Contacts of the helix formed by residues 501 - 508 (chain B) 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 TYR 501 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474B LYS* 6.0 2.7 - - - -
491B LEU* 4.1 2.5 - - - -
498B PHE* 3.6 26.5 - + - +
499B ARG 3.2 1.0 - - - -
500B GLN* 1.3 105.2 + - + +
502B THR* 1.3 63.0 + - - +
503B TYR 3.5 0.7 - - - -
504B GLY* 3.4 5.1 + - - +
505B MSE 3.2 40.6 + - + +
527B CYS 5.2 3.9 - - - +
528B GLY 4.3 8.3 - - - -
529B ILE* 3.7 43.3 - - + +
530B HIS 5.0 1.0 + - - -
531B LEU* 4.6 8.5 + - - +
534B HIS* 2.7 38.8 + - + +
538B ILE* 4.1 17.7 - - + -
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Residues in contact with THR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B TYR* 3.7 33.2 - - + -
483B ASP* 3.9 11.2 - - - +
487B LEU* 4.7 2.9 - - + -
488B ALA* 3.3 33.2 - - + +
491B LEU* 3.7 11.5 - - - +
499B ARG 2.7 22.5 + - - -
500B GLN 3.1 2.4 - - - -
501B TYR* 1.3 77.3 - - - +
503B TYR* 1.3 63.9 + - - +
505B MSE 3.2 4.4 + - - +
506B VAL* 2.9 33.8 + - + +
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Residues in contact with TYR 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B PRO* 3.8 30.0 + - + +
441B ASP* 2.3 41.9 + - - +
444B LEU* 3.6 42.0 - - + +
445B ARG* 3.7 17.9 - - + -
474B LYS* 5.7 2.2 - - + -
479B TYR* 3.9 19.7 - + + +
482B CYS* 4.2 17.0 - - + -
500B GLN 4.3 4.2 + - - +
501B TYR 3.5 0.2 - - - -
502B THR* 1.3 79.7 - - - +
504B GLY* 1.3 57.6 + - - +
506B VAL* 3.8 6.5 - - + -
507B SER* 2.8 56.7 + - - -
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Residues in contact with GLY 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B LEU 5.9 0.6 + - - -
445B ARG* 6.1 2.2 - - - -
500B GLN 5.0 1.2 + - - -
501B TYR* 3.4 7.5 + - - +
502B THR 3.2 1.0 - - - -
503B TYR* 1.3 81.3 - - - +
505B MSE 1.3 60.6 + - - +
507B SER* 3.6 9.5 + - - -
508B CYS* 3.3 17.6 + - - -
526B ASP 4.2 2.9 - - - +
527B CYS* 3.8 24.7 - - - -
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Residues in contact with MSE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B LEU* 3.8 26.7 - - + -
491B LEU* 3.6 33.0 - - + -
501B TYR* 3.2 26.0 + - + +
502B THR 3.9 1.1 - - - +
504B GLY* 1.3 72.6 - - - +
506B VAL* 1.3 64.9 + - - +
508B CYS* 3.3 17.8 + - - -
510B LEU* 3.0 35.7 + - + +
515B LEU* 4.4 17.3 - - - -
523B MSE 5.9 2.9 - - + -
527B CYS* 4.0 16.8 - - + -
529B ILE* 3.5 28.3 - - + -
538B ILE* 3.9 11.9 - - + -
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Residues in contact with VAL 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B CYS* 3.2 39.9 - - + +
483B ASP* 4.0 24.2 - - + +
487B LEU* 4.4 8.5 - - + -
502B THR* 2.9 31.2 + - + +
503B TYR* 4.1 7.6 - - + +
505B MSE 1.3 77.6 - - - +
507B SER* 1.3 61.8 + - - +
509B GLY* 3.1 13.5 + - - -
510B LEU 4.1 15.5 - - - +
497C ARG* 5.5 3.5 + - - -
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Residues in contact with SER 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B ARG* 4.2 13.9 - - - -
503B TYR* 2.8 49.8 + - - -
504B GLY* 3.8 6.7 - - - -
505B MSE 3.2 0.4 - - - -
506B VAL* 1.3 78.0 - - - +
508B CYS* 1.3 57.0 + - - +
509B GLY 3.3 2.2 + - - -
497C ARG* 4.7 20.5 + - - +
531C LEU* 5.1 3.3 - - - +
534C HIS* 5.2 1.7 + - - -
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Residues in contact with CYS 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B GLY 3.3 18.6 - - - +
505B MSE 3.3 16.8 - - - -
507B SER* 1.3 76.6 - - - +
509B GLY* 1.3 60.6 + - - +
510B LEU* 3.5 6.7 + - - +
526B ASP 4.2 8.1 - - - +
527B CYS* 3.9 18.6 - - - -
497C ARG* 6.2 0.2 - - - -
531C LEU* 4.0 20.0 - - + -
533C VAL* 3.6 29.0 - - + +
534C HIS* 3.3 26.6 + - - -
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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