Contacts of the helix formed by residues 416 - 427 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ALA 3.0 13.0 + - - -
413B VAL 3.7 3.6 - - - -
415B ILE* 1.3 78.7 - - - +
417B LEU* 1.3 59.1 + - - -
418B PRO* 3.7 1.6 - - - -
419B PHE* 3.7 24.8 + - - +
420B LEU* 3.3 31.4 + - - +
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Residues in contact with LEU 417 (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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413B VAL* 3.3 35.5 + - + +
414B ALA 4.4 0.7 - - - +
415B ILE 3.3 1.4 + - - -
416B GLY* 1.3 71.5 - - - +
418B PRO* 1.4 70.3 - - + +
419B PHE 3.2 1.3 - - - -
420B LEU* 3.4 6.5 + - + +
421B ALA* 3.0 26.9 + - - +
445B ALA* 4.5 8.1 - - + +
448B ALA* 4.8 1.6 - - + -
449B SER* 4.1 22.2 - - - +
452B ILE* 3.8 28.7 - - + -
501B TRP* 5.3 2.0 - - + -
761B PRO* 4.3 17.7 - - + -
763B PRO* 5.0 3.1 - - + -
764B PHE* 3.6 25.8 - - + -
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Residues in contact with PRO 418 (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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414B ALA 5.8 0.2 - - - +
415B ILE 4.3 7.2 - - - +
416B GLY* 4.0 1.3 - - - -
417B LEU* 1.4 91.3 - - + +
419B PHE* 1.3 66.6 + - + +
421B ALA* 3.5 1.9 - - + +
422B LEU* 2.9 33.6 + - + +
425B TRP* 5.5 0.9 - - - -
764B PHE* 3.9 25.6 - - + -
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Residues in contact with PHE 419 (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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415B ILE* 4.8 5.8 - - + -
416B GLY* 3.7 28.7 - - - +
417B LEU 3.2 0.6 - - - -
418B PRO* 1.3 86.4 - - + +
420B LEU* 1.3 59.0 + - + +
422B LEU* 3.2 13.3 + - + +
423B ILE* 2.9 35.4 + - + +
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Residues in contact with LEU 420 (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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413B VAL* 3.8 36.3 - - + -
416B GLY 3.3 20.3 + - - +
417B LEU* 3.4 6.8 + - + +
419B PHE* 1.3 75.1 - - + +
421B ALA* 1.3 61.2 + - - +
423B ILE* 3.5 15.5 - - + +
424B TYR* 2.9 23.7 + - - +
432B MET* 4.0 21.5 - - + -
436B MET* 3.4 40.9 - - + +
441B MET* 5.9 2.9 - - + -
760B LEU* 5.0 0.7 - - - -
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Residues in contact with ALA 421 (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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417B LEU 3.0 18.3 + - - +
418B PRO 3.5 6.1 - - - +
419B PHE 3.2 0.2 - - - -
420B LEU* 1.3 76.4 - - - +
422B LEU* 1.3 56.7 + - - +
424B TYR* 3.4 2.6 + - - +
425B TRP* 2.9 39.3 + - + +
760B LEU* 3.8 18.9 - - + +
764B PHE* 3.7 38.6 - - + -
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Residues in contact with LEU 422 (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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418B PRO* 2.9 20.3 + - + +
419B PHE* 3.2 13.0 + - + +
421B ALA* 1.3 73.0 - - - +
423B ILE* 1.3 60.2 + - + +
425B TRP* 3.6 24.1 - - + +
426B PHE* 2.9 70.4 + - + +
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Residues in contact with ILE 423 (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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419B PHE* 2.9 21.0 + - + +
420B LEU* 3.5 26.7 - - + +
421B ALA 3.3 0.2 - - - -
422B LEU* 1.3 76.6 - - - +
424B TYR* 1.3 63.6 + - - +
427B ALA* 2.9 43.5 + - + +
430B SER* 6.1 1.1 - - - -
432B MET* 4.1 29.4 - - + -
433B GLY* 4.7 5.6 - - - +
436B MET* 4.7 6.7 - - + -
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Residues in contact with TYR 424 (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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420B LEU 2.9 15.8 + - - +
421B ALA 3.9 3.1 - - - +
423B ILE* 1.3 79.2 - - - +
425B TRP* 1.3 65.9 + + - +
427B ALA 4.9 0.7 - - - -
428B PRO* 3.4 25.3 - - + +
433B GLY* 4.7 12.8 - - - -
436B MET* 3.7 17.3 - - + -
437B ARG* 3.4 44.0 + - + -
757B GLY 5.2 0.7 + - - -
759B THR* 3.4 41.3 + - + -
760B LEU* 3.7 31.0 - - + -
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Residues in contact with TRP 425 (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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418B PRO 5.5 0.7 - - - -
421B ALA* 2.9 25.8 + - + +
422B LEU* 3.6 28.5 - - + +
423B ILE 3.3 0.2 - - - -
424B TYR* 1.3 81.7 - + - +
426B PHE* 1.3 78.0 + + + +
428B PRO* 4.3 4.5 - - - +
760B LEU* 3.5 23.5 - - + +
764B PHE* 3.6 42.9 + + + -
767B VAL* 3.6 48.2 - - + +
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Residues in contact with PHE 426 (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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422B LEU* 2.9 42.8 + - + +
425B TRP* 1.3 88.9 - + + +
427B ALA* 1.3 61.5 + - + +
428B PRO* 3.4 8.2 - - - +
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Residues in contact with ALA 427 (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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422B LEU 4.3 0.2 + - - -
423B ILE* 2.9 27.9 + - + +
426B PHE* 1.3 81.0 - - + +
428B PRO* 1.3 64.7 - - - +
430B SER* 3.5 18.1 + - - +
433B GLY* 4.9 1.7 - - - -
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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