Contacts of the helix formed by residues 509 - 516 (chain C) in PDB entry 3UOA
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 GLY 509 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361C ALA* 3.7 3.6 - - - +
365C ASP* 2.9 24.6 + - - -
462C ASP* 5.5 2.2 - - - -
499C PHE 3.9 8.1 - - - -
500C GLU* 3.9 17.3 - - - -
508C ASN* 1.3 77.2 - - - +
510C ILE* 1.3 62.0 + - - -
511C PHE 3.4 2.2 - - - -
512C MET 3.5 2.4 + - - -
513C LYS* 2.9 24.8 + - - +
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Residues in contact with ILE 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C ASP* 5.7 0.2 + - - -
499C PHE* 3.0 26.6 + - + +
500C GLU* 4.7 1.8 - - - +
501C ILE* 4.4 25.1 - - + -
509C GLY* 1.3 71.9 - - - -
511C PHE* 1.3 63.3 + - - +
513C LYS* 3.3 16.1 + - + +
514C PHE* 3.1 39.9 - - + -
536C MET* 4.2 13.9 - - + -
539C CYS* 4.1 18.4 - - - -
541C LEU* 4.7 6.7 - - + -
542C THR* 3.8 24.0 - - + +
546C GLN* 3.7 21.3 - - - +
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Residues in contact with PHE 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C TYR* 4.1 15.0 - + - -
460C LEU* 4.1 21.3 - - + -
462C ASP* 3.5 34.7 + - + +
489C GLY 4.1 18.4 - - - -
491C ALA* 3.6 30.7 - - + -
499C PHE 4.8 0.4 + - - -
509C GLY 3.4 0.4 - - - -
510C ILE* 1.3 78.2 - - - +
512C MET* 1.3 58.4 + - - +
514C PHE* 3.2 5.0 + - - +
515C LEU* 2.8 59.4 + - + +
529C LEU* 4.7 2.5 - - + -
532C VAL* 4.6 1.8 - - + -
536C MET* 4.1 11.2 - - + -
546C GLN* 4.2 2.5 - - - +
548C LEU* 3.7 31.4 - - + -
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Residues in contact with MET 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C ASP* 3.4 34.3 - - - +
368C GLU* 5.1 3.1 - - + +
369C LEU* 3.8 36.6 - - + -
372C LEU* 5.4 0.2 - - - -
411C TYR* 3.4 40.4 - - + +
462C ASP* 4.2 0.8 + - - -
508C ASN* 3.7 17.9 - - + +
509C GLY 3.5 1.4 + - - -
510C ILE 3.4 0.2 - - - -
511C PHE* 1.3 77.4 - - + +
513C LYS* 1.3 66.5 + - - +
515C LEU* 4.0 22.4 - - + -
516C LYS* 3.0 40.8 + - + +
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Residues in contact with LYS 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C ILE* 5.5 7.6 - - + -
508C ASN* 3.7 15.8 - - + +
509C GLY 2.9 19.4 + - - +
510C ILE* 3.4 17.7 - - + +
511C PHE 3.2 0.4 - - - -
512C MET* 1.3 77.5 - - - +
514C PHE* 1.3 95.0 + - + +
516C LYS* 3.5 17.3 - - - +
517C ASP* 4.1 9.9 - - - +
539C CYS* 5.2 5.4 - - - -
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Residues in contact with PHE 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510C ILE* 3.1 28.3 - - + -
511C PHE 3.2 4.2 + - - +
512C MET 3.0 0.2 - - - -
513C LYS* 1.3 111.3 - - + +
515C LEU* 1.3 66.1 + - - +
516C LYS 3.2 1.9 + - - -
517C ASP* 3.3 14.9 + - - +
518C ARG* 3.8 14.2 + - - +
532C VAL* 3.9 19.7 - - + +
535C ASP* 3.7 37.2 - - + +
536C MET* 4.0 16.8 - - + -
538C LYS 5.4 0.4 - - - -
539C CYS* 3.7 32.5 - - + -
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Residues in contact with LEU 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C LEU* 4.5 3.1 - - + -
460C LEU* 4.1 18.2 - - + -
511C PHE* 2.8 48.5 + - + +
512C MET* 4.0 25.1 - - + -
514C PHE* 1.3 76.8 - - - +
516C LYS* 1.3 62.2 + - - +
518C ARG* 3.0 13.0 + - - -
519C LEU* 3.0 37.9 + - + +
528C LEU* 4.1 6.1 - - + -
529C LEU* 4.1 20.4 - - + -
532C VAL* 3.9 21.6 - - + +
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Residues in contact with LYS 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C GLU* 2.9 39.1 + - + +
372C LEU* 3.7 37.2 - - + +
508C ASN* 3.2 23.2 - - - +
512C MET* 3.0 26.8 + - + +
513C LYS* 3.5 14.4 - - - +
515C LEU* 1.3 77.7 - - - +
517C ASP* 1.3 72.9 + - - +
518C ARG 3.5 0.7 + - - -
519C LEU* 4.0 4.2 + - - +
520C LEU* 5.2 3.3 + - - +
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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