Contacts of the strand formed by residues 316 - 326 (chain B) in PDB entry 5O67
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 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B TYR* 3.1 7.0 - - - +
289B THR* 2.8 41.1 + - - +
291B ASN* 5.4 0.3 + - - -
314B GLY 4.7 0.9 + - - -
315B ASP* 1.3 78.8 - - - +
317B PHE* 1.3 61.9 + - - +
318B GLN* 2.9 23.1 + - - -
340B LEU* 4.2 6.6 - - - +
341B ILE 3.1 16.6 - - - -
342B GLN* 4.0 16.7 + - - -
343B ARG* 4.4 6.8 - - - +
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Residues in contact with PHE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 5.9 4.5 - - + -
287B SER 3.4 13.0 - - - +
288B TYR* 3.8 9.0 - - + -
316B SER* 1.3 73.9 - - - +
318B GLN* 1.3 69.6 + - - +
319B PHE* 4.3 20.6 - + + -
339B ASP 4.0 0.9 - - - +
340B LEU* 3.4 0.7 - - - -
341B ILE* 2.8 76.5 + - + +
343B ARG* 3.5 23.6 - - - +
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 4.3 2.8 - - - +
286B VAL* 3.7 4.0 - - - +
287B SER* 2.7 55.3 + - - +
288B TYR* 3.8 3.3 + - - -
289B THR* 3.7 13.5 + - - -
316B SER* 2.9 39.6 + - - -
317B PHE* 1.3 75.9 - - - +
319B PHE* 1.3 66.4 + - - +
339B ASP 3.3 9.4 - - - +
340B LEU* 3.6 32.5 - - + +
501B LDA 3.7 23.3 - - + -
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B SER 3.3 14.8 - - - +
286B VAL* 4.5 9.2 - - + -
317B PHE* 4.3 23.8 - + + -
318B GLN* 1.3 79.5 - - - +
320B GLY* 1.3 63.5 + - - +
321B VAL* 5.9 3.4 - - + -
338B SER* 3.2 7.1 - - - +
339B ASP* 3.0 54.8 + - + -
341B ILE* 4.7 5.8 - - + -
501B LDA 4.3 6.1 - - - -
116C TYR* 6.1 2.9 - + - -
398C PHE* 3.7 35.7 - + - -
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 5.5 0.6 - - - -
284B GLY* 3.1 3.1 - - - -
285B SER* 3.0 37.4 + - - -
319B PHE* 1.3 85.6 - - - +
321B VAL* 1.3 67.3 + - - +
337B VAL* 3.1 15.9 - - - -
338B SER* 4.2 3.1 - - - -
501B LDA 4.8 2.2 - - - -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 3.2 14.6 - - - +
284B GLY* 4.1 4.9 - - - -
319B PHE* 5.9 3.8 - - + -
320B GLY* 1.3 80.2 - - - +
322B GLY* 1.3 58.7 + - - +
336B SER* 3.4 4.7 - - - -
337B VAL* 3.0 44.5 + - + +
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Residues in contact with GLY 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 3.5 6.8 - - - +
283B PHE* 2.9 46.6 + - - +
321B VAL* 1.3 77.9 - - - +
323B VAL* 1.3 66.7 + - - +
335B PHE 3.2 13.0 - - - -
336B SER* 3.8 1.1 - - - -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 4.1 19.1 - - + -
281B VAL 3.5 6.1 - - - +
282B LEU* 4.0 12.8 - - + -
283B PHE* 3.8 1.7 - - - -
322B GLY* 1.3 78.7 - - - +
324B ALA* 1.3 65.9 + - - +
325B PHE* 4.1 16.2 - - + -
334B SER* 3.5 2.1 - - - -
335B PHE* 2.9 33.9 + - + +
333C MET* 4.2 20.2 - - + -
371C MET* 3.9 40.2 - - + -
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Residues in contact with ALA 324 (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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95B LEU* 3.5 32.3 - - + -
279B PRO 3.8 0.3 - - - +
280B ALA* 3.5 0.9 - - - -
281B VAL* 2.9 32.8 + - - +
283B PHE* 4.0 8.1 - - + -
323B VAL* 1.3 78.3 - - - +
325B PHE* 1.3 75.1 + - - +
332B SER* 5.8 0.9 - - - +
333B MET 3.4 13.7 - - - +
334B SER* 3.7 12.1 - - - -
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.1 7.6 - - - -
279B PRO* 3.7 24.2 - - + +
280B ALA* 3.8 21.3 - - + -
281B VAL* 5.6 0.2 - - - -
323B VAL* 4.1 11.0 - - + -
324B ALA* 1.3 84.8 - - - +
326B ALA* 1.3 66.1 + - - +
327B LEU* 3.5 11.9 + - + +
332B SER* 3.2 6.1 - - - -
333B MET* 3.0 41.9 + - + -
335B PHE* 4.2 27.1 - + - -
327C LEU* 4.1 21.5 - - + -
333C MET* 4.1 20.6 - - - -
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B SER* 3.7 21.5 - - - +
92B VAL* 4.3 18.6 - - + +
95B LEU* 4.1 7.1 - - + +
279B PRO* 4.5 8.4 + - - +
281B VAL* 6.1 0.2 - - - +
325B PHE* 1.3 72.8 - - - +
327B LEU* 1.3 63.2 + - - +
328B ASN 4.3 2.5 - - - +
331B MET 3.8 5.4 - - - -
332B SER* 4.5 3.1 - - - +
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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