Contacts of the strand formed by residues 325 - 330 (chain B) in PDB entry 1ADI
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 SER 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ARG* 3.3 28.2 + - - +
260B ASP 4.3 1.0 + - - -
261B TYR* 3.7 27.0 - - - -
262B VAL 2.9 34.7 + - - -
323B SER 3.4 1.0 + - - -
324B LEU* 1.3 75.8 - - - +
326B GLY* 1.3 56.5 + - - +
408B VAL* 3.3 3.9 - - - +
409B PRO* 3.2 24.4 - - - +
411B ASP* 4.3 0.7 - - - +
426B ARG* 5.3 1.7 + - - -
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Residues in contact with GLY 326 (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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261B TYR* 3.4 20.4 + - - -
262B VAL 3.4 2.4 + - - -
263B LEU* 3.7 2.8 - - - -
264B GLY* 2.9 25.1 + - - -
324B LEU* 3.8 4.3 - - - +
325B SER* 1.3 80.3 - - - +
327B PHE* 1.3 60.9 + - - -
408B VAL* 3.4 7.4 - - - +
409B PRO 3.3 11.2 - - - -
411B ASP* 3.5 4.3 - - - -
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Residues in contact with PHE 327 (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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9B THR* 4.0 12.1 - - + -
263B LEU* 4.2 4.2 - - - +
264B GLY 3.4 15.3 - - - -
266B LEU* 3.8 31.0 - - + -
315B VAL* 3.7 24.7 - - + -
319B VAL* 4.0 15.7 - - + -
324B LEU* 3.5 20.4 - - + -
326B GLY* 1.3 76.4 - - - -
328B CYS* 1.3 62.7 + - - +
329B LEU 3.8 0.9 - - - +
402B ILE* 4.8 4.0 - - + -
403B GLU* 6.1 0.2 - - + -
406B THR* 3.7 23.6 - - + -
408B VAL* 3.9 22.4 - - + -
409B PRO 2.8 10.5 + - - +
410B ILE* 3.6 20.8 - - + -
411B ASP* 2.9 23.2 + - - +
412B ILE 3.1 8.7 + - - +
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Residues in contact with CYS 328 (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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19B ILE* 3.1 39.7 - - - -
263B LEU* 4.2 13.7 - - + +
264B GLY 2.9 10.8 + - - +
265B ILE* 3.7 14.2 - - + -
266B LEU 2.8 28.6 + - - +
327B PHE* 1.3 73.8 - - - +
329B LEU* 1.3 66.3 + - - +
330B THR* 3.6 4.1 + - - +
412B ILE* 3.3 29.6 - - + -
414B SER* 4.7 4.9 - - - -
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Residues in contact with LEU 329 (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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266B LEU* 3.3 27.8 - - + +
267B LYS 4.6 1.1 - - - +
268B ALA* 4.1 21.8 - - + -
327B PHE* 3.8 2.6 - - + +
328B CYS* 1.3 72.3 - - - +
330B THR* 1.3 63.6 + - - +
332B LEU* 4.4 17.7 - - + -
398B TYR* 5.7 0.2 - - + -
399B ILE* 3.6 35.2 - - + -
402B ILE* 4.8 12.6 - - + -
410B ILE* 4.0 23.5 - - + +
412B ILE 3.0 14.4 + - - +
413B ILE* 4.0 12.7 - - + +
414B SER* 3.2 25.8 + - - +
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Residues in contact with THR 330 (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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14B GLU 2.6 29.1 + - - +
15B GLY* 3.8 17.9 - - - +
19B ILE* 4.2 13.0 - - + -
265B ILE* 4.3 6.7 - - + -
266B LEU 2.7 11.3 + - - -
267B LYS* 3.4 14.4 - - - +
268B ALA* 2.8 33.4 + - - +
328B CYS* 4.3 3.6 - - - +
329B LEU* 1.3 79.0 - - - +
331B LYS* 1.3 69.7 + - - +
332B LEU* 3.4 2.7 - - - -
414B SER* 4.5 14.8 - - - +
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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