Contacts of the helix formed by residues 531 - 544 (chain C) in PDB entry 6O0T
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 LEU 531 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B SER 5.1 2.5 - - - +
508B CYS* 4.0 19.1 - - + -
525B GLU 5.6 0.2 - - - +
526B ASP* 3.6 33.0 - - + +
501C TYR* 4.4 3.9 + - - +
529C ILE* 3.5 1.6 - - - +
530C HIS* 1.3 77.1 - - + +
532C GLY* 1.3 65.5 + - - +
533C VAL* 4.3 2.0 - - + -
534C HIS* 3.2 53.4 + - + +
535C ARG* 3.2 15.3 + - - +
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Residues in contact with GLY 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B GLN* 3.7 11.2 + - - -
525B GLU* 5.8 2.4 + - - -
526B ASP* 3.1 18.4 + - - -
530C HIS 3.3 4.0 + - - -
531C LEU* 1.3 69.6 - - - +
533C VAL* 1.3 65.0 + - - +
535C ARG* 3.2 27.0 + - - +
536C ALA* 3.0 23.7 + - - +
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Residues in contact with VAL 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B CYS* 3.6 39.0 - - + +
510B LEU* 4.3 29.8 - - + -
518B VAL* 4.8 2.5 - - + -
522B GLN* 3.5 37.7 - - + +
526B ASP* 3.1 19.0 + - + +
527B CYS* 5.3 0.7 - - - -
531C LEU* 4.3 3.8 - - + -
532C GLY* 1.3 71.3 - - - +
534C HIS* 1.3 67.8 + - + +
536C ALA* 3.4 3.0 + - - +
537C ARG* 3.1 23.7 + - - +
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Residues in contact with HIS 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B SER 5.5 1.8 - - - -
508B CYS* 3.3 32.8 + - - -
509B GLY* 4.9 1.4 - - - -
497C ARG* 5.2 9.5 - - + +
498C PHE* 3.4 33.3 - + + -
500C GLN* 4.5 10.3 - - - -
501C TYR* 2.6 33.3 + + + +
529C ILE* 3.8 13.7 - - + -
531C LEU* 3.2 29.2 + - + +
532C GLY 3.2 0.6 - - - -
533C VAL* 1.3 81.7 - - + +
535C ARG* 1.3 64.3 + - - +
537C ARG* 3.2 2.3 + - - +
538C ILE* 3.0 29.9 + - + +
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Residues in contact with ARG 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B GLN* 5.5 6.1 - - - +
525B GLU* 5.3 5.5 + - - -
520C GLU* 3.7 37.5 + - + +
523C MSE 4.1 14.9 - - + +
524C LEU* 3.6 31.9 - - - +
529C ILE* 3.1 41.0 + - + +
530C HIS 3.0 27.9 + - - -
531C LEU 3.2 2.3 + - - +
532C GLY* 3.2 23.4 + - - +
534C HIS* 1.3 76.5 - - - +
536C ALA* 1.3 58.1 + - - +
538C ILE* 3.5 1.8 + - - +
539C LEU* 2.9 35.6 + - - +
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Residues in contact with ALA 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ARG* 5.1 2.9 + - - +
522B GLN* 3.5 29.2 - - - +
532C GLY 3.0 8.4 + - - +
533C VAL* 3.8 4.5 - - - +
535C ARG* 1.3 75.7 - - - +
537C ARG* 1.3 61.6 + - - +
539C LEU* 3.6 8.6 + - - +
540C THR* 3.1 29.1 + - - -
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Residues in contact with ARG 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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509B GLY 5.9 0.4 - - - -
514B LEU* 3.1 35.2 - - - +
517B ARG* 3.0 41.6 + - - +
494C LEU* 3.2 47.7 + - + +
495C ASP* 4.4 6.8 + - - +
498C PHE* 3.4 29.0 - - + -
533C VAL 3.1 16.8 + - - +
534C HIS 3.2 4.0 + - - +
536C ALA* 1.3 75.2 - - - +
538C ILE* 1.3 64.1 + - - +
540C THR* 3.6 5.2 + - - -
541C ALA* 3.2 18.5 + - - +
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Residues in contact with ILE 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C TRP* 4.0 18.5 - - + -
491C LEU* 4.1 17.3 - - + -
494C LEU* 4.0 8.5 - - + -
498C PHE* 4.1 20.4 - - + -
501C TYR* 4.0 20.4 - - + -
505C MSE 5.2 4.3 - - - -
515C LEU* 5.3 4.3 - - + -
523C MSE 3.7 23.6 - - + -
529C ILE* 3.7 26.5 - - + -
534C HIS 3.0 20.0 + - - +
535C ARG 4.1 2.7 - - - +
537C ARG* 1.3 73.6 - - - +
539C LEU* 1.3 67.1 + - - +
541C ALA* 3.4 1.9 + - - +
542C ALA* 2.9 23.3 + - + +
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Residues in contact with LEU 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C VAL 3.4 25.6 - - - +
519C SER* 4.6 0.4 - - - -
520C GLU* 3.5 39.9 - - + +
523C MSE 3.6 21.3 - - + -
535C ARG 2.9 22.5 + - - +
536C ALA* 3.8 7.4 - - - +
538C ILE* 1.3 77.6 - - - +
540C THR* 1.3 64.1 + - - +
542C ALA* 3.2 6.3 + - + +
543C ARG* 3.2 24.0 + - - +
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Residues in contact with THR 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ARG* 3.7 27.5 + - - +
536C ALA 3.1 17.3 + - - -
537C ARG 3.9 2.0 - - - -
538C ILE 3.3 0.2 - - - -
539C LEU* 1.3 77.1 - - - +
541C ALA* 1.3 62.8 + - - +
543C ARG* 3.3 29.6 + - - +
544C GLU* 3.3 39.0 + - + +
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Residues in contact with ALA 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C TRP* 3.8 17.2 - - + -
494C LEU* 3.7 31.2 - - + -
537C ARG 3.2 15.5 + - - +
539C LEU 3.3 0.2 - - - -
540C THR* 1.3 80.4 - - - +
542C ALA* 1.3 62.5 + - - +
543C ARG 3.4 0.7 + - - -
544C GLU* 3.5 19.5 + - - +
545C MSE 3.6 12.6 - - - +
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Residues in contact with ALA 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C TRP* 3.9 13.2 - - + -
515C LEU* 3.6 37.0 - - + +
516C HIS* 3.7 19.5 - - - +
523C MSE 5.2 4.3 - - + -
538C ILE 2.9 18.2 + - - +
539C LEU* 3.2 8.0 + - + +
541C ALA* 1.3 76.9 - - - +
543C ARG* 1.3 61.2 + - - +
545C MSE 3.6 17.6 + - - +
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Residues in contact with ARG 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C HIS* 5.1 9.0 - - - +
539C LEU 3.2 14.9 + - - +
540C THR* 3.9 24.6 + - - +
541C ALA 3.2 0.2 - - - -
542C ALA* 1.3 75.4 - - - +
544C GLU* 1.3 60.6 + - + +
545C MSE 3.1 15.8 + - - +
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Residues in contact with GLU 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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540C THR* 3.3 37.1 + - + +
541C ALA* 3.5 11.1 + - - +
542C ALA 3.4 0.8 - - - -
543C ARG* 1.3 80.4 - - + +
545C MSE 1.3 62.6 + - - +
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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