Contacts of the strand formed by residues 360 - 367 (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 LYS 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A LYS* 5.8 3.2 - - - +
334A GLN* 3.3 26.7 + - - +
335A TYR* 4.0 26.0 - - + -
359A ALA* 1.3 71.2 - - - +
361A LEU* 1.3 70.5 + - - +
362A ALA* 3.3 8.3 + - - +
376A TYR* 3.2 5.9 - - - -
377A LYS* 2.8 63.0 + - + +
500A ALA* 4.3 9.9 + - - +
502A SER* 5.3 3.2 - - - -
531A GLY* 3.1 34.6 + - - +
532A GLU 4.4 7.8 + - - +
534A GLY* 4.4 7.2 - - - +
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Residues in contact with LEU 361 (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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327A LYS* 4.0 13.0 + - + +
334A GLN 2.9 10.6 + - - +
335A TYR* 3.5 31.1 - - + +
336A LYS* 3.7 34.1 - - - +
337A VAL* 3.7 7.9 - - + +
353A ILE* 5.3 3.4 - - + -
359A ALA 3.6 2.2 + - - -
360A LYS* 1.3 72.7 - - - +
362A ALA* 1.3 60.2 + - - +
363A GLN 4.1 0.4 - - - +
364A VAL* 3.5 34.8 - - + -
374A ALA* 3.8 10.8 - - + -
375A ILE 3.8 13.7 - - - +
376A TYR* 3.7 34.7 - - + +
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LYS* 4.0 14.9 + - - -
360A LYS* 3.3 16.2 + - + +
361A LEU* 1.3 73.9 - - - +
363A GLN* 1.3 60.4 + - + +
375A ILE* 2.8 26.1 + - + +
377A LYS* 4.7 25.1 - - + +
382A ASP* 5.0 1.8 - - - +
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Residues in contact with GLN 363 (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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327A LYS* 4.4 6.7 - - - +
361A LEU 3.7 0.8 - - - -
362A ALA* 1.3 82.3 - - + +
364A VAL* 1.3 71.0 + - - +
365A ASN* 3.3 24.1 + - - +
373A VAL 4.5 0.4 - - - -
374A ALA* 3.4 0.3 - - - -
375A ILE* 2.8 40.6 + - + +
405A ALA 4.5 1.2 - - - +
406A SER* 3.6 13.7 + - - -
407A ILE* 3.3 46.1 + - + +
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 3.8 38.2 - - + +
327A LYS* 4.5 9.5 - - + +
337A VAL* 3.8 12.1 - - + -
353A ILE* 5.3 2.7 - - + -
361A LEU* 3.5 36.6 - - + -
363A GLN* 1.3 81.4 - - - +
365A ASN* 1.3 68.8 + - - +
372A PHE* 4.1 28.0 - - + -
373A VAL 3.3 11.4 - - - +
374A ALA* 4.0 7.6 - - + -
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Residues in contact with ASN 365 (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* 4.3 4.0 - - - -
363A GLN* 3.3 25.2 + - - +
364A VAL* 1.3 81.6 - - - +
366A CYS* 1.3 63.6 + - - +
372A PHE* 3.3 2.0 - - - -
373A VAL* 2.8 39.8 + - + +
407A ILE* 3.5 33.7 + - + +
409A ASN* 2.9 30.6 + - - +
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Residues in contact with CYS 366 (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* 3.8 9.7 + - + +
318A THR* 3.8 33.9 - - + -
320A HIS* 5.0 0.2 - - - -
365A ASN* 1.3 72.8 - - - +
367A ALA* 1.3 61.0 + - - +
369A GLU 3.2 28.9 - - - -
370A GLU* 4.5 1.6 - - - -
371A TYR 3.3 12.6 - - - -
372A PHE* 4.1 8.1 - - + -
409A ASN* 2.8 19.1 + - - +
411A GLN* 3.5 34.8 - - + +
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Residues in contact with ALA 367 (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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365A ASN 3.7 0.2 + - - -
366A CYS* 1.3 76.0 - - - +
368A ASN* 1.3 74.0 + - - +
369A GLU 3.2 2.6 + - - -
371A TYR* 2.8 30.9 + - + +
373A VAL* 3.9 15.9 - - + -
409A ASN* 3.7 15.0 - - - +
411A GLN 4.0 1.1 - - - -
415A HIS 5.2 1.3 - - - +
416A PHE* 3.9 26.9 - - + -
434A PHE* 4.3 6.7 - - + -
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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