Contacts of the helix formed by residues 526 - 542 (chain C) in PDB entry 1UEX
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 SER 526 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C SER 5.2 0.7 - - - -
524C ARG 4.3 0.2 - - - -
525C LEU* 1.3 79.0 - - - +
527C GLU* 1.3 65.4 + - - +
528C ALA* 3.4 8.6 + - - +
529C GLU* 2.7 39.5 + - - +
530C PHE 3.1 14.6 + - - -
586C TYR* 3.5 6.6 - - - -
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Residues in contact with GLU 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C SER* 1.3 73.8 - - - +
528C ALA* 1.3 63.0 + - - +
530C PHE* 3.0 16.1 + - - +
531C GLU* 3.1 21.3 + - + +
586C TYR* 3.6 45.4 + - + +
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Residues in contact with ALA 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C SER* 3.2 7.3 + - - +
527C GLU* 1.3 81.8 - - - +
529C GLU* 1.3 62.4 + - + +
531C GLU* 3.2 13.4 + - - +
532C VAL* 3.1 25.3 + - + +
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Residues in contact with GLU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C ARG 3.9 5.1 - - - +
525C LEU* 3.3 26.2 - - + +
526C SER* 2.7 42.7 + - - +
527C GLU 3.2 0.2 - - - -
528C ALA* 1.3 77.1 - - + +
530C PHE* 1.3 58.0 + - - +
532C VAL* 3.2 6.2 + - - +
533C LEU* 3.0 25.3 + - - +
679C SER* 5.5 4.3 - - - -
680C VAL* 3.8 30.8 + - + +
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Residues in contact with PHE 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C LEU* 4.1 10.3 - - + -
520C ASP 3.5 25.4 - - - -
521C GLY* 4.9 2.9 - - - -
525C LEU* 4.2 8.7 - - + +
526C SER 3.1 4.8 + - - +
527C GLU 3.0 11.0 + - - +
529C GLU* 1.3 73.4 - - - +
531C GLU* 1.3 58.1 + - - +
533C LEU* 3.1 25.6 + - + +
534C LYS* 2.8 67.4 + - + +
557C GLU* 4.1 13.7 - - + -
584C VAL* 3.5 18.6 - - + -
585C LYS 3.5 21.8 - - - -
586C TYR* 3.4 39.9 - + + -
587C ALA 5.5 0.7 - - - -
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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
----------------------------------------------------------
527C GLU* 3.1 22.1 + - + +
528C ALA* 3.2 14.6 + - - +
530C PHE* 1.3 77.2 - - - +
532C VAL* 1.3 56.1 + - + +
534C LYS* 2.9 41.8 + - - +
535C ALA* 2.7 36.5 + - - +
582C SER 4.7 1.7 - - - +
584C VAL 4.8 0.5 - - - +
586C TYR* 5.5 2.9 - - - +
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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
----------------------------------------------------------
528C ALA 3.1 15.2 + - - +
529C GLU* 3.2 10.1 + - - +
531C GLU* 1.3 76.5 - - + +
533C LEU* 1.3 62.0 + - - +
535C ALA* 3.4 10.0 - - + +
536C PHE* 3.1 19.2 + - - +
680C VAL* 3.5 44.2 - - + +
681C ASP* 4.5 10.5 - - - +
683C LEU* 4.3 1.6 - - + +
684C GLU* 6.1 1.8 - - + +
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Residues in contact with LEU 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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519C LEU* 3.6 40.8 - - + -
520C ASP* 4.4 4.3 - - + +
525C LEU* 4.2 15.7 - - + -
529C GLU 3.0 11.8 + - - +
530C PHE* 3.2 27.1 - - + +
531C GLU 3.0 0.2 - - - -
532C VAL* 1.3 76.6 - - - +
534C LYS* 1.3 61.0 + - - +
536C PHE* 2.9 25.2 + - + +
537C VAL* 3.2 8.4 + - - +
621C LEU* 4.3 15.7 - - + +
653C ILE* 3.6 31.2 - - + -
680C VAL* 4.9 2.7 - - + -
683C LEU* 3.6 15.7 - - + -
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Residues in contact with LYS 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C LEU* 4.4 7.9 - - + -
530C PHE* 2.8 58.0 + - + +
531C GLU* 2.9 39.4 + - - +
533C LEU* 1.3 72.9 - - - +
535C ALA* 1.3 62.3 + - - +
537C VAL* 3.2 12.5 + - - +
538C VAL* 3.1 26.2 + - - +
581C ALA 3.5 19.1 - - - +
