130E PHE* 3.7 29.9 - - + -
277E CYS* 3.3 17.7 + - - +
278E HIS* 1.3 78.1 - - - +
280E SER* 1.3 61.3 + - - +
289E MET* 3.9 3.6 - - - +
305E TYR* 2.7 43.3 + - + +
309E LEU* 4.4 1.2 - - - +
364E ARG* 3.2 18.3 - - - +
365E LEU* 2.9 32.3 + - + +
367E PHE* 3.4 23.4 - - - +
383E MET* 3.7 24.7 - - - +
501E IQ1 4.2 0.9 - - - -
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Residues in contact with SER 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E THR 3.9 0.2 - - - +
128E ALA* 3.5 4.9 - - - +
129E TYR* 2.9 34.2 + - - +
279E GLN* 1.3 77.0 - - - +
281E LEU* 1.3 64.7 + - - +
282E TRP* 3.2 24.1 + - - -
289E MET* 3.6 22.9 - - - -
305E TYR* 6.3 0.7 - - - -
363E LYS 4.1 9.2 - - - -
364E ARG* 4.1 0.2 - - - -
501E IQ1 2.9 24.9 + - - -
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Residues in contact with LEU 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E LEU* 4.3 9.4 - - + -
124E ILE* 4.2 10.5 - - + -
125E ALA* 3.9 9.4 - - + -
127E THR 3.5 2.9 - - - +
128E ALA* 3.7 29.8 - - + -
280E SER* 1.3 74.9 - - - +
282E TRP* 1.3 67.7 + - - +
288E LEU* 3.0 35.2 + - + +
289E MET* 3.5 15.5 + - - +
301E THR* 4.5 6.3 - - + -
305E TYR* 3.9 19.5 - - + -
384E LEU* 3.9 15.3 - - + -
388E LEU* 4.2 8.3 - - + -
391E ILE* 3.6 31.0 - - + -
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Residues in contact with TRP 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ALA* 3.3 3.3 - - - +
126E ASP* 2.9 26.3 + - - +
127E THR* 2.9 21.1 + - - +
129E TYR* 3.4 39.0 - + + -
232E PHE* 5.9 4.7 - + - -
280E SER* 3.2 24.1 + - - -
281E LEU* 1.3 83.8 - - - +
283E LYS* 1.3 60.4 + - - +
285E GLY* 3.6 27.1 - - - +
286E ALA 3.3 17.3 - - - +
287E PRO* 3.7 24.7 - - + +
288E LEU* 4.3 1.1 - - - -
289E MET* 5.6 0.2 - - - +
361E LYS* 3.6 53.9 + - + -
363E LYS 5.8 0.2 + - - -
501E IQ1 5.2 6.0 + + - -
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Residues in contact with LYS 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E GLY* 2.7 38.3 + - - +
124E ILE 4.2 2.9 - - - +
125E ALA* 4.0 17.7 - - - +
126E ASP* 3.4 11.7 - - - +
282E TRP* 1.3 74.8 - - - +
284E ASP* 1.3 90.5 + - - +
285E GLY 3.2 1.6 - - - -
286E ALA* 3.0 25.1 + - - +
288E LEU* 4.1 17.8 - - + +
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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