Contacts of the helix formed by residues 501 - 508 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D LYS* 6.1 1.3 - - - -
491D LEU* 4.0 8.3 - - + -
497D ARG 4.3 0.7 - - - -
498D PHE* 3.5 33.7 - + - +
499D ARG 3.1 1.2 - - - -
500D GLN* 1.3 100.7 + - + +
502D THR* 1.3 63.7 + - - +
503D TYR 3.5 0.9 - - - -
504D GLY* 3.5 5.2 + - - +
505D MSE 3.2 26.1 + - + +
527D CYS 5.2 2.8 - - - +
528D GLY 4.4 8.3 - - - -
529D ILE* 3.7 54.3 - - + +
530D HIS 5.0 1.4 + - - -
531D LEU* 4.6 7.8 + - - +
534D HIS* 2.6 38.5 + - + -
538D ILE* 4.1 10.3 - - + -
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Residues in contact with THR 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D TYR* 3.8 26.0 - - + -
483D ASP* 3.9 12.3 - - - +
487D LEU* 4.7 2.5 - - + -
488D ALA* 3.2 40.2 - - + +
491D LEU* 3.8 11.2 - - - +
499D ARG 2.7 22.5 + - - -
500D GLN 3.1 2.4 - - - -
501D TYR* 1.3 76.9 - - - +
503D TYR* 1.3 60.1 + - - +
505D MSE 3.1 4.1 + - - +
506D VAL* 2.8 43.4 + - + +
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Residues in contact with TYR 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D PRO* 3.9 30.5 + - + +
441D ASP* 2.4 45.5 + - - +
444D LEU* 3.6 41.1 - - + +
445D ARG* 3.9 17.5 - - + -
474D LYS* 6.0 1.3 - - + -
479D TYR* 4.2 11.5 - + + +
482D CYS* 4.3 17.0 - - + -
500D GLN 4.2 4.9 + - - +
501D TYR 3.5 0.2 - - - -
502D THR* 1.3 80.6 - - - +
504D GLY* 1.3 58.2 + - - +
506D VAL* 3.8 6.6 - - + +
507D SER* 2.8 56.6 + - - -
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Residues in contact with GLY 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D ARG* 6.2 2.0 - - - -
500D GLN 4.9 1.2 + - - -
501D TYR* 3.5 7.5 + - - +
502D THR 3.2 0.6 - - - -
503D TYR* 1.3 81.5 - - - +
505D MSE 1.3 60.6 + - - +
507D SER* 3.9 7.7 + - - -
508D CYS* 3.4 16.1 + - - +
526D ASP 4.0 3.7 - - - +
527D CYS* 3.7 28.5 - - - -
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Residues in contact with MSE 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D LEU* 4.0 21.1 - - + -
491D LEU* 4.0 29.8 - - - -
501D TYR* 3.2 15.2 + - + +
502D THR 3.1 4.0 + - - +
504D GLY* 1.3 72.6 - - - +
506D VAL* 1.3 68.2 + - - +
507D SER 3.2 1.3 - - - -
508D CYS* 3.2 16.7 - - - -
510D LEU* 3.1 31.1 + - + +
515D LEU* 4.1 20.9 - - + -
518D VAL* 5.2 0.7 - - + -
523D MSE 4.3 15.7 - - + -
527D CYS* 3.8 19.5 - - + -
529D ILE* 3.8 24.9 - - + -
538D ILE* 4.3 14.8 - - + -
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Residues in contact with VAL 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D CYS* 3.3 41.1 - - + +
483D ASP* 4.1 22.7 - - + +
487D LEU* 4.7 7.2 - - + -
502D THR* 2.8 35.2 + - + +
503D TYR* 4.1 7.4 - - + +
505D MSE 1.3 77.5 - - - +
507D SER* 1.3 63.6 + - - +
509D GLY* 3.1 9.9 + - - -
510D LEU 4.2 14.8 - - - +
497E ARG* 3.6 18.8 + - - +
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Residues in contact with SER 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D ASP* 5.1 0.2 + - - -
445D ARG* 4.6 10.1 - - - -
503D TYR* 2.8 48.4 + - - -
504D GLY* 4.0 7.4 - - - -
505D MSE 3.2 0.4 - - - -
506D VAL* 1.3 78.2 - - - +
508D CYS* 1.3 56.4 + - - +
509D GLY 3.2 2.7 + - - -
497E ARG* 4.1 16.1 + - - +
531E LEU* 5.0 3.4 - - - +
534E HIS* 5.0 1.4 + - - -
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Residues in contact with CYS 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D GLY 3.4 14.4 - - - -
505D MSE 3.2 21.3 - - - -
507D SER* 1.3 75.9 - - - +
509D GLY* 1.3 60.5 + - - +
510D LEU* 3.4 14.8 + - - +
526D ASP 4.6 5.2 - - - +
527D CYS* 3.8 17.7 - - - -
531E LEU* 3.9 21.5 - - + -
533E VAL* 3.6 25.5 - - + +
534E HIS* 3.2 26.0 + - - -
537E ARG* 5.6 2.8 + - - -
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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