Contacts of the helix formed by residues 505 - 511 (chain B) in PDB entry 5OQN
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 505 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A PHE* 3.4 9.0 - - - -
395B ASP* 3.4 15.3 - - - -
503B HIS* 2.9 12.5 + - - -
504B PHE* 1.3 73.7 - - - +
506B THR* 1.3 65.8 + - - +
507B ASP* 3.1 15.1 + - - +
508B ARG* 3.2 19.1 + - - +
509B ILE* 3.4 14.9 - - - +
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Residues in contact with THR 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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749A PHE* 3.4 15.7 - - - -
391B MET* 3.2 49.3 - - + +
394B PHE* 5.6 2.6 - - - -
395B ASP* 2.8 33.2 + - - +
505B SER* 1.3 75.3 - - - +
507B ASP* 1.3 61.3 + - + +
509B ILE* 3.5 5.0 + - - +
510B THR* 3.1 30.1 + - - +
523B PHE* 4.3 11.3 - - - -
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Residues in contact with ASP 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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391B MET* 5.1 7.6 - - + +
505B SER* 3.1 10.3 + - - +
506B THR* 1.3 80.5 - - + +
508B ARG* 1.3 65.9 + - - +
509B ILE 3.0 4.4 + - - -
510B THR* 2.9 20.5 + - - -
511B ARG* 3.1 52.8 + - - +
519B LYS* 3.6 14.0 + - - -
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Residues in contact with ARG 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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704A VAL* 5.8 2.6 - - - +
708A GLU* 3.5 26.3 + - - +
712A LYS* 5.8 0.2 - - - -
502B PHE* 2.9 43.9 + - - +
503B HIS 4.4 4.9 - - - +
504B PHE* 4.4 27.1 - - + -
505B SER* 3.2 21.5 + - - +
507B ASP* 1.3 81.6 + - - +
509B ILE* 1.3 60.0 + - + +
511B ARG* 4.1 12.9 - - - +
513B PHE* 5.6 1.7 - - - -
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Residues in contact with ILE 509 (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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708A GLU* 3.6 33.2 - - + +
711A CYS* 6.2 0.2 - - + -
712A LYS* 3.4 40.6 - - + +
715A LEU* 6.0 3.8 - - + -
749A PHE* 4.3 16.4 - - + -
750A CYS* 4.2 18.4 - - - -
753A VAL* 6.4 2.0 - - + -
504B PHE* 4.0 18.2 - - + -
505B SER 3.4 15.9 + - - +
506B THR* 4.0 8.1 - - - +
507B ASP 3.0 0.8 - - - -
508B ARG* 1.3 79.0 - - - +
510B THR* 1.3 66.9 + - + +
511B ARG 3.4 1.1 - - - +
522B LEU* 4.6 19.4 - - + +
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Residues in contact with THR 510 (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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387B GLU* 6.3 2.2 - - + -
391B MET* 4.3 21.1 - - + +
506B THR* 3.1 20.7 + - - +
507B ASP* 2.9 19.1 + - - -
509B ILE* 1.3 79.5 - - + +
511B ARG* 1.3 58.1 + - - +
519B LYS* 3.2 25.3 + - - +
520B MET* 3.0 36.1 + - - +
522B LEU* 3.7 30.3 - - + +
523B PHE* 5.5 1.1 - - + -
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Residues in contact with ARG 511 (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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712A LYS* 3.7 10.4 + - - -
507B ASP* 3.1 47.2 + - - +
508B ARG* 4.1 11.6 - - - +
509B ILE 3.4 3.3 - - - +
510B THR* 1.3 78.7 - - - +
512B LEU* 1.3 71.1 + - - +
513B PHE* 5.2 1.4 - - - -
516B PRO* 3.0 36.6 + - + +
517B GLY* 4.8 5.9 + - - -
518B GLN 3.7 6.1 - - - -
519B LYS* 3.6 22.8 - - - +
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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