Contacts of the strand formed by residues 275 - 283 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C ALA* 4.4 7.9 - - + -
133C GLU 3.2 8.1 - - - +
134C ALA* 4.4 0.4 - - - -
242C MET* 3.8 37.7 - - + -
274C GLY* 1.3 71.5 - - - -
276C HIS* 1.3 65.5 + - - +
277C CYS* 3.4 24.5 - - - -
370C PRO* 2.9 32.2 + - + +
371C ASP* 3.5 31.1 - - - +
372C SER* 3.6 17.3 - - - +
376C PRO* 5.1 6.7 - - + -
379C ALA* 4.5 11.2 - - + -
380C PHE* 4.0 13.9 - - + -
383C MET* 4.5 4.7 - - + -
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Residues in contact with HIS 276 (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 GLY 3.5 1.3 - - - +
132C ALA* 3.2 6.1 - - - -
133C GLU* 2.9 50.9 + - + +
135C GLU* 4.5 4.2 + - - -
274C GLY* 4.7 0.7 - - - -
275C MET* 1.3 73.8 - - - +
277C CYS* 1.3 60.4 + - - +
278C HIS 4.0 0.7 - - - -
329C ARG* 4.2 2.5 - - - -
366C GLU* 3.1 16.1 + - + +
367C PHE 3.5 5.8 - - - +
368C ARG* 3.4 40.2 + - + +
502C MG 4.4 2.2 - - - -
503C MG 2.4 21.9 - - - -
505C P3S 2.7 61.9 + - + +
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Residues in contact with CYS 277 (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 PHE* 4.6 5.4 - - + -
131C GLY 3.4 4.5 - - - -
132C ALA* 4.7 2.5 - - - -
275C MET* 3.4 21.8 - - - -
276C HIS* 1.3 72.9 - - - +
278C HIS* 1.3 62.1 + - - +
279C GLN* 3.2 29.7 + - + +
365C LEU 3.6 0.2 - - - +
367C PHE 2.9 35.7 + - - +
370C PRO* 4.3 0.9 - - - -
380C PHE* 3.6 23.3 - - - -
383C MET* 3.6 30.7 - - - -
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Residues in contact with HIS 278 (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 PHE* 3.4 3.6 - - - -
131C GLY 2.7 39.1 + - - +
133C GLU* 2.9 27.9 + - - -
276C HIS 4.6 1.1 - - - -
277C CYS* 1.3 72.0 - - - +
279C GLN* 1.3 58.8 + - - +
352C ARG* 4.6 1.6 - - - -
354C PRO* 4.2 10.7 - - + +
364C ARG* 3.1 38.5 + - + +
365C LEU 3.2 5.8 - - - -
366C GLU* 3.5 24.6 + - + +
501C IQ1 3.3 41.0 - - + +
506C PO4 3.2 25.4 + - - -
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Residues in contact with GLN 279 (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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129C TYR 3.3 4.5 - - - +
130C PHE* 3.6 29.5 - - + -
277C CYS* 3.2 17.3 + - - +
278C HIS* 1.3 77.5 - - - +
280C SER* 1.3 60.1 + - - +
289C MET* 3.8 3.7 - - - +
305C TYR* 2.8 41.0 + - + +
309C LEU* 4.4 1.7 - - - +
364C ARG* 3.3 18.3 - - - +
365C LEU* 2.9 33.9 + - + +
367C PHE* 3.3 23.0 - - - +
383C MET* 3.6 25.9 - - - +
501C IQ1 4.2 0.6 - - - -
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Residues in contact with SER 280 (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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127C THR 3.9 0.2 - - - +
128C ALA* 3.5 3.8 - - - +
129C TYR* 2.8 34.9 + - - +
279C GLN* 1.3 76.2 - - - +
281C LEU* 1.3 63.9 + - - +
282C TRP* 3.1 23.7 + - - -
289C MET* 3.6 22.7 - - - -
305C TYR* 6.3 0.4 - - - -
363C LYS 4.0 9.4 - - - -
364C ARG* 4.1 0.2 - - - -
501C IQ1 2.9 25.4 + - - -
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Residues in contact with LEU 281 (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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119C LEU* 4.2 9.9 - - + -
124C ILE* 4.3 10.1 - - + -
125C ALA* 3.9 9.4 - - + -
127C THR 3.4 2.9 - - - +
128C ALA* 3.8 29.6 - - + -
280C SER* 1.3 74.2 - - - +
282C TRP* 1.3 66.6 + - - +
288C LEU* 3.1 33.0 + - + +
289C MET* 3.4 16.4 - - - +
301C THR* 4.5 6.1 - - + -
305C TYR* 3.8 20.6 - - + +
384C LEU* 3.9 15.3 - - + -
388C LEU* 4.2 8.5 - - + -
391C ILE* 3.6 30.3 - - + -
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Residues in contact with TRP 282 (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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125C ALA* 3.2 3.8 - - - +
126C ASP* 2.9 24.7 + - - +
127C THR* 2.9 23.2 + - - +
129C TYR* 3.4 38.7 - + + -
232C PHE* 5.8 5.4 - + - -
280C SER* 3.1 23.2 + - - -
281C LEU* 1.3 84.3 + - - +
283C LYS* 1.3 61.0 + - - +
285C GLY* 3.5 28.3 - - - +
286C ALA 3.3 18.2 - - - +
287C PRO* 3.7 24.7 - - + +
288C LEU* 4.2 1.1 - - - -
289C MET* 5.7 0.4 - - - +
361C LYS* 3.5 54.2 + - + -
363C LYS 5.8 0.2 + - - -
501C IQ1 5.2 5.0 + + - -
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Residues in contact with LYS 283 (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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123C GLY* 2.7 35.9 + - - +
124C ILE 4.1 7.6 - - - +
125C ALA* 4.0 13.7 - - - +
126C ASP* 3.5 11.9 - - - +
282C TRP* 1.3 74.1 - - - +
284C ASP* 1.3 90.9 - - - +
285C GLY 3.2 1.3 - - - -
286C ALA* 2.9 25.0 + - - +
288C LEU* 4.1 17.4 - - + +
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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