Contacts of the strand formed by residues 275 - 283 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA* 4.4 7.4 - - + -
133B GLU 3.1 8.1 - - - +
134B ALA* 4.4 0.7 - - - -
242B MET* 4.0 37.5 - - + -
274B GLY* 1.3 72.2 - - - -
276B HIS* 1.3 66.2 + - - +
277B CYS* 3.4 22.9 + - - -
320B THR 5.4 0.2 - - - +
370B PRO* 2.9 39.1 + - + +
371B ASP* 3.5 31.9 - - - +
372B SER* 3.7 17.0 - - - +
376B PRO* 5.1 6.7 - - + -
379B ALA* 4.5 10.5 - - + -
380B PHE* 4.0 14.1 - - + -
383B MET* 4.5 4.5 - - + -
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLY 3.5 1.2 - - - +
132B ALA* 3.3 5.5 - - - -
133B GLU* 3.0 49.1 + - + +
135B GLU* 4.5 4.6 + - - -
274B GLY* 4.7 0.7 - - - -
275B MET* 1.3 75.1 - - - +
277B CYS* 1.3 60.3 + - - +
278B HIS 4.0 0.4 - - - -
329B ARG* 4.2 2.7 + - - -
366B GLU* 3.1 17.4 + - + +
367B PHE 3.4 6.3 - - - +
368B ARG* 3.4 39.3 + - + +
502B MG 4.3 2.5 - - - -
503B MG 2.3 22.2 - - - -
505B P3S 2.7 62.3 + - + +
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Residues in contact with CYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 4.6 4.5 - - + -
131B GLY 3.4 4.0 - - - +
132B ALA* 4.8 2.7 - - - -
275B MET* 3.5 21.5 - - - -
276B HIS* 1.3 73.3 - - - +
278B HIS* 1.3 61.7 + - - +
279B GLN* 3.3 28.3 + - + +
365B LEU 3.5 1.0 - - - +
367B PHE 2.8 38.7 + - - +
370B PRO* 4.4 1.1 - - + -
380B PHE* 3.5 31.9 - - - -
383B MET* 3.6 22.9 - - - -
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Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 3.4 4.5 - - - +
131B GLY 2.7 41.0 + - - +
133B GLU* 2.9 27.4 + - - -
276B HIS 4.5 1.8 - - - -
277B CYS* 1.3 71.3 - - - +
279B GLN* 1.3 61.0 + - - +
352B ARG* 4.6 1.1 - - - -
354B PRO* 4.1 10.5 - - + +
364B ARG* 3.1 37.7 + - + +
365B LEU 3.2 4.7 - - - -
366B GLU* 3.3 25.7 + - + +
501B IQ1 3.4 40.0 - - + +
506B PO4 3.3 25.2 + - - -
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR 3.4 4.0 - - - +
130B PHE* 3.7 28.2 - - + -
277B CYS* 3.3 27.3 + - - +
278B HIS* 1.3 78.8 - - - +
280B SER* 1.3 60.4 + - - +
289B MET* 4.0 3.5 - - - +
305B TYR* 2.8 41.5 + - + +
309B LEU* 4.5 1.1 - - - +
364B ARG* 3.2 19.2 - - - +
365B LEU* 2.9 33.2 + - + +
367B PHE* 3.3 22.8 - - - +
383B MET* 3.6 20.1 - - - +
501B IQ1 4.3 0.9 - - - -
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Residues in contact with SER 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 3.6 4.0 - - - +
129B TYR* 2.9 35.5 + - - +
279B GLN* 1.3 77.1 - - - +
281B LEU* 1.3 65.1 + - - +
282B TRP* 3.1 23.7 + - - -
289B MET* 3.6 22.0 - - - -
305B TYR* 6.3 0.2 - - - -
361B LYS 5.9 0.2 - - - -
363B LYS 4.0 10.3 - - - -
501B IQ1 2.8 26.0 + - - -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 4.3 9.4 - - + -
124B ILE* 4.3 10.3 - - + -
125B ALA* 3.9 9.2 - - + -
127B THR 3.4 2.7 - - - +
128B ALA* 3.7 28.9 - - + -
280B SER* 1.3 75.4 - - - +
282B TRP* 1.3 67.8 + - - +
288B LEU* 3.1 34.0 + - + +
289B MET* 3.4 15.6 - - - +
301B THR* 4.6 5.6 - - + -
305B TYR* 3.8 19.5 - - + +
384B LEU* 3.9 15.0 - - + -
388B LEU* 4.2 9.0 - - + -
391B ILE* 3.6 31.6 - - + -
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Residues in contact with TRP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ALA* 3.2 4.3 - - - +
126B ASP* 2.9 25.4 + - - +
127B THR* 2.9 21.8 + - - +
129B TYR* 3.4 41.9 - + + -
232B PHE* 5.8 5.2 - + - -
280B SER* 3.1 22.6 + - - -
281B LEU* 1.3 94.8 + - - +
283B LYS* 1.3 61.2 + - - +
285B GLY* 3.4 33.0 - - - +
286B ALA 3.4 11.0 - - - +
287B PRO* 3.7 24.7 - - + +
288B LEU* 4.3 1.3 - - - -
289B MET* 5.6 0.4 - - - +
361B LYS* 3.6 55.5 + - + -
501B IQ1 5.2 4.8 + + - -
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLY* 2.7 37.7 + - - +
124B ILE 4.2 7.0 - - - +
125B ALA* 4.0 13.0 - - - +
126B ASP* 3.4 11.7 - - - +
282B TRP* 1.3 75.2 - - - +
284B ASP* 1.3 91.3 + - - +
285B GLY 3.2 1.3 - - - -
286B ALA* 3.0 24.6 + - - +
288B LEU* 4.1 17.2 - - + +
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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