Contacts of the strand formed by residues 348 - 358 (chain A) in PDB entry 4OI9
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 ARG 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A GLU* 5.4 9.7 + - - +
337A LEU* 5.5 3.0 - - - +
339A LEU* 3.3 31.3 - - - +
344A ASN 4.8 3.4 - - - +
345A ASP* 3.2 40.1 + - - +
346A ASP 3.2 0.9 - - - +
347A ARG* 1.3 78.6 - - - +
349A SER* 1.3 69.7 + - - +
350A PHE* 3.5 33.5 + - + -
369A ALA 3.8 0.2 - - - +
370A GLU* 3.4 1.5 - - - -
371A LEU* 2.9 29.1 + - + +
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Residues in contact with SER 349 (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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324A GLU* 3.9 6.1 - - - +
347A ARG 4.0 2.1 + - - -
348A ARG* 1.3 81.0 + - - +
350A PHE* 1.3 65.9 + - - +
351A PHE* 3.5 33.8 - - - -
368A SER* 4.0 0.7 - - - -
369A ALA 3.1 8.1 - - - -
370A GLU* 3.4 9.2 + - - +
2337A EDO 3.1 32.3 + - - -
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Residues in contact with PHE 350 (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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296A LEU* 3.3 8.1 - - + +
298A LEU* 4.0 21.1 - - + -
309A VAL* 6.2 0.2 - - + -
311A VAL* 4.0 35.0 - - + -
323A LEU* 5.0 3.1 - - + -
324A GLU* 3.3 18.2 - - + +
337A LEU* 4.4 9.9 - - + -
339A LEU* 4.0 16.4 - - + -
348A ARG* 3.5 52.5 - - - -
349A SER* 1.3 75.7 - - - +
351A PHE* 1.3 63.5 + - - +
368A SER* 3.2 7.3 + - - -
369A ALA 2.8 32.7 + - - +
371A LEU* 4.1 27.4 - - + -
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Residues in contact with PHE 351 (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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296A LEU* 4.4 1.8 - - - -
322A THR 3.6 0.9 - - - +
323A LEU* 3.5 6.1 - - - +
324A GLU* 2.9 53.6 + - - +
349A SER* 3.5 33.0 - - - -
350A PHE* 1.3 74.8 - - - +
352A CYS* 1.3 61.5 + - - +
353A ASP* 4.9 6.5 - - - +
366A ASN* 6.0 1.1 - - - -
367A ARG 3.4 5.4 - - - +
368A SER* 3.4 28.9 - - - -
2337A EDO 4.2 5.6 - - - -
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Residues in contact with CYS 352 (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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294A PRO* 4.4 2.7 - - - +
296A LEU* 4.1 6.4 - - + +
313A CYS* 1.7 80.1 - - + -
321A VAL* 3.5 24.9 - - - -
322A THR 3.2 6.7 - - - -
323A LEU* 4.6 2.9 - - - -
351A PHE* 1.3 75.0 - - - +
353A ASP* 1.3 64.0 + - - +
365A LYS 4.0 1.4 - - - +
366A ASN* 3.7 0.9 - - - -
367A ARG* 2.9 35.3 + - + +
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Residues in contact with ASP 353 (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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294A PRO* 5.2 1.1 - - - -
320A LEU 3.2 4.3 - - - +
321A VAL* 3.3 3.7 - - - +
322A THR* 2.7 57.2 + - - +
351A PHE* 4.8 6.5 - - - +
352A CYS* 1.3 87.5 + - - +
354A ALA* 1.3 60.8 + - - +
355A THR* 5.0 6.0 + - - +
364A ILE* 5.3 9.1 - - + +
365A LYS 3.9 2.7 - - - -
366A ASN* 3.4 23.3 - - - +
367A ARG 4.5 0.2 + - - -
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Residues in contact with ALA 354 (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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291A PHE* 3.4 23.8 - - + -
292A PRO 5.4 0.2 - - - +
294A PRO* 4.2 21.7 - - + +
315A ALA* 4.6 11.0 - - + -
319A ALA* 4.3 7.4 - - + -
320A LEU 3.4 4.7 - - - -
321A VAL* 4.8 0.9 - - + +
353A ASP* 1.3 74.6 - - - +
355A THR* 1.3 61.0 + - - +
364A ILE* 3.2 7.0 - - - +
365A LYS 3.1 34.9 + - - +
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Residues in contact with THR 355 (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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319A ALA* 3.3 3.4 - - - +
320A LEU* 2.9 57.0 + - + +
322A THR* 5.6 1.6 + - - -
353A ASP* 5.0 4.5 - - - +
354A ALA* 1.3 71.9 + - - +
356A LEU* 1.3 62.7 + - - +
357A ASP* 4.3 9.5 + - - +
362A THR* 3.9 28.0 - - + +
363A LEU 3.3 2.5 - - - -
364A ILE* 3.2 17.2 - - + +
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Residues in contact with LEU 356 (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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289A TYR* 5.7 1.6 - - + -
290A SER 4.1 11.7 - - - +
291A PHE* 3.7 43.7 - - + -
318A GLN* 3.6 39.9 - - + +
319A ALA* 3.8 11.0 - - + -
355A THR* 1.3 73.7 - - - +
357A ASP* 1.3 79.8 + - - +
358A VAL* 4.5 14.1 - - + -
361A GLU 3.3 2.4 - - - +
362A THR* 3.6 0.7 - - - -
363A LEU* 2.7 44.6 + - + +
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Residues in contact with ASP 357 (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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355A THR* 4.3 8.2 + - - +
356A LEU* 1.3 86.6 - - - +
358A VAL* 1.3 65.7 + - - +
359A ASP 4.3 0.6 + - - -
360A GLY* 5.3 8.5 - - - +
361A GLU 3.2 5.6 - - - +
362A THR* 3.3 23.7 + - - -
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Residues in contact with VAL 358 (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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207A LEU* 4.0 15.7 - - + +
287A THR* 5.5 2.7 - - + -
289A TYR* 3.6 33.2 - - + -
356A LEU* 4.5 15.9 - - + +
357A ASP* 1.3 77.9 - - - +
359A ASP* 1.3 66.1 + - - +
360A GLY 3.1 0.7 - - - -
361A GLU* 2.7 41.1 + - + +
363A LEU* 3.6 32.1 - - + -
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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