Contacts of the strand formed by residues 275 - 283 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132F ALA* 4.3 7.2 - - + -
133F GLU 3.0 8.7 - - - +
134F ALA* 4.5 0.4 - - - -
242F MET* 3.9 38.8 - - + -
274F GLY* 1.3 72.3 - - - -
276F HIS* 1.3 64.7 + - - +
277F CYS* 3.4 22.4 - - - -
370F PRO* 2.9 39.7 + - + +
371F ASP* 3.5 31.3 - - - +
372F SER* 3.6 16.6 - - - +
376F PRO* 5.1 6.3 - - + -
379F ALA* 4.5 11.0 - - + -
380F PHE* 3.9 15.3 - - + -
383F MET* 4.4 4.9 - - + -
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Residues in contact with HIS 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F GLY 3.6 1.0 - - - +
132F ALA* 3.3 6.1 - - - -
133F GLU* 3.0 48.5 + - + +
135F GLU* 4.5 5.0 + - - -
274F GLY* 4.6 0.7 - - - -
275F MET* 1.3 74.6 - - - +
277F CYS* 1.3 60.0 + - - +
278F HIS 4.0 0.4 - - - -
329F ARG* 4.2 2.5 - - - -
366F GLU* 3.1 16.5 + - + +
367F PHE 3.5 6.3 - - - +
368F ARG* 3.4 40.8 + - + +
502F MG 4.3 2.7 - - - -
503F MG 2.5 21.0 - - - -
505F P3S 2.7 62.1 + - + +
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Residues in contact with CYS 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PHE* 4.6 5.2 - - + -
131F GLY 3.4 4.5 - - - +
132F ALA* 4.6 2.9 - - - -
275F MET* 3.4 23.3 - - - -
276F HIS* 1.3 72.5 - - - +
278F HIS* 1.3 62.6 + - - +
279F GLN* 3.2 28.0 + - + +
365F LEU 3.6 1.0 - - - +
367F PHE* 2.8 37.8 + - + +
370F PRO* 4.3 0.4 - - - -
380F PHE* 3.6 22.4 - - - -
383F MET* 3.6 30.1 - - - -
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Residues in contact with HIS 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PHE* 3.4 4.5 - - - -
131F GLY 2.7 37.9 + - - +
133F GLU* 3.0 28.1 + - - -
276F HIS 4.6 1.3 - - - -
277F CYS* 1.3 71.1 - - - +
279F GLN* 1.3 59.2 + - - +
352F ARG* 4.6 1.6 - - - -
354F PRO* 4.2 10.7 - - + +
364F ARG* 3.1 37.5 + - + +
365F LEU 3.2 5.2 - - - -
366F GLU* 3.4 25.4 + - + +
501F IQ1 3.4 41.1 - - + +
506F PO4 3.2 24.4 + - - -
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Residues in contact with GLN 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F TYR 3.4 4.0 - - - +
130F PHE* 3.7 29.9 - - + -
277F CYS* 3.2 18.5 + - - +
278F HIS* 1.3 78.2 - - - +
280F SER* 1.3 61.3 + - - +
289F MET* 3.8 3.3 - - - +
305F TYR* 2.8 42.4 + - + +
309F LEU* 4.4 1.1 - - - +
364F ARG* 3.1 18.7 - - - +
365F LEU* 2.8 35.1 + - + +
367F PHE* 3.3 23.0 - - - +
383F MET* 3.5 26.8 - - - +
501F IQ1 4.3 0.7 - - - -
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Residues in contact with SER 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F THR 3.9 0.2 - - - +
128F ALA* 3.6 3.5 - - - -
129F TYR* 2.9 35.8 + - - +
279F GLN* 1.3 76.4 - - - +
281F LEU* 1.3 63.9 + - - +
282F TRP* 3.2 22.7 + - - -
289F MET* 3.6 22.9 - - - -
305F TYR* 6.3 0.7 - - - -
361F LYS 6.0 0.2 - - - -
363F LYS 4.0 9.6 - - - -
364F ARG* 4.1 0.2 - - - -
501F IQ1 2.9 25.2 + - - -
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Residues in contact with LEU 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F LEU* 4.3 8.7 - - + -
124F ILE* 4.3 10.5 - - + -
125F ALA* 3.9 9.2 - - + -
127F THR 3.4 4.5 - - - +
128F ALA* 3.7 28.3 - - + -
280F SER* 1.3 73.6 - - - +
282F TRP* 1.3 67.2 + - - +
288F LEU* 3.0 34.1 + - + +
289F MET* 3.4 15.1 - - - +
301F THR* 4.6 5.8 - - + -
305F TYR* 3.9 19.7 - - + -
384F LEU* 3.9 15.3 - - + -
388F LEU* 4.2 8.7 - - + -
391F ILE* 3.6 30.7 - - + -
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Residues in contact with TRP 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ALA* 3.2 3.9 - - - +
126F ASP* 2.9 24.1 + - - +
127F THR* 2.9 21.4 + - - +
129F TYR* 3.4 40.5 - + + -
232F PHE* 5.8 4.9 - + - -
280F SER* 3.2 22.4 + - - -
281F LEU* 1.3 85.2 - - - +
283F LYS* 1.3 60.5 + - - +
285F GLY* 3.5 33.9 - - - +
286F ALA 3.3 11.2 - - - +
287F PRO* 3.7 24.9 - - + +
288F LEU* 4.2 1.6 - - - -
289F MET* 5.7 0.2 - - - +
361F LYS* 3.6 53.5 + - + -
363F LYS 5.8 0.2 + - - -
501F IQ1 5.2 5.0 + + - -
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Residues in contact with LYS 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F GLY* 2.8 36.2 + - - +
124F ILE 4.2 7.2 - - - +
125F ALA* 4.0 11.9 - - - +
126F ASP* 3.4 13.2 - - - +
282F TRP* 1.3 76.0 - - - +
284F ASP* 1.3 90.9 + - - +
285F GLY 3.2 1.3 - - - -
286F ALA* 2.9 25.4 + - - +
288F LEU* 4.1 17.6 - - + +
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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