582C SER* 2.6 32.1 + - - -
583C GLN* 3.9 2.4 - - - +
584C VAL* 3.2 23.6 + - + +
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Residues in contact with ALA 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C GLU 2.7 20.8 + - - +
532C VAL* 3.4 11.9 - - + +
533C LEU 3.1 0.2 - - - -
534C LYS* 1.3 73.2 - - - +
536C PHE* 1.3 57.2 + - - +
538C VAL* 3.3 7.5 + - - +
539C ASP* 2.9 39.1 + - - +
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Residues in contact with PHE 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PHE* 4.7 0.4 - + - -
532C VAL 3.1 11.5 + - - +
533C LEU* 2.9 14.3 + - + +
535C ALA* 1.3 74.2 - - - +
537C VAL* 1.3 66.7 + - - +
539C ASP* 3.2 7.7 + - + +
540C MET* 2.9 63.1 + - + +
619C LEU* 3.9 16.8 - - + -
621C LEU* 3.5 33.9 - - + -
651C VAL* 6.0 0.2 - - + -
683C LEU* 3.7 58.1 - - + -
684C GLU* 5.6 0.2 - - - -
687C ARG* 4.1 14.8 - - + -
690C ILE* 4.3 13.5 - - + -
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Residues in contact with VAL 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PHE* 3.8 39.5 - - + -
519C LEU* 3.9 31.2 - - + -
533C LEU 3.7 11.9 - - - +
534C LYS* 3.2 8.0 + - - +
536C PHE* 1.3 78.1 - - + +
538C VAL* 1.3 62.4 + - - +
540C MET* 3.4 2.1 + - - +
541C MET* 3.0 48.5 + - - +
555C VAL* 3.9 13.2 - - + -
581C ALA* 4.1 8.5 - - + -
621C LEU* 4.5 7.2 - - + -
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Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C LYS 3.1 14.4 + - - +
535C ALA* 3.6 9.9 - - - +
537C VAL* 1.3 73.2 - - - +
539C ASP* 1.3 69.6 + - - +
541C MET* 3.1 11.8 + - - +
542C GLU* 2.8 45.5 + - - +
578C ARG* 3.6 36.1 - - + +
581C ALA* 4.0 5.4 - - + -
582C SER* 3.9 21.3 - - - +
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Residues in contact with ASP 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C ALA* 2.9 24.3 + - - +
536C PHE* 3.6 10.9 - - + +
538C VAL* 1.3 77.0 - - - +
540C MET* 1.3 65.5 + - - +
542C GLU* 2.9 25.7 + - - +
543C ARG* 2.9 31.6 + - - +
684C GLU* 4.4 8.7 - - - +
687C ARG* 4.0 26.7 + - + +
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Residues in contact with MET 540 (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* 4.7 2.7 - - + -
517C PHE* 3.7 21.5 - - + -
536C PHE* 2.9 48.9 + - + +
537C VAL 3.5 6.5 - - - +
539C ASP* 1.3 74.4 - - - +
541C MET* 1.3 55.7 + - - +
543C ARG* 2.6 29.8 + - - +
544C LEU* 2.9 19.7 - - + +
619C LEU* 4.2 10.3 - - + -
687C ARG* 3.9 8.7 - - - +
690C ILE* 4.0 9.6 - - + -
691C VAL* 3.3 34.8 - - + -
694C LEU* 3.5 32.5 - - + -
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Residues in contact with MET 541 (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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517C PHE* 4.1 15.3 - - + -
537C VAL* 3.0 33.1 + - - +
538C VAL* 3.5 6.7 - - - +
540C MET* 1.3 74.7 - - - +
542C GLU* 1.3 58.2 + - - +
543C ARG 3.0 2.0 + - - -
544C LEU* 3.6 16.0 + - - +
546C ILE* 3.4 32.2 - - + +
553C VAL* 3.8 23.6 - - + -
555C VAL* 4.8 0.9 - - - -
566C ILE* 4.6 5.2 - - + -
577C LEU* 3.7 33.0 - - + +
578C ARG* 3.8 25.1 + - + +
581C ALA* 4.0 14.4 - - - -
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Residues in contact with GLU 542 (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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504C LEU* 3.5 35.9 + - + +
505C HIS* 3.0 41.3 + - + -
507C PHE 4.1 0.7 - - - +
508C TYR* 5.2 3.1 - - - -
538C VAL* 2.8 41.6 - - - +
539C ASP* 2.9 20.4 + - - +
541C MET* 1.3 78.1 - - - +
543C ARG* 1.3 58.7 + - - +
544C LEU 3.6 1.6 - - - -
578C ARG* 3.4 19.4 + - - +
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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