Contacts of the strand formed by residues 370 - 376 (chain A) in PDB entry 1NU6
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 SER 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A PHE* 3.3 7.8 - - - -
365A THR* 2.7 63.0 + - - +
367A ASP* 4.4 1.0 + - - -
368A GLY 3.2 1.6 + - - -
369A ASN* 1.3 83.9 - - - +
371A PHE* 1.3 62.5 + - - +
386A TYR* 3.8 23.0 + - - -
387A PHE 3.2 15.5 - - - -
388A GLN* 4.2 5.8 - - - -
389A ILE 4.3 1.3 - - - +
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Residues in contact with PHE 371 (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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325A MET* 3.2 34.3 - - + -
327A ILE* 4.5 0.2 - - + -
345A HIS* 4.0 21.5 - + + -
362A PRO* 4.0 12.3 - - + -
363A HIS 3.2 17.0 - - - +
364A PHE* 3.6 32.5 - + + -
365A THR* 4.6 0.2 - - - +
370A SER* 1.3 77.5 - - - +
372A TYR* 1.3 72.2 + - - +
373A LYS* 4.2 7.0 - - + -
386A TYR* 3.7 2.1 - - - -
387A PHE* 2.9 76.4 + + + -
389A ILE* 4.2 16.2 - - + -
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Residues in contact with TYR 372 (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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362A PRO* 3.5 0.7 - - - +
363A HIS* 2.8 46.8 + - + +
365A THR* 3.6 26.1 - - + +
371A PHE* 1.3 76.3 - - - +
373A LYS* 1.3 64.2 + - - +
384A ILE* 4.0 11.2 - - + -
385A CYS 3.3 6.5 - - - +
386A TYR* 3.3 45.1 - + + -
397A ILE* 4.3 9.0 - - + -
407A ILE* 4.0 5.6 - - + -
410A LEU* 4.1 18.2 - - + -
415A LEU* 3.6 33.0 - - + -
436A LEU* 3.8 32.3 - - + +
439A TYR* 5.1 3.6 + - - -
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Residues in contact with LYS 373 (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 GLN* 3.2 17.8 + - - -
325A MET* 4.3 10.5 - - - -
347A GLU* 2.6 35.4 + - - +
359A PRO* 4.8 0.2 - - - +
360A SER* 2.7 53.9 + - - +
361A GLU 3.9 10.8 - - - +
362A PRO* 4.2 7.9 - - + -
371A PHE* 4.2 18.6 - - + -
372A TYR* 1.3 78.5 - - - +
374A ILE* 1.3 62.8 + - - +
375A ILE* 3.6 12.6 + - + +
384A ILE* 4.4 0.4 - - - -
385A CYS 2.9 28.3 + - - +
387A PHE* 4.2 12.6 - - + -
407A ILE* 3.8 9.7 - - - +
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Residues in contact with ILE 374 (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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347A GLU* 5.1 0.5 - - - +
356A ARG* 4.5 6.3 - - - +
360A SER* 2.6 39.2 + - - -
361A GLU 4.7 0.6 + - - -
363A HIS* 6.5 0.4 - - + -
373A LYS* 1.3 75.1 - - - +
375A ILE* 1.3 65.6 + - - +
382A ARG* 3.6 36.4 + - + +
383A HIS 3.3 8.3 - - - +
384A ILE* 4.5 2.0 - - + -
404A VAL* 4.0 24.0 - - + +
405A ILE 3.9 9.0 - - - +
406A GLY* 3.7 31.6 - - - +
407A ILE* 4.1 16.1 - - + +
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Residues in contact with ILE 375 (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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347A GLU* 3.6 36.6 - - + +
373A LYS* 3.7 17.0 - - + +
374A ILE* 1.3 83.1 - - - +
376A SER* 1.3 77.1 + - - +
377A ASN 3.3 1.2 + - - -
382A ARG* 4.2 3.6 - - - +
383A HIS 2.9 26.5 + - - +
385A CYS* 4.0 12.8 - - + -
387A PHE* 4.1 19.5 - - + -
394A CYS* 5.4 2.5 - - - -
396A PHE* 3.6 21.7 - - + -
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Residues in contact with SER 376 (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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375A ILE* 1.3 84.1 - - - +
377A ASN* 1.3 63.8 + - - +
380A GLY* 3.5 17.3 - - - -
381A TYR 3.6 8.7 - - - -
382A ARG* 4.1 22.9 - - - +
396A PHE* 4.1 0.9 - - - -
588A ASP* 2.6 27.7 + - - -
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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