Contacts of the strand formed by residues 292 - 299 (chain A) in PDB entry 5I4A
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 PRO 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A GLU 4.5 1.6 - - - +
291A GLN* 1.3 97.9 - - + +
293A LEU* 1.3 60.7 + - - +
294A LYS* 3.8 29.3 + - + +
332A PHE* 4.3 0.9 - - - -
333A SER* 3.2 14.3 - - - +
334A LYS* 3.5 26.9 - - + +
369A ASN* 5.2 2.9 - - - +
423A ILE* 4.2 14.2 - - - +
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Residues in contact with LEU 293 (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 GLN 3.8 1.0 + - - -
292A PRO* 1.3 70.3 - - - +
294A LYS* 1.3 58.3 + - - +
295A ALA* 5.5 2.6 - - + +
323A PHE* 4.2 26.5 - - + -
327A ALA* 4.2 20.9 - - + -
332A PHE* 3.7 20.9 - - + -
334A LYS 2.8 13.5 + - - +
335A VAL* 3.3 10.3 - - + +
336A GLU 2.8 31.2 + - - +
371A MET* 4.0 12.3 - - + -
416A VAL* 4.3 13.9 - - + -
419A MET* 4.0 31.6 - - + -
423A ILE* 4.3 13.9 - - + -
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Residues in contact with LYS 294 (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 PRO* 3.8 27.2 + - + +
293A LEU* 1.3 77.6 - - - +
295A ALA* 1.3 63.4 + - - +
336A GLU* 3.1 33.2 - - + +
338A LEU* 4.2 15.9 - - + +
367A GLU 4.3 3.2 + - - -
368A ASP* 3.1 38.5 + - - +
369A ASN* 3.3 23.8 + - - +
370A VAL* 3.5 14.1 - - + +
371A MET* 2.9 28.1 + - - +
423A ILE* 5.9 0.4 - - - +
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Residues in contact with ALA 295 (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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293A LEU* 5.5 5.6 - - + +
294A LYS* 1.3 76.5 - - - +
296A ILE* 1.3 62.0 + - - +
323A PHE* 5.9 1.8 - - + -
335A VAL* 6.3 0.4 - - + -
336A GLU 3.0 6.4 + - - +
337A PHE* 3.2 33.8 - - + +
338A LEU 3.2 23.8 + - - +
370A VAL* 4.1 3.5 - - - +
371A MET* 3.2 18.6 - - + +
373A ILE* 3.9 16.6 - - + -
419A MET* 5.5 2.0 - - + -
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Residues in contact with ILE 296 (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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295A ALA* 1.3 78.8 - - - +
297A PHE* 1.3 67.8 + - - +
298A PHE* 3.6 31.2 - - + -
338A LEU* 3.4 36.1 - - + +
346A SER* 3.7 8.1 - - - +
348A PHE* 4.0 17.9 - - + -
362A PHE* 4.3 4.9 - - + -
363A ILE* 5.1 3.1 - - + -
366A ILE* 3.8 23.6 - - + -
370A VAL* 4.4 7.0 - - + -
371A MET 2.9 13.9 + - - +
372A ALA* 3.7 2.1 - - - -
373A ILE* 2.9 28.8 + - - +
394A LEU* 4.2 9.4 - - + -
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Residues in contact with PHE 297 (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 ILE* 1.3 76.2 - - - +
298A PHE* 1.3 62.6 + - - +
299A PHE* 3.5 31.0 - + + -
312A LEU* 4.5 6.5 - - + -
316A PHE* 3.6 40.6 - + + -
337A PHE* 3.4 42.2 - + - -
346A SER* 3.0 30.2 + - - +
347A ALA* 4.2 2.2 - - + -
348A PHE* 2.8 33.4 + - - -
373A ILE* 3.4 34.1 - - + +
375A LEU* 4.7 1.8 - - + -
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Residues in contact with PHE 298 (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 ILE* 3.6 28.5 - - + -
297A PHE* 1.3 76.5 - - - +
299A PHE* 1.3 61.8 + - - +
348A PHE* 3.2 21.8 - - + -
349A LEU 4.0 16.8 - - - -
350A TYR* 3.8 15.6 - - + -
357A VAL* 3.6 37.0 - - + -
363A ILE* 4.5 9.2 - - + -
372A ALA* 3.8 18.4 - - + -
373A ILE 2.8 9.8 + - - +
374A VAL* 4.0 12.6 - - + -
375A LEU* 3.0 30.3 + - - +
390A PHE* 3.8 22.0 - + - -
394A LEU* 3.9 16.4 - - + -
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Residues in contact with PHE 299 (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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297A PHE* 3.5 29.6 - + + -
298A PHE* 1.3 74.5 - - - +
300A SER* 1.3 63.7 + - - +
301A SER 3.2 15.2 + - - +
304A GLN* 3.2 17.7 - - - +
305A PHE* 3.5 28.9 - + + -
308A VAL* 4.2 0.2 - - + -
312A LEU* 3.5 37.0 - - + -
347A ALA* 3.6 20.2 - - + -
348A PHE 2.8 17.1 + - - +
349A LEU* 3.2 11.7 - - + -
350A TYR* 2.9 26.0 + - - -
375A LEU* 3.6 29.2 - - + -
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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