Contacts of the strand formed by residues 543 - 549 (chain C) 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 MET 543 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511C ILE* 3.6 15.9 - - + +
512C GLY* 3.6 19.6 - - - +
513C LEU* 3.8 16.7 + - + -
529C LEU* 3.7 30.5 - - + -
533C ILE* 3.7 7.4 - - - +
537C GLU 5.2 0.9 - - - +
538C ASP* 4.1 8.8 - - - +
541C GLY 3.7 1.2 - - - -
542C ASP* 1.3 82.4 + - - +
544C ASP* 1.3 61.5 + - - +
545C PHE* 3.5 32.5 - - + -
560C ASP 3.1 13.9 - - - +
561C ILE* 4.0 11.9 - - + -
562C LYS* 4.0 4.6 - - - +
566C ILE* 4.0 25.6 - - + -
570C ILE* 5.2 1.1 - - + -
574C ALA* 4.0 9.4 - - + -
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Residues in contact with ASP 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C CIT 2.5 31.4 - - - +
510C ALA* 3.3 25.1 - - - +
511C ILE 4.1 1.1 - - - -
533C ILE* 3.8 7.0 - - - +
538C ASP* 3.3 22.8 - - - +
543C MET* 1.3 71.9 - - - +
545C PHE* 1.3 58.2 + - - +
546C LYS* 3.4 8.5 + - - +
558C GLN 3.3 4.0 - - - +
560C ASP* 2.8 41.0 + - + +
562C LYS* 4.9 0.9 - - + +
670C CIT 3.4 23.1 - - - +
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Residues in contact with PHE 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C LEU* 4.4 3.4 - - + -
509C VAL 3.6 1.7 - - - +
510C ALA* 3.2 1.7 - - - -
511C ILE* 2.8 49.2 + - + +
543C MET* 3.5 29.6 - - + -
544C ASP* 1.3 71.1 + - - +
546C LYS* 1.3 60.6 + - - +
547C ILE* 3.7 14.8 + - + +
557C LEU* 3.6 25.4 - - + -
558C GLN 3.9 2.9 - - - -
559C ALA* 3.5 28.0 - - + +
561C ILE* 5.3 0.9 - - + -
571C VAL* 4.1 27.4 - - + -
574C ALA* 4.1 17.0 - - + -
575C ILE* 3.6 33.0 - - + -
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Residues in contact with LYS 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C CIT 2.8 26.3 + - - -
450C HIS* 4.0 1.2 + - - -
453C LEU* 4.2 8.1 - - + +
482C SER* 5.8 0.9 - - - -
484C SER* 3.6 6.7 - - - +
485C MET* 4.0 22.0 - - + +
509C VAL 3.6 4.3 - - - -
510C ALA* 3.9 9.4 - - + -
544C ASP* 3.6 22.2 - - - +
545C PHE* 1.3 69.6 - - - +
547C ILE* 1.3 61.7 + - - +
556C ALA 4.1 0.3 - - - +
557C LEU* 3.4 3.4 - - - +
558C GLN* 2.8 67.5 + - - +
560C ASP* 3.0 21.3 - - - -
670C CIT 2.7 37.9 + - - +
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Residues in contact with ILE 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C PHE* 4.8 1.3 - - + -
485C MET* 3.8 3.1 - - - -
508C GLY* 3.4 0.5 - - - -
509C VAL* 3.0 35.8 + - - +
545C PHE* 4.4 9.6 - - + +
546C LYS* 1.3 76.3 - - - +
548C ALA* 1.3 65.4 + - - +
554C ILE* 3.9 35.4 - - + -
556C ALA 3.3 12.3 - - - +
557C LEU* 3.9 22.4 - - + -
575C ILE* 4.3 23.3 - - + +
578C ALA* 3.3 33.0 - - + -
582C LYS* 5.7 2.1 - - - +
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Residues in contact with ALA 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C ALA* 3.8 28.3 - - + -
485C MET* 4.2 9.4 - - + +
488C ALA* 4.8 2.0 - - + -
506C VAL* 4.7 2.7 - - + -
507C ALA 3.3 14.8 - - - +
508C GLY* 3.7 9.4 - - - -
547C ILE* 1.3 75.6 - - - +
549C GLY* 1.3 59.4 + - - +
554C ILE* 3.7 7.7 - - - +
555C THR* 2.9 19.9 + - - +
556C ALA* 2.9 15.9 + - + +
582C LYS* 4.5 4.7 - - - -
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Residues in contact with GLY 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C VAL* 3.3 7.1 - - - +
507C ALA 3.0 31.0 + - - +
548C ALA* 1.3 77.6 - - - +
550C THR* 1.3 64.3 + - - -
553C GLY 3.1 13.5 - - - -
555C THR* 3.2 16.8 + - - -
582C LYS* 3.6 8.4 - - - +
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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