Contacts of the strand formed by residues 388 - 393 (chain A) in PDB entry 5KYT
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 GLY 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A VAL* 2.9 19.4 - - - +
374A VAL 3.3 10.8 - - - -
375A ASP* 5.4 0.2 - - - -
376A LEU* 4.6 5.2 - - - -
382A LEU* 4.0 1.8 - - - -
387A ARG* 1.3 74.1 - - - +
389A GLU* 1.3 63.2 + - - -
423A ILE* 3.2 14.9 - - - +
424A ALA 2.9 27.7 + - - +
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Residues in contact with GLU 389 (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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373A VAL* 3.2 4.0 - - - -
374A VAL* 2.9 42.7 + - + +
376A LEU* 3.7 21.7 - - + +
388A GLY* 1.3 71.6 - - - -
390A LEU* 1.3 72.6 + - - +
391A CYS* 3.5 1.7 + - - -
419A HIS* 3.2 41.3 + - - +
421A GLY* 2.9 30.5 + - - +
422A ASP 3.3 11.0 - - - +
423A ILE* 4.1 3.4 - - + -
438A LEU* 6.0 4.3 - - + -
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A TYR* 3.4 39.5 - - + +
350A LEU* 3.8 14.4 - - + -
371A ALA* 4.3 5.6 - - + -
372A LYS 3.5 16.2 - - - +
373A VAL* 4.1 6.1 - - + -
388A GLY 3.5 1.6 + - - -
389A GLU* 1.3 72.9 - - - +
391A CYS* 1.3 65.3 + - - +
392A VAL* 4.2 10.1 - - + -
420A SER* 2.7 40.7 + - - +
422A ASP* 2.9 11.3 + - + +
424A ALA* 3.8 14.1 - - + -
432A PHE* 3.5 30.3 - - + -
434A ILE* 4.0 10.3 - - + -
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Residues in contact with CYS 391 (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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371A ALA* 3.3 0.7 - - - +
372A LYS* 2.9 42.3 + - + +
374A VAL* 3.9 19.3 - - - -
389A GLU* 3.8 12.6 - - - -
390A LEU* 1.3 77.6 - - - +
392A VAL* 1.3 70.4 + - - +
417A TRP* 3.6 19.9 - - + -
418A LEU 3.0 9.2 - - - +
419A HIS* 3.4 38.8 - - - -
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Residues in contact with VAL 392 (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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340A TYR* 5.3 0.4 - - + -
342A LEU* 5.6 2.0 - - + -
345A THR* 3.9 27.6 - - + -
349A ILE* 3.9 29.2 - - + -
350A LEU* 5.4 2.0 - - + -
369A PHE* 4.3 2.5 - - + -
370A GLU 3.4 9.0 - - - +
371A ALA* 3.9 15.9 - - + -
390A LEU* 4.2 17.9 - - + -
391A CYS* 1.3 82.3 - - - +
393A ARG* 1.3 59.7 + - - +
397A ILE* 4.2 7.2 - - + +
416A GLY 3.7 0.2 - - - +
417A TRP* 3.6 3.6 - - - -
418A LEU* 2.7 40.6 + - + +
420A SER* 6.0 2.0 - - - -
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Residues in contact with ARG 393 (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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368A PHE 4.2 0.2 - - - +
369A PHE* 3.0 8.8 - - - -
370A GLU* 2.9 65.4 + - + +
392A VAL* 1.3 73.5 - - - +
394A GLY* 1.3 58.4 + - - +
397A ILE* 4.2 2.2 - - - -
415A ASP* 3.0 41.9 + - - +
416A GLY* 3.1 25.4 - - - +
417A TRP* 3.5 34.7 - - + +
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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