Contacts of the helix formed by residues 524 - 537 (chain C) in PDB entry 3UO8
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 LYS 524 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530B ASP* 2.8 23.1 + - - +
534B GLU* 2.7 37.0 + - - +
523C LYS* 1.3 75.6 - - - +
525C ILE* 1.3 69.7 + - - +
526C THR* 3.2 25.4 - - - +
527C VAL* 3.0 24.2 + - + +
528C LEU* 3.1 9.4 + - - +
554C LEU* 3.1 41.5 + - + -
556C GLU 3.5 7.8 + - - +
557C LYS* 4.1 11.4 - - + -
558C ARG 3.4 22.0 - - - +
559C ALA* 4.2 2.0 - - - +
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Residues in contact with ILE 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C LEU* 4.8 5.4 - - + -
458C VAL* 4.7 19.1 - - + -
460C LEU* 5.6 3.1 - - + -
487C VAL* 3.7 30.5 - - + -
519C LEU* 5.4 1.8 - - + -
523C LYS 3.3 4.7 + - - -
524C LYS* 1.3 71.0 - - - +
526C THR* 1.3 64.7 + - - +
528C LEU* 3.5 18.3 + - + -
529C LEU* 3.0 44.5 + - + +
554C LEU* 3.9 13.9 - - + -
558C ARG 3.2 10.6 + - - +
559C ALA* 4.2 2.4 - - - +
560C LEU* 4.0 39.5 - - + +
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Residues in contact with THR 526 (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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530B ASP* 2.7 31.9 + - - +
487C VAL* 3.9 18.6 - - + -
524C LYS* 3.2 21.1 - - - +
525C ILE* 1.3 77.9 - - - +
527C VAL* 1.3 56.6 + - - -
529C LEU* 3.4 6.0 + - - +
530C ASP* 2.9 28.8 + - - +
550C ILE* 4.1 10.2 - - + +
552C SER* 3.3 36.8 - - - +
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Residues in contact with VAL 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B VAL* 5.7 15.5 - - + -
530B ASP* 4.0 16.2 - - - +
523C LYS* 4.2 24.5 - - + -
524C LYS* 3.0 22.5 + - + +
526C THR* 1.3 76.4 + - - +
528C LEU* 1.3 62.9 + - - +
530C ASP* 3.0 10.7 + - + +
531C GLU* 2.9 31.0 + - + +
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Residues in contact with LEU 528 (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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515C LEU* 4.2 14.4 - - + -
518C ARG* 3.3 42.6 - - + +
519C LEU* 3.7 18.2 - - + +
521C GLU* 3.9 21.1 - - + +
523C LYS* 4.7 10.7 - - + +
524C LYS 3.1 8.7 + - - +
525C ILE* 3.6 25.1 - - + +
527C VAL* 1.3 80.0 - - - +
529C LEU* 1.3 63.1 + - + +
531C GLU* 3.0 15.8 + - - +
532C VAL* 3.0 26.7 + - + +
560C LEU* 5.4 3.4 - - + -
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Residues in contact with LEU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C LEU* 4.2 17.0 - - + -
487C VAL* 3.8 28.9 - - + -
488C PHE 4.2 1.8 - - - +
489C GLY* 3.9 21.8 - - - +
511C PHE* 4.7 9.2 - - + -
515C LEU* 4.1 25.6 - - + -
525C ILE* 3.0 30.8 + - + +
526C THR 3.9 1.1 - - - +
528C LEU* 1.3 72.8 - - + +
530C ASP* 1.3 61.7 + - - +
532C VAL* 3.2 5.4 + - + +
533C ALA* 2.8 29.5 + - - +
548C LEU* 3.8 10.6 - - + +
550C ILE* 3.5 21.9 - - + +
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Residues in contact with ASP 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LYS* 2.9 27.8 + - - +
526B THR* 2.8 33.1 + - - +
527B VAL* 3.9 16.6 - - - +
552B SER* 5.1 1.2 + - - -
554B LEU 4.3 2.8 - - - +
526C THR 2.9 14.3 + - - +
527C VAL* 3.0 17.2 + - + +
529C LEU* 1.3 78.2 - - - +
531C GLU* 1.3 58.8 + - + +
533C ALA* 3.2 6.7 + - - +
534C GLU* 3.2 25.9 + - - +
550C ILE* 3.4 14.6 - - + +
