Contacts of the strand formed by residues 382 - 392 (chain A) in PDB entry 2RD0
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 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A LEU* 3.7 25.1 + - - +
340A CYS* 3.6 35.4 - - + +
375A ARG* 4.5 13.5 - - - +
376A VAL* 4.5 4.5 - - - +
380A ASN 3.4 8.6 + - - +
381A PRO* 1.3 77.8 - - - +
383A TRP* 1.3 72.6 + - - +
384A ASN* 3.9 28.2 + - + +
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Residues in contact with TRP 383 (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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338A ILE* 3.8 8.3 - - + +
339A LEU 2.8 19.1 + - - +
340A CYS* 4.4 3.6 - - - -
341A ALA* 4.2 14.8 - - + -
354A ILE* 3.6 19.7 - - + -
355A TYR* 3.5 25.6 - - - +
356A VAL* 3.9 22.2 - - + -
372A ASN* 3.3 27.2 + - - +
373A THR 2.7 29.6 + - - -
375A ARG* 4.0 18.3 - - + +
381A PRO* 3.8 31.4 - - + -
382A ARG* 1.3 81.7 - - - +
384A ASN* 1.3 59.1 + - - +
385A GLU* 2.7 40.2 + - - +
406A ILE* 5.3 4.7 - - + -
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Residues in contact with ASN 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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337A LYS* 3.4 32.6 + - - +
338A ILE 3.3 5.1 + - - -
339A LEU* 3.3 16.5 + - - +
382A ARG* 3.9 26.3 + - + +
383A TRP* 1.3 77.5 - - - +
385A GLU* 1.3 59.1 + - - +
386A TRP* 4.9 0.9 - - - -
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Residues in contact with GLU 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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337A LYS* 3.2 10.9 - - - +
338A ILE* 3.1 28.6 + - + +
372A ASN* 3.6 16.0 - - - +
373A THR* 2.9 50.1 + - - -
383A TRP* 2.7 38.8 + - - +
384A ASN* 1.3 74.6 - - - +
386A TRP* 1.3 67.8 + - - +
387A LEU* 4.2 9.5 - - + +
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Residues in contact with TRP 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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335A ARG* 3.2 70.1 - - + +
336A ILE 3.8 2.5 - - - -
337A LYS* 3.2 61.1 - - + +
384A ASN 4.9 1.1 - - - -
385A GLU* 1.3 76.6 - - - +
387A LEU* 1.3 70.4 + - - +
388A ASN* 4.1 11.6 + - - +
476A GLU* 3.2 40.6 - - - -
478A ASP* 3.9 15.9 - - - -
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Residues in contact with LEU 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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335A ARG* 2.9 26.5 - - - -
336A ILE 2.9 20.6 + - - +
338A ILE* 3.5 27.6 - - + -
358A THR* 3.3 17.7 - - + +
370A ASN* 3.5 22.4 - - - +
372A ASN* 3.5 31.6 - - + -
385A GLU* 4.2 8.5 - - + +
386A TRP* 1.3 84.2 - - - +
388A ASN* 1.3 58.8 + - - +
389A TYR* 3.1 35.5 - - + +
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Residues in contact with ASN 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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333A ALA* 4.6 7.1 - - + +
334A LEU 3.7 4.5 - - - +
335A ARG* 3.5 27.3 - - - +
370A ASN* 4.2 14.2 + - - +
386A TRP* 4.5 11.9 + - - +
387A LEU* 1.3 70.7 - - - +
389A TYR* 1.3 62.9 + - - +
390A ASP 4.0 0.9 + - - -
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Residues in contact with TYR 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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333A ALA* 4.2 8.0 - - - +
334A LEU* 3.0 29.5 + - + +
336A ILE* 3.4 32.6 - - + +
358A THR* 2.9 43.7 + - - +
360A ILE* 3.4 26.7 - - + -
367A LEU* 3.2 29.2 - - + -
368A CYS 5.3 1.8 - - - -
370A ASN* 4.0 21.1 - - + -
387A LEU* 3.1 43.9 - - + +
388A ASN* 1.3 74.3 - - - +
390A ASP* 1.3 58.1 + - - +
391A ILE 2.8 19.0 + - - +
402A LEU* 5.1 0.2 - - + -
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Residues in contact with ASP 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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333A ALA* 5.6 2.7 - - - -
367A LEU* 3.6 6.6 - - - +
368A CYS* 3.6 39.5 + - - +
388A ASN 4.0 2.9 + - - +
389A TYR* 1.3 69.1 - - - +
391A ILE* 1.3 68.1 + - - +
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Residues in contact with ILE 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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333A ALA* 3.6 6.2 - - - -
334A LEU* 3.4 25.5 + - + +
360A ILE* 4.4 7.9 - - + -
366A PRO* 5.3 2.0 - - + -
367A LEU* 3.6 31.6 - - + -
389A TYR 2.8 8.0 + - - +
390A ASP* 1.3 84.8 - - - +
392A TYR* 1.3 73.3 + - - +
395A ASP* 4.9 6.7 - - + +
396A LEU* 3.4 39.0 - - + +
397A PRO* 5.4 1.1 - - + -
575A ASN* 4.0 35.7 - - + +
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Residues in contact with TYR 392 (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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330A ILE 4.6 3.4 - - - -
331A ASN* 3.9 28.7 + - - -
332A SER 4.1 8.7 - - - -
333A ALA* 4.5 4.5 - - + +
334A LEU* 4.9 0.3 - - - +
391A ILE* 1.3 95.3 - - - +
393A ILE* 1.3 62.6 + - - +
394A PRO* 3.6 27.4 - - + -
395A ASP* 3.6 29.5 + - + +
396A LEU* 4.2 2.9 - - - +
577A ARG* 4.5 13.9 - - - -
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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