Contacts of the helix formed by residues 531 - 544 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507G SER 5.1 2.0 - - - +
508G CYS* 3.9 19.5 - - + -
526G ASP* 3.4 36.3 - - + +
501H TYR* 4.5 4.2 + - - +
529H ILE* 3.5 1.2 - - - +
530H HIS* 1.3 77.8 - - + +
532H GLY* 1.3 65.2 + - - +
533H VAL* 4.3 1.3 - - + -
534H HIS* 3.2 49.1 + - + +
535H ARG* 3.1 23.5 + - - +
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Residues in contact with GLY 532 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522G GLN* 3.7 11.0 + - - -
525G GLU* 5.9 1.8 + - - -
526G ASP* 3.0 19.2 + - - -
520H GLU* 4.1 3.8 - - - +
530H HIS 3.4 4.0 + - - -
531H LEU* 1.3 68.7 - - - +
533H VAL* 1.3 61.1 + - - +
535H ARG* 3.2 27.5 + - - +
536H ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 533 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508G CYS* 3.6 41.1 - - + +
510G LEU* 4.3 28.3 - - + -
518G VAL* 4.7 1.6 - - + -
522G GLN* 3.4 38.1 - - + +
526G ASP* 3.3 13.7 + - + +
527G CYS* 5.2 0.7 - - - -
531H LEU* 4.3 4.3 - - + -
532H GLY* 1.3 72.7 - - - +
534H HIS* 1.3 66.4 + - + +
536H ALA* 3.8 2.3 - - - +
537H ARG* 3.1 33.3 + - - +
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Residues in contact with HIS 534 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507G SER 5.3 0.9 - - - -
508G CYS* 3.3 32.9 + - - -
509G GLY* 4.9 0.8 - - - -
497H ARG* 4.2 22.6 - - + -
498H PHE* 3.3 31.2 - + + -
500H GLN* 4.9 2.9 - - - -
501H TYR* 2.5 30.2 + + + -
529H ILE* 3.9 13.5 - - + -
531H LEU* 3.2 31.9 + - + +
532H GLY 3.2 0.8 - - - -
533H VAL* 1.3 81.2 - - + +
535H ARG* 1.3 65.6 + - - +
537H ARG* 3.3 3.0 + - - +
538H ILE* 3.0 30.7 + - - +
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Residues in contact with ARG 535 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521G GLN* 5.7 2.2 + - - -
525G GLU* 5.3 6.1 + - - -
520H GLU* 3.3 56.0 + - + +
523H MSE 3.9 17.2 - - + +
524H LEU* 3.8 31.0 - - - +
529H ILE* 3.0 45.5 + - + +
530H HIS 3.0 22.0 + - - -
531H LEU 3.1 6.7 + - - +
532H GLY* 3.2 19.1 + - - +
534H HIS* 1.3 74.9 - - - +
536H ALA* 1.3 58.7 + - - +
538H ILE* 4.8 0.9 - - - -
539H LEU* 2.9 32.4 + - - +
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Residues in contact with ALA 536 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G ARG 5.8 2.7 - - - +
522G GLN* 3.6 19.5 - - - +
520H GLU* 4.7 9.6 + - - +
532H GLY 2.9 16.5 + - - +
533H VAL* 3.8 4.5 - - - +
535H ARG* 1.3 76.0 - - - +
537H ARG* 1.3 59.8 + - + +
539H LEU* 3.9 6.4 - - - +
540H THR* 2.9 32.9 + - - -
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Residues in contact with ARG 537 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508G CYS 5.0 2.3 + - - -
509G GLY* 3.1 24.4 + - - -
510G LEU* 5.6 2.2 - - - -
514G LEU* 3.5 35.5 - - + +
494H LEU* 3.8 28.4 + - + +
495H ASP* 2.8 29.8 + - - +
498H PHE* 4.0 23.3 - - + -
533H VAL* 3.1 22.8 + - - +
534H HIS* 3.9 4.5 - - - +
536H ALA* 1.3 77.4 - - + +
538H ILE* 1.3 59.3 + - - +
540H THR* 3.4 5.8 + - - -
541H ALA* 3.0 28.6 + - - +
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Residues in contact with ILE 538 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490H TRP* 4.2 18.6 - - + -
491H LEU* 4.1 11.9 - - + -
494H LEU* 4.2 8.7 - - + -
498H PHE* 3.8 24.7 - - + -
501H TYR* 4.1 19.7 - - + -
505H MSE 3.9 28.5 - - + -
515H LEU* 5.3 4.7 - - + -
523H MSE 4.1 18.6 - - + -
529H ILE* 4.2 8.1 - - + -
534H HIS 3.0 17.7 + - - +
535H ARG 4.1 2.2 - - - +
537H ARG* 1.3 72.3 - - - +
539H LEU* 1.3 62.0 + - - +
541H ALA* 3.3 1.6 + - - +
542H ALA* 2.9 28.7 + - + +
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Residues in contact with LEU 539 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518H VAL 4.2 15.0 - - - +
519H SER* 4.3 1.3 - - - -
520H GLU* 3.8 40.4 - - + +
523H MSE 4.1 11.0 - - + +
535H ARG 2.9 18.8 + - - +
536H ALA* 3.9 6.1 - - - +
538H ILE* 1.3 76.7 - - - +
540H THR* 1.3 68.9 + - - +
542H ALA* 3.2 13.7 + - + +
543H ARG* 3.2 22.7 + - + +
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Residues in contact with THR 540 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G ARG* 4.5 19.8 - - - +
536H ALA 2.9 18.9 + - - -
537H ARG* 3.8 5.8 - - - -
538H ILE 3.3 0.2 - - - -
539H LEU* 1.3 82.4 - - - +
541H ALA* 1.3 62.5 + - - +
543H ARG* 3.1 18.4 + - - +
544H GLU* 3.2 32.6 + - + +
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Residues in contact with ALA 541 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490H TRP* 3.9 18.1 - - + -
494H LEU* 3.6 33.2 - - + -
537H ARG 3.0 17.8 + - - +
538H ILE 3.8 2.9 - - - +
540H THR* 1.3 77.8 - - - +
542H ALA* 1.3 62.1 + - - +
544H GLU* 3.3 28.2 + - - +
545H MSE 4.3 3.1 + - - +
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Residues in contact with ALA 542 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490H TRP* 4.1 10.0 - - + -
515H LEU* 3.6 38.4 - - + +
516H HIS* 3.6 16.5 - - - +
523H MSE 5.4 2.7 - - + -
538H ILE 2.9 17.5 + - - +
539H LEU* 3.2 8.9 + - - +
541H ALA* 1.3 76.9 - - - +
543H ARG* 1.3 58.4 + - - +
545H MSE 3.2 24.3 - - - +
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Residues in contact with ARG 543 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516H HIS* 5.2 4.3 - - - +
539H LEU* 3.2 18.5 + - + +
540H THR* 3.1 13.0 + - - +
542H ALA* 1.3 76.0 - - - +
544H GLU* 1.3 58.3 + - + +
545H MSE 3.0 13.6 + - - -
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Residues in contact with GLU 544 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G ARG* 5.2 6.6 + - - -
540H THR* 3.2 30.2 + - + +
541H ALA* 3.3 16.3 + - - +
543H ARG* 1.3 76.1 - - + +
545H MSE 1.3 60.6 + - - +
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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
------------------------------------------------------------
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