Contacts of the strand formed by residues 275 - 283 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ALA* 4.4 7.4 - - + -
133A GLU 3.1 8.5 - - - +
134A ALA* 4.4 0.7 - - - -
242A MET* 3.9 39.0 - - + -
274A GLY* 1.3 71.2 - - - -
276A HIS* 1.3 65.4 + - - +
277A CYS* 3.2 25.4 + - - -
370A PRO* 2.8 33.3 + - + +
371A ASP* 3.5 32.0 - - - +
372A SER* 3.7 16.2 - - - +
376A PRO* 5.0 6.3 - - + -
379A ALA* 4.5 15.0 - - + -
380A PHE* 4.0 16.2 - - + -
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Residues in contact with HIS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLY 3.5 1.4 - - - +
132A ALA* 3.3 5.7 - - - -
133A GLU* 3.0 50.9 + - + +
135A GLU* 4.5 4.2 + - - -
274A GLY* 4.7 1.3 - - - -
275A MET* 1.3 73.4 - - - +
277A CYS* 1.3 59.5 + - - +
278A HIS 4.0 0.4 - - - -
329A ARG* 4.2 2.5 - - - -
366A GLU* 3.1 15.2 + - + +
367A PHE 3.5 6.1 - - - -
368A ARG* 3.4 41.0 + - + +
502A MG 4.4 2.0 - - - -
503A MG 2.5 21.4 - - - -
505A P3S 2.8 62.6 + - + +
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Residues in contact with CYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 4.6 6.3 - - + -
131A GLY 3.4 4.0 - - - +
132A ALA* 4.7 2.5 - - - -
275A MET* 3.2 23.8 - - - -
276A HIS* 1.3 73.3 - - - +
278A HIS* 1.3 61.9 + - - +
279A GLN* 3.2 27.6 + - + +
365A LEU 3.6 1.0 - - - +
367A PHE 2.9 36.4 + - - +
370A PRO* 4.3 1.3 - - - -
380A PHE* 3.7 21.1 - - - -
383A MET* 3.7 30.1 - - - -
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.4 4.3 - - - -
131A GLY 2.7 39.6 + - - +
133A GLU* 2.9 29.2 + - - -
276A HIS 4.5 1.1 - - - -
277A CYS* 1.3 72.1 - - - +
279A GLN* 1.3 60.6 + - - +
352A ARG* 4.6 1.8 - - - -
354A PRO* 4.2 9.8 - - + +
364A ARG* 3.1 38.4 + - + +
365A LEU 3.2 5.6 - - - -
366A GLU* 3.4 25.9 + - + +
501A IQ1 3.4 40.3 - - + +
506A PO4 3.2 23.9 + - - -
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR 3.4 3.8 - - - +
130A PHE* 3.7 29.1 - - + -
277A CYS* 3.2 18.1 + - - +
278A HIS* 1.3 79.8 - - - +
280A SER* 1.3 60.6 + - - +
289A MET* 3.9 4.1 - - - +
305A TYR* 2.7 41.4 + - + +
309A LEU* 4.4 1.5 - - - +
364A ARG* 3.2 18.5 - - - +
365A LEU* 2.9 32.4 + - + +
367A PHE* 3.4 23.0 - - - +
383A MET* 3.6 25.4 - - - +
501A IQ1 4.1 0.6 - - - -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A THR 3.9 0.2 - - - +
128A ALA* 3.5 4.7 - - - +
129A TYR* 2.9 36.2 + - - +
279A GLN* 1.3 76.0 - - - +
281A LEU* 1.3 65.3 + - - +
282A TRP* 3.1 24.6 + - - -
289A MET* 3.6 21.8 - - - -
305A TYR* 6.2 0.7 - - - -
361A LYS 6.0 0.4 - - - -
363A LYS 4.1 8.5 - - - -
364A ARG* 4.1 0.2 - - - -
501A IQ1 2.9 24.7 + - - -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 4.2 9.4 - - + -
124A ILE* 4.2 10.3 - - + -
125A ALA* 3.8 10.1 - - + -
127A THR 3.4 4.7 - - - +
128A ALA* 3.8 28.3 - - + -
280A SER* 1.3 74.9 - - - +
282A TRP* 1.3 67.5 + - - +
288A LEU* 3.1 32.9 + - + +
289A MET* 3.4 14.9 - - - +
301A THR* 4.6 5.6 - - + -
305A TYR* 3.9 20.0 - - + -
384A LEU* 3.9 14.4 - - + -
388A LEU* 4.1 9.0 - - + -
391A ILE* 3.6 31.0 - - + -
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Residues in contact with TRP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA* 3.2 4.1 - - - +
126A ASP* 2.9 24.6 + - - +
127A THR* 2.9 20.5 + - - +
129A TYR* 3.4 34.9 - + + -
232A PHE* 5.8 5.4 - + - -
280A SER* 3.1 27.5 + - - -
281A LEU* 1.3 93.1 + - - +
283A LYS* 1.3 61.2 + - - +
285A GLY* 3.5 27.8 - - - +
286A ALA 3.3 18.4 - - - +
287A PRO* 3.7 24.5 - - + +
288A LEU* 4.2 1.3 - - - -
289A MET* 5.7 0.2 - - - +
361A LYS* 3.6 53.7 + - + -
501A IQ1 5.2 6.1 + + - -
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLY* 2.7 37.5 + - - +
124A ILE 4.3 3.4 - - - +
125A ALA* 4.0 16.6 - - - +
126A ASP* 3.5 11.7 - - - +
282A TRP* 1.3 75.4 - - - +
284A ASP* 1.3 90.8 + - - +
285A GLY 3.2 1.6 - - - -
286A ALA* 2.9 24.5 + - - +
288A LEU* 4.1 17.0 - - + +
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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