Contacts of the strand formed by residues 369 - 374 (chain A) in PDB entry 4YKN
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 THR 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A VAL* 3.3 8.3 - - - +
358A ARG* 2.8 62.0 + - - +
359A ASP 4.0 9.8 + - - -
368A TYR* 1.3 76.0 + - - +
370A LEU* 1.3 60.4 + - - +
371A THR* 3.9 2.4 + - - +
380A LEU* 3.4 38.5 - - + +
381A ILE 3.9 3.8 - - - +
382A LYS* 4.7 4.3 - - - +
383A ILE* 4.9 0.4 - - - -
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Residues in contact with LEU 370 (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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355A PHE* 4.0 23.1 - - + -
356A LEU 3.3 17.5 - - - +
357A VAL* 4.1 9.2 - - + -
368A TYR 4.3 0.4 - - - -
369A THR* 1.3 72.7 - - - +
371A THR* 1.3 68.8 + - - +
372A LEU* 4.9 9.2 - - + +
379A LYS 3.7 0.9 - - - +
380A LEU* 3.6 1.0 - - - -
381A ILE* 2.7 57.8 + - + +
383A ILE* 4.1 15.6 - - + +
392A PHE* 3.5 28.9 - - + -
404A LEU* 5.8 0.2 - - + -
405A ILE* 5.9 3.1 - - + -
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Residues in contact with THR 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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343A VAL* 3.8 25.7 - - + +
344A ASN* 5.9 0.9 - - - +
347A LEU* 3.8 16.3 - - + +
354A THR 4.0 0.2 - - - +
355A PHE* 3.2 25.8 - - - +
356A LEU* 3.2 18.7 + - - +
358A ARG* 3.0 26.7 + - - +
369A THR* 3.9 2.3 + - - +
370A LEU* 1.3 72.2 - - - +
372A LEU* 1.3 61.3 + - - +
378A ASN* 4.2 13.0 - - + -
379A LYS 3.4 8.7 - - - +
380A LEU* 3.4 14.8 - - + +
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Residues in contact with LEU 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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347A LEU* 4.4 2.2 - - - -
353A GLY* 3.9 10.8 - - - +
354A THR 3.6 10.8 - - - +
355A PHE* 4.3 8.7 - - + -
370A LEU* 3.9 13.2 + - + -
371A THR* 1.3 75.1 - - - +
373A ARG* 1.3 79.3 + - - +
374A LYS* 4.7 4.3 - - + +
378A ASN* 3.3 3.3 - - - -
379A LYS* 2.5 49.2 + - + +
381A ILE* 5.1 7.0 - - + -
420A LEU* 4.2 32.5 - - + -
422A VAL 5.0 0.9 - - - +
423A LYS* 3.4 35.9 - - + -
424A LEU 4.3 0.4 - - - +
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Residues in contact with ARG 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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347A LEU* 3.2 23.1 + - + +
348A ARG* 4.4 1.8 - - - +
349A ASP* 3.4 29.3 + - - +
350A THR* 3.4 22.3 + - - +
351A ALA 3.4 26.2 - - - +
352A ASP* 3.4 5.2 + - - +
353A GLY 2.9 27.5 + - - -
354A THR* 2.8 24.5 + - - +
372A LEU* 1.3 74.9 - - - +
374A LYS* 1.3 61.6 + - - +
376A GLY* 3.3 33.9 + - - -
377A ASN* 3.4 7.6 - - - +
378A ASN* 3.1 31.0 + - - +
1357A ARG* 5.7 0.4 - - - +
1369A ASP* 4.4 5.7 + - - -
1370A ASN* 5.5 3.8 + - - -
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Residues in contact with LYS 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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352A ASP* 3.7 7.0 - - + +
372A LEU* 3.7 9.8 + - + -
373A ARG* 1.3 74.8 - - - +
375A GLY* 1.3 65.5 + - - +
376A GLY 3.2 2.7 - - - -
377A ASN* 3.0 25.3 + - - +
379A LYS* 4.3 11.5 - - + +
420A LEU* 4.2 27.4 - - + -
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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