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Residues in contact with GLU 531 (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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518C ARG* 3.5 28.8 + - - +
521C GLU* 2.6 30.5 - - - +
523C LYS* 2.9 30.8 + - - +
527C VAL* 2.9 24.3 + - + +
528C LEU* 3.0 10.7 + - - +
530C ASP* 1.3 74.5 - - + +
532C VAL* 1.3 65.4 + - - +
534C GLU* 3.1 15.4 + - - +
535C ASP* 3.0 27.1 + - - +
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Residues in contact with VAL 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C PHE* 4.4 6.3 - - + -
514C PHE* 4.0 19.1 - - + +
515C LEU* 4.0 31.6 - - + +
518C ARG* 3.8 24.5 - - + -
528C LEU* 3.0 19.6 + - + +
529C LEU* 3.2 9.4 + - + +
531C GLU* 1.3 75.1 - - - +
533C ALA* 1.3 63.8 + - - +
535C ASP* 3.2 10.3 + - - +
536C MET* 3.0 28.4 + - + +
548C LEU* 3.4 20.4 - - + -
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Residues in contact with ALA 533 (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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552B SER 6.1 0.4 - - - +
553B SER* 5.7 2.0 - - - +
554B LEU 4.3 16.4 - - - +
555B SER* 3.5 13.4 - - - -
529C LEU 2.8 16.5 + - - +
530C ASP* 3.3 15.0 - - - +
531C GLU 3.2 0.4 - - - -
532C VAL* 1.3 73.7 - - - +
534C GLU* 1.3 62.6 + - - +
536C MET* 3.4 3.9 + - - +
537C GLY 3.1 16.1 + - - -
548C LEU* 4.0 34.5 + - + +
550C ILE* 4.7 2.9 - - + -
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Residues in contact with GLU 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LYS* 2.9 41.0 + - - +
555B SER 3.6 22.6 - - - +
556B GLU* 4.6 0.7 - - - +
557B LYS* 3.1 44.1 + - + +
530C ASP* 3.2 14.0 + - - +
531C GLU* 3.1 16.5 + - - +
533C ALA* 1.3 75.6 - - - +
535C ASP* 1.3 68.3 + - - +
537C GLY* 3.1 13.2 + - - -
538C LYS* 3.6 18.4 + - - +
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Residues in contact with ASP 535 (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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514C PHE* 3.7 36.0 - - + +
517C ASP* 5.8 1.4 - - - +
518C ARG* 2.8 49.5 + - - +
531C GLU 3.0 15.4 + - - +
532C VAL* 3.6 7.8 - - - +
534C GLU* 1.3 77.7 - - - +
536C MET* 1.3 59.0 + - - +
538C LYS* 3.0 42.4 + - - +
539C CYS 3.8 0.5 + - - -
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Residues in contact with MET 536 (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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491C ALA 4.0 11.4 - - - +
510C ILE* 4.0 17.9 - - + -
511C PHE* 4.0 27.1 - - + -
514C PHE* 4.0 16.6 - - + -
532C VAL* 3.0 18.5 + - + +
533C ALA* 3.7 4.7 - - - +
534C GLU 3.2 0.2 - - - -
535C ASP* 1.3 72.6 - - - +
537C GLY* 1.3 60.7 + - - +
538C LYS 3.0 5.6 - - - -
539C CYS* 3.1 17.0 + - - +
542C THR* 4.0 9.1 + - - +
543C LYS* 5.7 0.3 - - - +
546C GLN* 4.1 22.3 - - - +
547C ALA* 4.3 2.9 - - - -
548C LEU* 3.7 50.5 - - + +
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Residues in contact with GLY 537 (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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555B SER* 4.0 21.3 - - - -
533C ALA 3.1 10.0 + - - -
534C GLU 3.1 12.0 + - - -
536C MET* 1.3 75.6 - - - +
538C LYS* 1.3 52.1 + - - +
539C CYS 3.3 0.4 - - - -
543C LYS* 2.7 29.4 + - - +
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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