Contacts of the helix formed by residues 450 - 457 (chain C) in PDB entry 5Q14
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 HIS 450 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365C TYR* 3.7 25.3 + + + -
446C THR 4.2 7.3 + - - +
447C PHE 3.8 4.1 + - - -
448C ASN 3.3 0.2 - - - -
449C HIS* 1.3 97.6 + - + +
451C HIS* 1.3 63.7 + - - +
452C ALA 3.4 2.5 - - - -
453C GLU* 2.8 32.4 + - - +
454C MET* 2.9 25.0 + - - +
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Residues in contact with HIS 451 (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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329C VAL* 3.5 36.7 - - + +
332C MET* 4.9 2.5 - - + -
333C PHE* 3.9 8.3 - + - -
447C PHE 3.4 16.9 + - - +
448C ASN* 3.6 11.6 + - - +
450C HIS* 1.3 76.9 - - - +
452C ALA* 1.3 62.2 + - - +
454C MET* 3.4 29.5 - - + +
455C LEU* 3.2 46.3 + - + +
473C TRP* 3.2 53.6 + + + -
501C 9MM 4.3 8.5 - - + -
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Residues in contact with ALA 452 (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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448C ASN 5.2 0.6 + - - -
450C HIS 3.4 0.4 - - - -
451C HIS* 1.3 77.8 - - - +
453C GLU* 1.4 59.4 + - + +
455C LEU* 3.4 11.7 + - - +
456C MET* 3.0 37.2 + - + +
473C TRP 4.9 6.7 - - - +
474C ASP 5.3 3.6 - - - +
475C VAL* 4.3 15.9 - - + -
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Residues in contact with GLU 453 (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 TYR* 3.5 17.4 + - - +
449C HIS 4.4 5.9 - - - +
450C HIS* 2.8 43.3 + - - +
452C ALA* 1.4 78.1 - - + +
454C MET* 1.3 52.4 + - - +
456C MET* 3.6 4.4 + - - +
457C SER* 2.8 38.4 + - - -
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Residues in contact with MET 454 (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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333C PHE* 4.4 0.9 - - + -
361C ILE* 3.8 21.1 - - + +
362C SER* 5.3 0.5 + - - -
365C TYR* 3.6 40.5 - - + -
369C MET* 4.0 11.2 - - + -
450C HIS 2.9 15.6 + - - +
451C HIS* 3.4 37.0 - - + +
453C GLU* 1.3 74.3 - - - +
455C LEU* 1.3 70.7 + - + +
457C SER* 3.1 16.8 + - - -
458C TRP* 3.4 18.3 + - - +
501C 9MM 3.1 33.2 - - + -
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Residues in contact with LEU 455 (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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288C PHE* 3.9 6.2 - - + -
291C LEU* 4.0 23.8 - - + -
451C HIS* 3.2 43.5 + - + +
452C ALA 3.4 4.2 + - - +
454C MET* 1.3 90.5 - - + +
456C MET* 1.3 62.1 + - + +
458C TRP* 3.3 15.6 - - + +
463C HIS* 3.1 19.2 - - - -
465C PHE* 4.0 16.4 - - + -
473C TRP* 3.5 35.7 - - + -
475C VAL* 4.2 16.4 - - + -
501C 9MM 4.4 2.2 - - + -
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Residues in contact with MET 456 (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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452C ALA* 3.0 24.1 + - + +
453C GLU* 4.2 4.3 - - - +
455C LEU* 1.3 75.5 - - + +
457C SER* 1.3 56.7 + - - +
458C TRP 3.4 0.4 - - - -
463C HIS* 2.9 52.0 + - + +
465C PHE* 3.8 29.6 - - + -
475C VAL* 4.7 10.3 - - + -
476C GLN* 5.4 5.4 - - + +
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Residues in contact with SER 457 (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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360C GLY 4.3 1.2 - - - +
362C SER* 3.4 26.2 + - - -
365C TYR* 3.5 9.2 - - - -
453C GLU 2.8 22.0 + - - -
454C MET* 3.1 13.7 + - - -
455C LEU 3.3 0.2 - - - -
456C MET* 1.3 74.1 - - - +
458C TRP* 1.4 64.5 + - - +
459C ARG* 3.4 6.8 + - - +
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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