Contacts of the strand formed by residues 371 - 378 (chain A) in PDB entry 5N4D
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 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A CYS* 3.3 7.6 - - - -
367A ALA* 2.8 34.7 + - + +
368A ASN* 3.6 22.9 - - - -
370A GLU* 1.3 105.5 + - + +
372A PHE* 1.3 66.4 + - - +
386A LEU* 4.1 9.6 - - + -
387A TYR 3.4 20.0 - - - +
388A SER* 4.1 8.7 - - - -
389A LYS 5.5 0.4 - - - -
394A LEU* 3.8 24.2 - - + -
434A PHE* 3.5 35.2 - + + -
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Residues in contact with PHE 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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317A ILE* 3.9 21.3 - - + -
318A THR* 3.9 25.6 - - + -
320A HIS* 4.8 7.2 - + - -
325A TYR* 3.7 32.8 - + + -
337A VAL* 5.9 1.1 - - + -
352A PHE* 3.5 33.7 - + - -
353A ILE* 5.0 3.8 - - + -
364A VAL* 4.1 17.7 - - + -
365A ASN 3.3 4.7 - - - +
366A CYS* 4.1 7.6 - - + -
370A GLU 3.8 14.6 - - - -
371A TYR* 1.3 79.0 - - - +
373A VAL* 1.3 63.3 + - - +
374A ALA 4.1 0.2 + - - -
385A TYR 3.9 0.2 - - - +
386A LEU* 3.5 4.3 - - - +
387A TYR* 2.8 46.2 + - + +
388A SER 3.9 9.6 - - - -
389A LYS* 4.6 2.9 - - - -
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 3.3 4.8 - - - +
365A ASN* 2.8 32.1 + - + +
367A ALA* 3.9 11.7 - - + -
372A PHE* 1.3 74.5 - - - +
374A ALA* 1.3 62.0 + - - +
384A ILE* 3.9 21.1 - - + -
385A TYR 3.4 9.9 - - - +
386A LEU* 3.9 7.4 - - + -
397A LEU* 5.3 0.4 - - + -
407A ILE* 3.5 30.8 - - + +
416A PHE* 3.5 52.5 - - + -
418A LEU* 4.5 0.2 - - + -
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Residues in contact with ALA 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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353A ILE* 5.3 2.9 - - + -
361A LEU* 3.8 21.8 - - + -
363A GLN 3.4 3.8 - - - -
364A VAL* 4.0 8.1 - - + -
372A PHE 4.1 0.4 - - - -
373A VAL* 1.3 75.1 - - - +
375A ILE* 1.3 63.5 + - - +
376A TYR* 4.1 6.5 + - + -
383A GLU 3.7 0.9 - - - +
384A ILE* 3.4 4.0 - - - +
385A TYR* 2.8 34.6 + - - +
387A TYR* 3.8 28.7 - - + -
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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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361A LEU* 3.7 3.2 - - - +
362A ALA* 2.8 37.1 + - + +
363A GLN* 2.8 31.7 + - + +
374A ALA* 1.3 71.8 - - - +
376A TYR* 1.3 57.6 + - - +
382A ASP* 3.7 36.1 - - + +
383A GLU 3.4 4.5 - - - +
384A ILE* 3.5 33.9 - - + -
405A ALA* 4.0 19.1 - - + +
407A ILE* 3.6 35.0 - - + -
418A LEU* 4.6 1.6 - - + -
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Residues in contact with TYR 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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335A TYR 5.8 0.7 - - - -
353A ILE* 3.4 27.5 - - - +
354A PRO 4.2 3.8 + - - -
356A GLU* 3.7 31.0 + - + +
359A ALA* 3.9 22.2 - - + -
360A LYS 3.2 17.9 - - - -
361A LEU* 3.7 30.9 - - + +
362A ALA* 5.1 0.2 - - - -
374A ALA* 4.2 8.5 - - + -
375A ILE* 1.3 75.1 - - - +
377A LYS* 1.4 59.1 + - - +
378A ARG* 3.9 0.8 + - - +
381A LYS 3.7 1.4 - - - +
382A ASP* 3.3 4.9 - - - -
383A GLU* 2.8 43.2 + - + +
385A TYR* 3.8 27.6 - + + -
387A TYR* 3.7 18.8 + - - -
393A GLN* 5.1 1.1 - - - -
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Residues in contact with LYS 377 (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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359A ALA* 3.7 1.9 - - - -
360A LYS* 2.8 52.3 + - + +
362A ALA* 4.7 16.0 - - + +
375A ILE 4.3 0.2 - - - -
376A TYR* 1.4 69.2 - - - +
378A ARG* 1.3 59.0 + - - +
379A ASN 4.1 1.1 + - - -
380A VAL* 3.6 29.7 + - - +
381A LYS 3.6 1.1 - - - -
382A ASP* 2.9 37.2 + - - +
502A SER* 3.4 27.8 - - - +
504A ASP* 2.9 32.9 + - - +
532A GLU* 4.2 17.1 - - - +
533A PHE* 6.1 0.5 - - - -
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Residues in contact with ARG 378 (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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356A GLU* 4.0 19.8 + - - +
358A ASP* 3.4 28.2 + - - +
359A ALA* 3.6 28.4 - - + +
376A TYR* 3.9 1.3 + - + +
377A LYS* 1.3 72.3 - - - +
379A ASN* 1.3 87.8 + - - +
381A LYS* 3.0 23.8 + - - +
383A GLU* 3.4 35.0 + - - +
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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