Contacts of the helix formed by residues 519 - 526 (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 SER 519 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517H ARG 3.8 1.9 + - - -
518H VAL* 1.3 75.2 - - - +
520H GLU* 1.3 65.7 + - - +
521H GLN* 3.9 6.9 + - - +
522H GLN* 3.1 47.3 + - - +
523H MSE 3.2 17.8 + - - +
539H LEU* 4.3 4.5 - - - -
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Residues in contact with GLU 520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522G GLN* 5.2 2.8 + - - -
519H SER* 1.3 74.7 - - - +
521H GLN* 1.3 62.2 + - - +
523H MSE 3.3 8.1 + - - -
524H LEU* 3.2 16.6 + - - +
532H GLY* 4.1 7.6 - - - +
535H ARG* 3.3 55.9 + - + +
536H ALA* 4.9 9.3 - - - +
539H LEU* 3.8 21.8 - - + +
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Residues in contact with GLN 521 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519H SER* 3.3 7.0 + - - +
520H GLU* 1.3 76.3 - - - +
522H GLN* 1.3 60.7 + - + +
524H LEU* 3.2 9.7 + - + +
525H GLU* 2.4 64.1 + - + +
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Residues in contact with GLN 522 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A GLU* 5.1 3.8 + - - -
532A GLY* 3.8 9.2 + - - -
533A VAL* 3.4 27.2 - - + +
536A ALA* 3.7 27.5 - - - +
517H ARG 3.8 5.2 + - - +
518H VAL* 3.4 10.2 - - + -
519H SER* 3.1 38.5 + - - +
521H GLN* 1.3 76.9 - - + +
523H MSE 1.3 56.2 + - - +
525H GLU* 4.9 1.6 - - - -
526H ASP* 2.8 51.6 + - - +
527H CYS* 3.3 4.6 + - - -
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Residues in contact with MSE 523 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505H MSE 6.0 3.1 - - - -
515H LEU* 4.9 8.1 - - + +
518H VAL* 3.6 39.9 - - + +
519H SER 3.2 11.8 + - - +
520H GLU* 3.6 9.9 - - - +
521H GLN 3.2 0.2 - - - -
522H GLN* 1.3 76.3 - - - +
524H LEU* 1.3 57.9 + - - +
527H CYS* 3.4 14.0 + - - +
528H GLY 3.0 11.8 + - - -
529H ILE* 3.0 44.5 + - + -
535H ARG* 3.9 35.9 - - - +
538H ILE* 4.1 17.5 - - + +
539H LEU* 4.1 24.2 - - + -
542H ALA* 5.4 1.3 - - + -
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Residues in contact with LEU 524 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520H GLU 3.2 13.0 + - - +
521H GLN* 3.2 12.1 + - + +
523H MSE 1.3 80.8 - - - +
525H GLU* 1.3 70.5 + - + +
528H GLY* 3.6 13.3 + - - -
529H ILE 3.8 9.6 - - - +
530H HIS* 4.1 23.3 + - + +
535H ARG* 3.8 32.7 - - - +
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Residues in contact with GLU 525 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A LEU* 5.5 0.2 - - - +
532A GLY* 5.7 1.2 + - - -
535A ARG* 4.9 10.7 + - - -
521H GLN* 2.4 60.7 + - + +
522H GLN* 5.4 0.7 - - - -
524H LEU* 1.3 81.9 - - + +
526H ASP* 1.3 73.1 + - - +
528H GLY* 5.0 0.5 + - - -
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Residues in contact with ASP 526 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A HIS 4.1 3.3 - - - +
531A LEU* 3.6 29.6 - - + +
532A GLY* 2.9 35.6 + - - -
533A VAL* 3.1 22.9 + - + -
504H GLY 4.2 2.9 - - - +
508H CYS* 4.2 9.8 - - - +
522H GLN* 2.8 33.2 + - - +
525H GLU* 1.3 87.2 - - - +
527H CYS* 1.3 61.1 + - - +
528H GLY 3.6 0.7 - - - -
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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