Contacts of the strand formed by residues 383 - 391 (chain A) in PDB entry 6RUT
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 TYR 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A PRO* 3.6 1.5 - - - +
319A SER* 3.1 35.6 + - - -
340A PHE* 3.6 37.2 - + + -
343A THR 5.0 2.2 + - - -
345A LEU* 3.3 25.7 - - + +
347A TRP* 3.3 20.9 - + - -
379A THR* 5.5 0.9 + - - +
380A GLN* 3.3 36.9 + - + +
382A ALA* 1.3 75.3 - - - +
384A LEU* 1.3 63.4 + - - +
385A ILE* 3.4 22.0 + - + -
397A PHE* 6.2 2.7 - + - -
399A GLY 5.5 1.6 - - - -
400A PHE 3.4 7.0 - - - +
401A LYS* 3.7 24.7 - - + -
402A ALA* 4.0 2.7 - - - +
543A VAL* 4.0 20.6 - - + -
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Residues in contact with LEU 384 (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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314A ASN 4.3 4.0 - - - -
315A SER* 3.4 26.2 - - - +
316A PHE 3.7 10.5 - - - +
317A LEU* 3.6 24.5 - - - -
318A PRO* 3.8 8.3 - - + -
383A TYR* 1.3 71.9 - - - +
385A ILE* 1.3 60.4 + - - +
386A SER 3.5 0.3 + - - -
399A GLY* 3.1 3.2 - - - -
400A PHE* 2.7 43.4 + - + +
402A ALA* 4.0 19.5 - - + +
504A ALA 3.7 21.8 - - - +
505A THR* 4.0 21.3 - - - -
506A PRO* 4.2 9.2 - - + -
626A SER* 4.3 4.1 + - - +
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Residues in contact with ILE 385 (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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301A LYS* 5.6 0.7 - - + +
312A MET* 4.1 33.4 - - + -
313A GLY 4.0 14.0 - - - +
314A ASN* 3.5 7.5 + - - +
315A SER* 3.0 27.4 + - - -
319A SER* 3.6 21.8 - - - +
340A PHE* 3.9 18.6 - - + -
383A TYR* 3.4 27.3 + - + +
384A LEU* 1.3 68.8 - - - +
386A SER* 1.4 59.8 + - - +
387A GLY* 3.5 31.6 - - - +
397A PHE* 5.0 8.7 - - + -
398A SER 3.7 10.5 - - - +
399A GLY* 5.2 0.4 - - - -
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Residues in contact with SER 386 (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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301A LYS* 5.4 3.9 - - - -
315A SER* 3.7 3.3 + - - -
384A LEU 3.5 3.8 + - - -
385A ILE* 1.4 70.6 - - - +
387A GLY* 1.3 56.6 + - - +
398A SER* 2.9 34.1 + - - -
399A GLY* 3.7 4.5 - - - -
542A PHE* 3.7 2.6 - - - -
626A SER* 2.7 42.7 + - - -
627A VAL* 3.4 5.2 - - - +
628A GLY* 3.2 23.6 + - - -
629A LEU* 4.2 2.5 - - - -
650A VAL* 3.3 16.9 - - - +
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Residues in contact with GLY 387 (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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301A LYS* 4.6 16.4 - - - -
385A ILE* 3.3 19.3 - - - +
386A SER* 1.3 81.3 - - - +
388A ILE* 1.3 63.2 + - - +
397A PHE* 3.7 2.4 - - - +
398A SER 3.7 9.5 + - - -
628A GLY* 5.8 0.2 - - - -
629A LEU* 3.4 25.1 - - - +
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Residues in contact with ILE 388 (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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301A LYS* 3.9 37.4 - - + +
302A LEU 4.1 10.3 - - - +
303A ALA* 3.9 21.5 - - + +
310A VAL* 3.9 20.4 - - + +
312A MET* 3.4 37.9 - - + -
387A GLY* 1.3 73.3 - - - +
389A ASP* 1.3 64.6 + - - +
395A ILE* 3.7 24.9 - - + -
396A ILE 3.4 11.9 - - - +
397A PHE* 4.2 4.0 - - + -
629A LEU* 3.9 8.2 + - - +
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Residues in contact with ASP 389 (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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70A THR* 5.3 4.2 + - - -
302A LEU 5.6 0.2 - - - -
303A ALA* 4.3 8.4 - - - +
388A ILE* 1.3 75.9 - - - +
390A SER* 1.4 76.7 + - - +
395A ILE* 3.4 8.8 - - - +
396A ILE* 2.8 36.9 + - + +
629A LEU* 4.3 6.7 - - + +
630A LYS* 3.6 27.1 + - - +
631A ALA* 3.0 46.4 + - + +
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Residues in contact with SER 390 (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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72A HIS* 5.2 0.7 + - - -
303A ALA* 4.8 0.3 - - - -
304A VAL 2.7 34.6 + - - -
305A THR* 5.1 2.2 - - - -
389A ASP* 1.4 89.8 + - - +
391A VAL* 1.3 69.5 + - - +
393A ASP* 5.3 1.8 - - - -
394A GLN 3.1 15.5 - - - -
395A ILE* 3.9 13.5 - - - -
396A ILE 4.9 0.2 - - - +
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Residues in contact with VAL 391 (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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390A SER* 1.3 78.4 - - - +
392A ASN* 1.4 60.7 + - - +
393A ASP 3.3 1.8 - - - -
394A GLN* 2.9 34.7 + - - +
396A ILE* 3.5 30.7 - - + -
631A ALA* 3.7 13.9 - - + +
632A GLY* 4.6 14.1 - - - +
633A ILE* 3.8 32.8 - - + -
646A TYR* 3.7 24.1 - - + -
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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