Contacts of the strand formed by residues 360 - 367 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LYS* 6.2 0.2 - - - +
334B GLN* 3.3 26.9 + - - +
335B TYR* 4.0 27.5 - - + -
359B ALA* 1.3 71.5 - - - +
361B LEU* 1.3 73.8 + - - +
362B ALA* 3.2 9.6 + - - +
376B TYR* 3.2 4.1 - - - -
377B LYS* 2.8 57.3 + - + +
500B ALA* 4.3 8.9 + - - +
502B SER* 4.1 7.1 + - - -
531B GLY* 3.2 35.6 + - - +
532B GLU 4.4 8.1 - - - +
534B GLY* 4.3 6.7 - - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LYS* 4.0 13.2 + - + +
334B GLN 2.9 15.4 + - - +
335B TYR* 3.5 26.0 - - + +
336B LYS* 3.7 34.3 - - - +
337B VAL* 3.7 18.2 - - + +
353B ILE* 5.3 2.5 - - + -
359B ALA 3.7 2.2 + - - -
360B LYS* 1.3 75.5 - - - +
362B ALA* 1.3 59.4 + - - +
363B GLN 4.1 0.7 - - - +
364B VAL* 3.6 23.8 - - + -
374B ALA* 3.9 7.6 - - + -
375B ILE 3.9 11.0 - - - +
376B TYR* 3.6 40.1 - - + +
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Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LYS* 3.8 15.7 + - - -
360B LYS* 3.2 15.8 + - + +
361B LEU* 1.3 74.7 - - - +
363B GLN* 1.3 63.4 + - + +
375B ILE* 2.8 24.3 + - + +
377B LYS* 4.6 24.9 - - + +
382B ASP* 4.9 1.6 - - - +
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Residues in contact with GLN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LYS* 4.4 6.7 - - - +
361B LEU* 3.7 1.0 - - - +
362B ALA* 1.3 81.2 - - + +
364B VAL* 1.3 69.8 + - - +
365B ASN* 3.3 31.1 + - - +
373B VAL 3.9 0.4 - - - +
374B ALA* 3.3 3.3 - - - -
375B ILE* 2.8 40.6 + - + +
405B ALA 4.5 1.2 - - - +
406B SER* 3.6 12.9 - - - -
407B ILE* 3.3 41.2 + - + +
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 3.9 36.4 - - + +
327B LYS* 4.5 9.3 - - + +
337B VAL* 3.8 14.4 - - + -
353B ILE* 5.3 2.5 - - + -
361B LEU* 3.6 35.4 - - + -
363B GLN* 1.3 83.2 - - - +
365B ASN* 1.3 69.8 + - - +
372B PHE* 4.0 29.4 - - + -
373B VAL 3.2 10.3 - - - +
374B ALA* 4.1 7.2 - - + -
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Residues in contact with ASN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ILE* 4.3 3.8 - - - -
363B GLN* 3.3 24.9 + - - +
364B VAL* 1.3 84.2 - - - +
366B CYS* 1.3 63.2 + - - +
367B ALA 3.6 0.3 + - - -
372B PHE* 3.3 1.7 - - - -
373B VAL* 2.8 37.6 + - + +
407B ILE* 3.6 33.7 + - + +
409B ASN* 2.9 30.3 + - - +
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Residues in contact with CYS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ILE* 3.9 9.3 + - + +
318B THR* 3.9 27.8 - - + -
320B HIS* 4.8 0.7 - - - -
365B ASN* 1.3 74.3 - - - +
367B ALA* 1.3 61.5 + - - +
369B GLU 3.3 28.3 - - - -
370B GLU* 4.2 1.8 - - - -
371B TYR 3.3 12.8 - - - -
372B PHE* 4.0 7.9 - - + -
409B ASN* 2.9 18.5 + - - +
411B GLN* 3.4 40.7 + - + +
101D GOL 5.1 0.7 + - - -
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B ASN 3.6 0.4 + - - -
366B CYS* 1.3 75.6 - - - +
368B ASN* 1.3 71.7 + - - +
369B GLU 3.1 3.0 + - - -
371B TYR* 2.8 31.4 + - + +
373B VAL* 4.0 14.4 - - + -
409B ASN* 3.7 15.5 - - - +
411B GLN 4.0 1.8 - - - -
415B HIS 5.0 1.6 - - - +
416B PHE* 3.9 28.3 - - + -
434B PHE* 4.3 7.2 - - + -
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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
------------------------------------------------------------
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