Contacts of the strand formed by residues 382 - 388 (chain A) in PDB entry 3U1K
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 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A LEU* 3.1 9.7 - - - +
381A HIS* 1.3 79.5 - - - +
383A SER* 1.3 63.8 + - - -
396A THR* 3.5 2.3 - - - -
397A VAL* 2.9 28.6 + - - +
494A ALA* 3.9 5.8 - - - -
497A ASP* 3.3 11.9 - - - -
498A SER* 3.7 16.7 - - - -
601A LYS* 4.7 0.2 - - - -
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Residues in contact with SER 383 (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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374A VAL* 3.2 6.8 - - - +
375A ASP* 3.0 22.5 + - - -
376A MET* 3.0 35.1 + - - +
377A PHE* 3.9 5.9 + - - -
380A LEU* 4.0 21.2 - - - +
382A GLY* 1.3 76.2 - - - -
384A ALA* 1.3 66.1 + - - +
394A LEU* 5.3 1.8 - - - -
395A CYS 3.2 12.8 - - - -
396A THR* 4.6 1.6 - - - -
494A ALA* 3.8 6.3 - - - +
497A ASP* 2.8 12.3 + - - +
601A LYS* 5.0 0.7 + - - -
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Residues in contact with ALA 384 (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 GLU 3.0 14.1 - - - +
374A VAL* 4.0 1.8 - - + +
376A MET* 4.1 7.2 - - - -
383A SER* 1.3 79.1 - - - +
385A LEU* 1.3 60.8 + - - +
393A VAL 3.9 0.5 - - - +
394A LEU* 3.5 4.9 - - - +
395A CYS* 2.8 33.5 + - - +
490A GLY* 3.7 10.3 - - - +
493A LEU* 3.6 33.0 - - + -
494A ALA* 3.7 8.5 - - + +
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Residues in contact with LEU 385 (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 SER 4.1 0.2 - - - +
372A CYS* 3.1 8.8 - - - +
373A GLU* 2.8 54.4 + - - +
376A MET* 3.9 22.8 - - + -
384A ALA* 1.3 74.8 - - - +
386A PHE* 1.3 61.9 + - - +
387A GLN* 4.9 5.6 - - + +
392A GLN* 4.0 35.2 - - + +
393A VAL 3.6 11.9 - - - +
394A LEU* 3.9 26.0 - - + -
477A LEU* 4.4 6.5 - - + -
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Residues in contact with PHE 386 (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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370A VAL* 4.0 26.7 - - + -
371A SER 3.9 1.1 - - - -
372A CYS* 4.1 6.7 - - - -
384A ALA 4.2 0.4 - - - -
385A LEU* 1.3 73.7 - - - +
387A GLN* 1.3 61.9 - - - +
388A ARG* 3.9 31.6 - - + -
391A THR 3.7 1.2 - - - +
392A GLN* 3.5 2.6 - - - +
393A VAL* 3.0 37.4 + - + +
486A ALA* 3.6 28.2 - - + +
489A CYS* 3.6 34.3 - - + -
490A GLY* 4.1 19.3 - - - +
493A LEU* 4.0 16.4 - - + -
585A ILE* 3.9 11.0 - - + -
589A MET* 4.1 15.3 - - + -
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Residues in contact with GLN 387 (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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369A ASN 5.5 1.1 - - - +
370A VAL* 3.2 8.3 - - - +
371A SER* 2.9 49.9 + - - +
385A LEU* 4.9 5.4 - - + +
386A PHE* 1.3 76.3 - - - +
388A ARG* 1.3 59.8 + - - +
389A GLY 2.8 26.0 + - - +
390A GLN* 3.9 4.0 - - - +
391A THR 3.3 16.1 + - - -
392A GLN* 2.9 32.5 + - - +
478A GLU* 3.2 19.5 + - - -
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Residues in contact with ARG 388 (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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367A LEU* 4.7 9.2 - - - -
368A ARG* 3.1 24.0 - - + +
369A ASN 3.6 3.4 - - - -
370A VAL* 4.4 17.5 - - + -
386A PHE* 3.9 18.2 - - + -
387A GLN* 1.3 75.5 - - - +
389A GLY* 1.3 68.0 + - - +
390A GLN 3.2 0.5 + - - -
391A THR* 2.8 32.4 + - + +
481A GLY 3.3 11.9 + - - -
482A SER* 3.0 29.2 + - - -
485A MET* 4.0 6.7 - - - +
486A ALA* 3.4 25.6 - - - +
508A GLY 4.7 2.1 + - - -
509A VAL* 5.3 3.1 - - - +
532A ASP* 2.9 44.4 + - - +
585A ILE* 4.6 11.1 - - - +
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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