Contacts of the strand formed by residues 543 - 549 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B ILE* 3.7 15.5 - - + +
512B GLY* 3.6 20.0 - - - +
513B LEU* 3.7 16.6 + - + -
529B LEU* 3.7 30.7 - - + -
533B ILE* 3.9 6.9 - - - +
537B GLU 4.9 0.7 - - - +
538B ASP* 4.1 9.7 - - - +
541B GLY 3.7 1.2 - - - -
542B ASP* 1.3 81.7 + - - +
544B ASP* 1.3 61.9 + - - +
545B PHE* 3.5 33.0 - - + -
560B ASP 3.1 14.6 - - - +
561B ILE* 4.1 11.0 - - + -
562B LYS* 4.5 4.8 - - - +
566B ILE* 4.0 26.9 - - + -
570B ILE* 5.2 1.1 - - + -
574B ALA* 4.0 9.0 - - + -
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Residues in contact with ASP 544 (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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1B CIT 3.5 19.3 - - - +
510B ALA* 3.3 27.0 - - - +
511B ILE 3.9 1.1 - - - -
533B ILE* 3.7 7.0 - - - +
538B ASP* 3.3 21.3 - - - +
543B MET* 1.3 72.7 - - - +
545B PHE* 1.3 58.9 + - - +
546B LYS* 3.5 9.7 + - - +
558B GLN 3.4 7.1 - - - +
560B ASP* 2.8 34.0 + - + +
562B LYS* 4.3 1.3 - - - +
670B CIT 2.7 38.6 - - - +
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Residues in contact with PHE 545 (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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229B LEU* 4.2 6.5 - - + -
509B VAL 3.6 1.9 - - - +
510B ALA* 3.4 1.4 - - - -
511B ILE* 2.8 50.2 + - + +
543B MET* 3.5 30.1 - - + -
544B ASP* 1.3 70.2 + - - +
546B LYS* 1.3 59.5 + - - +
547B ILE* 3.7 16.5 + - + -
557B LEU* 3.4 26.9 - - + -
558B GLN 4.0 2.0 - - - -
559B ALA* 3.5 26.7 - - + +
561B ILE* 5.5 2.0 - - + -
566B ILE* 5.8 0.2 - - + -
571B VAL* 4.0 24.7 - - + -
574B ALA* 4.2 12.3 - - + -
575B ILE* 3.6 34.3 - - + -
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Residues in contact with LYS 546 (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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1B CIT 2.7 36.8 + - - +
450B HIS* 4.0 1.6 + - - -
453B LEU* 4.2 6.3 - - + +
482B SER* 5.8 0.7 - - - -
484B SER* 3.7 7.2 - - - +
485B MET* 3.9 21.9 - - + +
509B VAL 3.6 4.9 - - - -
510B ALA* 4.1 8.1 - - + -
544B ASP* 3.7 25.6 - - - +
545B PHE* 1.3 70.1 - - - +
547B ILE* 1.3 59.4 + - - +
556B ALA 4.5 0.5 - - - -
557B LEU* 3.2 3.8 - - - +
558B GLN* 2.7 81.1 + - - +
560B ASP* 5.2 0.7 - - - -
670B CIT 2.9 30.7 + - - -
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Residues in contact with ILE 547 (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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241B PHE* 4.7 4.3 - - + -
485B MET* 3.8 2.8 - - - -
508B GLY* 3.2 1.2 - - - -
509B VAL* 3.0 33.1 + - + +
545B PHE* 4.3 9.4 - - + +
546B LYS* 1.3 75.8 - - - +
548B ALA* 1.3 69.0 - - - +
554B ILE* 4.2 21.8 - - + -
556B ALA 3.3 12.6 - - - +
557B LEU* 3.8 18.2 - - + -
575B ILE* 4.3 34.3 - - + +
578B ALA* 3.2 34.3 - - + -
582B LYS* 5.7 2.0 - - - +
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Residues in contact with ALA 548 (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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457B ALA* 3.7 29.2 - - + -
485B MET* 4.1 9.9 - - + -
488B ALA* 4.8 2.7 - - + -
506B VAL* 4.9 0.7 - - + -
507B ALA 3.2 15.0 - - - +
508B GLY* 3.7 7.2 - - - -
547B ILE* 1.3 76.6 - - - +
549B GLY* 1.3 58.7 + - - +
554B ILE* 3.7 7.6 - - - +
555B THR* 3.0 19.2 + - - +
556B ALA* 2.9 16.4 + - + +
582B LYS* 4.4 6.5 - - - -
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Residues in contact with GLY 549 (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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506B VAL* 3.2 7.4 - - - +
507B ALA 2.9 32.9 + - - +
548B ALA* 1.3 77.2 - - - +
550B THR* 1.3 65.8 + - - -
553B GLY 3.3 11.9 - - - -
555B THR* 3.4 17.1 + - - -
582B LYS* 3.7 8.3 - - - +
586B LEU* 4.5 0.2 - - - +
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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
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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