Contacts of the strand formed by residues 381 - 388 (chain A) in PDB entry 1RP1
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 THR 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A SER* 4.2 19.3 - - - -
344A ILE 3.0 13.5 - - - +
345A THR* 2.8 28.1 + - - +
379A GLY 4.9 1.2 + - - -
380A SER* 1.3 74.9 - - - +
382A HIS* 1.3 72.7 + - - +
383A SER* 4.9 2.7 - - - +
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Residues in contact with HIS 382 (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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343A SER* 3.5 0.4 - - - -
344A ILE* 2.9 35.0 + - + +
346A LEU* 3.8 18.3 - - + +
371A ILE* 4.0 6.3 - - + +
372A PHE* 3.5 69.4 - + + -
375A ILE 4.5 4.3 + - - -
377A LYS* 5.5 0.9 - - + +
380A SER* 3.1 27.4 + - - -
381A THR* 1.3 82.0 + - - +
383A SER* 1.3 63.3 + - - +
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Residues in contact with SER 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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294A ASN* 4.5 3.8 + - - -
342A VAL 3.1 11.7 - - - -
343A SER* 2.9 23.2 + - - -
371A ILE* 4.2 7.0 - - - +
381A THR* 4.9 2.6 - - - +
382A HIS* 1.3 75.3 - - - +
384A ASN* 1.3 69.1 + - - +
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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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292A GLU 5.7 0.2 - - - +
294A ASN* 2.9 25.2 + - - +
341A GLY* 3.5 2.1 - - - -
342A VAL* 3.0 32.3 + - - +
370A ASN 3.5 16.0 + - - -
371A ILE* 3.3 37.8 + - + +
383A SER* 1.3 79.4 - - - +
385A GLU* 1.3 77.5 + - - +
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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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291A PHE* 4.2 0.9 - - - +
294A ASN* 3.3 41.5 - - + +
296A CYS 5.3 0.2 + - - -
297A PHE* 3.4 40.2 - - + +
339A ARG* 2.6 46.3 + - - +
340A TYR 3.1 13.0 - - - +
341A GLY* 4.0 9.2 - - - -
384A ASN* 1.3 95.0 + - - +
386A PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 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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338A TRP 3.8 0.3 - - - +
339A ARG* 3.3 4.5 - - - +
340A TYR* 3.0 52.9 + + + -
342A VAL* 3.8 26.5 - - + -
357A VAL* 3.9 17.7 - - + -
359A LEU* 3.3 34.3 - - + -
369A PHE* 3.4 50.9 - + + -
370A ASN 5.5 3.1 - - - +
371A ILE* 3.8 17.9 - - + -
385A GLU* 1.3 76.4 - - - +
387A ASP* 1.3 64.3 + - - +
388A ALA* 4.3 4.0 - - + -
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Residues in contact with ASP 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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291A PHE* 5.0 0.7 - - - -
328A ASN* 3.0 39.6 + - + +
337A ARG* 3.8 33.2 + - + +
338A TRP 3.5 4.4 - - - +
339A ARG* 3.0 41.4 + - - +
369A PHE* 3.2 17.6 - - - -
386A PHE* 1.3 72.9 - - - +
388A ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 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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337A ARG* 3.1 12.5 - - - -
338A TRP 2.8 29.0 + - - -
340A TYR* 3.9 20.2 - - + -
366A THR* 3.7 31.0 - - + -
369A PHE* 3.6 18.4 - - + -
386A PHE* 3.9 2.5 + - + -
387A ASP* 1.3 74.0 - - - +
389A LYS* 1.3 61.6 + - - +
390A LEU 3.4 3.8 - - - +
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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