Contacts of the helix formed by residues 501 - 508 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474G LYS* 6.0 2.7 - - - -
491G LEU* 4.0 2.2 - - - -
498G PHE* 3.6 26.2 - + - +
499G ARG 3.1 1.2 - - - -
500G GLN* 1.3 103.6 + - + +
502G THR* 1.3 63.4 + - - +
503G TYR 3.5 0.9 - - - -
504G GLY* 3.4 5.3 + - - +
505G MSE 3.1 41.9 + - + +
527G CYS 5.3 3.5 - - - +
528G GLY 4.3 7.9 - - - -
529G ILE* 3.6 44.3 - - + +
530G HIS 4.9 1.4 + - - -
531G LEU* 4.6 7.8 + - - +
534G HIS* 2.6 39.6 + + + +
538G ILE* 4.0 17.7 - - + -
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Residues in contact with THR 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479G TYR* 3.6 33.7 - - + -
483G ASP* 3.8 20.6 - - - +
487G LEU* 4.9 2.0 - - + -
488G ALA* 3.4 26.3 - - + +
491G LEU* 3.8 10.3 - - - +
499G ARG* 2.7 22.7 + - - +
500G GLN 3.1 2.6 - - - -
501G TYR* 1.3 78.6 - - - +
503G TYR* 1.3 59.7 + - - +
505G MSE 3.2 2.6 + - - +
506G VAL* 2.9 41.5 + - + +
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Residues in contact with TYR 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410G PRO* 3.7 32.0 + - + +
441G ASP* 2.5 39.9 + - - +
444G LEU* 3.6 44.2 - - + +
445G ARG* 4.1 13.5 - - + -
474G LYS* 6.0 2.2 - - + -
479G TYR* 4.0 16.1 - + + +
482G CYS* 4.1 18.8 - - + -
500G GLN 4.3 4.2 + - - +
501G TYR 3.5 0.2 - - - -
502G THR* 1.3 80.4 - - - +
504G GLY* 1.3 58.4 + - - +
506G VAL* 3.7 6.4 - - + +
507G SER* 2.8 57.2 + - - -
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Residues in contact with GLY 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445G ARG* 6.3 1.8 - - - -
500G GLN 5.0 1.4 + - - -
501G TYR* 3.4 8.1 + - - +
502G THR 3.2 0.8 - - - -
503G TYR* 1.3 81.2 - - - +
505G MSE 1.3 61.4 + - - +
507G SER* 3.6 8.5 + - - -
508G CYS* 3.2 18.9 + - - +
526G ASP 4.3 2.5 - - - +
527G CYS* 3.8 24.9 - - - -
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Residues in contact with MSE 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487G LEU* 3.8 26.9 - - + -
491G LEU* 3.6 29.4 - - + -
501G TYR* 3.1 30.0 + - + +
502G THR* 3.9 0.7 - - - +
504G GLY* 1.3 72.5 - - - +
506G VAL* 1.3 65.4 + - - +
507G SER 3.5 0.2 + - - -
508G CYS* 3.5 13.8 - - - -
510G LEU* 3.0 39.4 + - + +
515G LEU* 4.3 17.0 - - - -
523G MSE 5.9 2.2 - - + -
527G CYS* 4.1 16.6 - - + -
529G ILE* 3.5 28.9 - - + -
538G ILE* 3.7 12.1 - - + -
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Residues in contact with VAL 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482G CYS* 3.2 41.1 - - + +
483G ASP* 4.1 31.6 - - + +
487G LEU* 4.5 10.8 - - + -
502G THR* 2.9 25.2 + - + +
503G TYR* 4.0 8.7 - - + +
505G MSE 1.3 76.8 - - - +
507G SER* 1.3 64.0 + - - +
509G GLY* 3.2 11.6 + - - -
510G LEU 4.2 10.5 - - - +
497H ARG* 3.3 16.8 + - - +
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Residues in contact with SER 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441G ASP* 4.9 0.5 + - - -
445G ARG* 4.6 11.8 - - - -
503G TYR* 2.8 49.4 + - - -
504G GLY* 3.9 6.7 - - - -
505G MSE 3.3 0.4 - - - -
506G VAL* 1.3 78.3 - - - +
508G CYS* 1.3 56.8 + - - +
509G GLY 3.3 0.4 - - - -
497H ARG* 2.7 32.4 + - - +
531H LEU* 5.1 3.0 - - - +
534H HIS* 5.0 1.0 + - - -
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Residues in contact with CYS 508 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504G GLY 3.2 18.6 - - - +
505G MSE 3.5 9.0 - - - -
507G SER* 1.3 75.9 - - - +
509G GLY* 1.3 60.2 + - - +
510G LEU* 3.6 6.1 + - - +
526G ASP 4.2 8.5 - - - +
527G CYS* 3.8 23.8 - - - -
497H ARG* 4.7 0.2 - - - -
531H LEU* 3.9 20.2 - - + -
533H VAL* 3.6 29.3 - - + +
534H HIS* 3.3 26.7 + - - -
537H ARG* 5.0 2.1 + - - -
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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