Contacts of the helix formed by residues 416 - 427 (chain C) in PDB entry 6UZA
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 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C ALA 3.0 13.7 + - - -
413C VAL 3.7 4.0 - - - -
415C ILE* 1.3 79.1 - - - +
417C LEU* 1.3 59.8 + - - -
418C PRO* 3.7 1.6 - - - -
419C PHE* 3.7 24.8 + - - +
420C LEU* 3.3 30.3 + - - +
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Residues in contact with LEU 417 (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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413C VAL* 3.3 35.1 + - + +
414C ALA 4.4 0.4 - - - +
415C ILE 3.3 1.4 + - - -
416C GLY* 1.3 72.8 - - - +
418C PRO* 1.4 68.9 - - + +
419C PHE 3.2 2.2 + - - -
420C LEU* 3.4 6.4 + - + +
421C ALA* 3.0 26.3 + - - +
445C ALA* 4.5 8.3 - - + +
448C ALA* 4.8 1.8 - - + -
449C SER* 4.1 21.1 - - - +
452C ILE* 3.8 29.6 - - + -
501C TRP* 5.3 2.0 - - + -
761C PRO* 4.3 17.9 - - + -
763C PRO* 5.0 3.4 - - + -
764C PHE* 3.6 26.2 - - + -
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Residues in contact with PRO 418 (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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415C ILE 4.3 7.6 - - - +
416C GLY* 4.0 1.3 - - - -
417C LEU* 1.4 92.3 - - + +
419C PHE* 1.3 67.6 + - + +
421C ALA* 3.5 2.7 - - + +
422C LEU* 2.9 32.9 + - + +
425C TRP* 5.5 0.5 - - - -
452C ILE* 6.3 0.2 - - + -
764C PHE* 3.9 24.5 - - + -
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Residues in contact with PHE 419 (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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415C ILE* 4.8 5.8 - - + -
416C GLY* 3.7 28.5 - - - +
417C LEU 3.2 1.0 - - - -
418C PRO* 1.3 85.6 - - + +
420C LEU* 1.3 59.2 + - + +
422C LEU* 3.2 12.8 + - + +
423C ILE* 2.9 34.9 + - + +
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Residues in contact with LEU 420 (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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412C ALA 5.6 0.2 - - - +
413C VAL* 3.8 35.7 - - + -
416C GLY 3.3 19.9 + - - +
417C LEU* 3.4 6.8 + - + +
419C PHE* 1.3 74.8 - - + +
421C ALA* 1.3 60.2 + - - +
423C ILE* 3.3 15.8 + - + +
424C TYR* 2.9 23.2 + - - +
432C MET* 4.0 21.5 - - + -
436C MET* 3.4 40.5 - - + +
441C MET* 5.9 3.1 - - + -
760C LEU* 5.0 0.4 - - - -
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Residues in contact with ALA 421 (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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417C LEU 3.0 17.2 + - - +
418C PRO 3.5 5.8 - - - +
419C PHE 3.2 0.2 - - - -
420C LEU* 1.3 77.2 - - - +
422C LEU* 1.3 56.5 + - - +
424C TYR* 3.4 2.1 + - - +
425C TRP* 2.9 40.9 + - + +
760C LEU* 3.8 17.8 - - + +
761C PRO* 6.1 0.2 - - + -
764C PHE* 3.7 38.6 - - + -
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Residues in contact with LEU 422 (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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418C PRO* 2.9 19.8 + - + +
419C PHE* 3.2 13.7 + - + +
421C ALA* 1.3 73.2 - - - +
423C ILE* 1.3 59.8 + - - +
425C TRP* 3.6 23.6 - - + +
426C PHE* 2.9 69.2 + - + +
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Residues in contact with ILE 423 (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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419C PHE* 2.9 20.2 + - + +
420C LEU* 3.5 26.0 - - + +
421C ALA 3.3 0.2 - - - -
422C LEU* 1.3 76.3 - - + +
424C TYR* 1.3 62.0 + - - +
427C ALA* 2.9 44.3 + - + +
430C SER* 6.1 1.6 - - - -
432C MET* 4.1 28.9 - - + -
433C GLY* 4.7 5.8 - - - +
436C MET* 4.7 6.3 - - + -
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Residues in contact with TYR 424 (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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420C LEU 2.9 16.9 + - - +
421C ALA 3.9 3.4 - - - +
423C ILE* 1.3 78.9 - - - +
425C TRP* 1.3 64.7 + + - +
427C ALA 4.9 1.1 - - - -
428C PRO* 3.4 23.5 - - + +
433C GLY* 4.7 13.0 - - - -
436C MET* 3.7 17.5 - - + -
437C ARG* 3.4 44.1 + - + -
757C GLY 5.2 0.5 + - - -
759C THR* 3.4 39.8 + - + -
760C LEU* 3.7 30.7 - - + -
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Residues in contact with TRP 425 (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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418C PRO 5.5 0.4 - - - -
421C ALA* 2.9 26.2 + - + +
422C LEU* 3.6 27.6 - - + +
423C ILE 3.3 0.4 - - - -
424C TYR* 1.3 82.8 - + - +
426C PHE* 1.3 75.1 + + + +
428C PRO* 4.3 4.5 - - - +
760C LEU* 3.5 22.7 - - + +
764C PHE* 3.6 42.9 + + + -
767C VAL* 3.6 47.6 - - + +
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Residues in contact with PHE 426 (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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422C LEU* 2.9 41.9 + - + +
425C TRP* 1.3 89.9 - + + +
427C ALA* 1.3 61.2 + - + +
428C PRO* 3.4 8.4 - - - +
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Residues in contact with ALA 427 (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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422C LEU 4.3 0.2 + - - -
423C ILE* 2.9 28.6 + - + +
426C PHE* 1.3 81.0 - - + +
428C PRO* 1.3 65.9 - - - +
430C SER* 3.5 17.1 + - - +
433C GLY* 4.9 0.9 - - - -
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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