Contacts of the helix formed by residues 478 - 489 (chain D) in PDB entry 2UZ1
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 TRP 478 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.9 29.4 - - + +
26C HIS* 5.4 3.1 - - + +
46C ASP* 4.9 5.2 + - - +
47C THR 4.1 10.9 + - - -
48C ARG* 4.1 17.3 - - - -
421D MET* 4.7 2.0 - - + -
449D GLY* 3.4 33.4 - - - -
450D SER* 3.8 3.4 - - - -
453D TYR* 3.6 26.9 - + - -
477D SER* 1.3 69.2 - - - +
479D GLY* 1.3 57.3 + - - +
480D ALA 3.7 0.4 - - - -
481D THR* 2.8 32.5 + - - +
482D LEU* 3.0 18.0 + - - +
496D GLY 3.8 18.6 + - - -
497D THR* 2.7 22.0 + - + +
498D ARG 5.0 0.2 - - - -
499D LEU* 3.6 26.0 - - + +
1556D TPP 3.4 50.0 - - + -
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Residues in contact with GLY 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D LEU* 3.5 14.4 - - - -
477D SER* 3.2 15.4 + - - -
478D TRP* 1.3 69.9 - - - +
480D ALA* 1.3 60.5 + - - +
482D LEU* 3.0 5.0 + - - +
483D HIS* 2.8 31.0 + - - -
546D LEU* 3.8 4.3 - - - -
1556D TPP 2.8 26.3 + - - -
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Residues in contact with ALA 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D ALA* 3.4 29.6 - - + -
395D LEU* 3.5 21.2 - - + +
398D LEU* 5.6 2.7 - - + -
479D GLY* 1.3 73.3 - - - +
481D THR* 1.3 57.5 + - - +
483D HIS* 3.4 3.8 + - - +
484D PHE* 2.9 26.0 + - - +
553D GLU* 4.0 8.6 - - - +
1556D TPP 3.0 16.0 + - - +
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Residues in contact with THR 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C HIS* 3.2 35.0 + - + +
27C GLY* 3.9 1.3 - - - -
28C ALA* 3.9 15.3 - - + +
478D TRP* 2.8 32.7 + - - +
480D ALA* 1.3 74.6 - - - +
482D LEU* 1.3 62.0 + - - +
484D PHE* 3.2 8.1 + - - +
485D GLN* 3.1 25.5 + - - +
497D THR* 3.9 3.3 - - - +
1556D TPP 3.5 37.4 - - + +
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Residues in contact with LEU 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477D SER* 3.9 16.6 - - - +
478D TRP 3.0 14.6 + - - +
479D GLY* 3.4 9.9 - - - +
481D THR* 1.3 74.3 - - - +
483D HIS* 1.3 67.5 + - + +
485D GLN* 3.1 6.7 + - - +
486D GLN* 3.0 53.5 + - + +
494D VAL* 3.9 10.3 - - + -
497D THR* 3.5 24.6 - - - +
498D ARG* 3.8 42.0 - - + +
546D LEU* 3.9 15.9 - - + -
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Residues in contact with HIS 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D LEU* 3.5 17.3 - - + +
479D GLY 2.8 16.6 + - - +
480D ALA 3.4 4.5 - - - +
482D LEU* 1.3 76.6 - - + +
484D PHE* 1.3 62.4 + - - +
486D GLN* 3.2 20.5 + - - +
487D LEU* 2.9 36.6 + - + +
546D LEU* 2.8 31.8 + - + +
547D ASP* 4.0 7.4 + - - -
548D PRO 3.1 28.9 - - - -
549D ILE* 4.1 7.0 - - + +
553D GLU* 2.5 42.4 + - - +
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Residues in contact with PHE 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C HIS* 4.9 0.4 - - - -
28C ALA* 3.7 34.3 - - + -
31C ASP* 3.7 35.4 - - + -
163C TRP* 4.1 20.6 - + - -
167C MET* 5.2 5.4 - - - -
1559C MPD 4.2 11.7 - - - -
480D ALA 2.9 14.1 + - - +
481D THR* 3.4 14.4 - - - +
482D LEU 3.2 0.2 - - - -
483D HIS* 1.3 76.0 - - - +
485D GLN* 1.3 60.5 + - + +
487D LEU* 4.9 2.2 - - - -
488D ALA* 2.8 58.3 + - + +
489D VAL* 4.3 4.3 - - + -
553D GLU* 5.0 0.4 + - - -
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Residues in contact with GLN 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C HIS* 3.3 8.4 - - + +
31C ASP* 2.8 31.4 + - - +
35C GLN* 3.6 4.3 - - - +
481D THR 3.1 11.2 + - - +
482D LEU* 3.1 6.1 + - - +
484D PHE* 1.3 77.3 - - + +
486D GLN* 1.3 51.8 + - - +
489D VAL* 3.0 15.6 + - - +
490D GLY 2.8 34.9 + - - +
493D ARG 3.7 14.1 - - - +
494D VAL* 3.3 5.2 - - - +
495D THR* 2.8 48.1 + - - +
497D THR* 2.9 31.2 + - - -
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Residues in contact with GLN 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D LEU* 3.0 39.6 + - - +
483D HIS* 3.8 20.0 + - - +
485D GLN* 1.3 75.8 - - - +
487D LEU* 1.3 67.9 + - + +
490D GLY* 3.3 29.6 + - - -
491D PRO* 3.8 16.2 - - + +
494D VAL* 3.7 19.8 - - + +
498D ARG* 4.5 6.9 + - - -
546D LEU* 5.7 0.2 - - - +
547D ASP* 4.9 11.8 + - - +
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Residues in contact with LEU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D HIS* 2.9 37.2 + - + +
484D PHE* 4.3 2.0 - - - +
486D GLN* 1.3 84.9 - - + +
488D ALA* 1.3 61.7 + - + +
489D VAL 3.6 0.2 - - - -
549D ILE* 4.4 28.3 - - + -
553D GLU* 4.7 13.0 - - + +
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Residues in contact with ALA 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1559C MPD 6.0 0.2 - - - +
484D PHE* 2.8 55.7 + - + +
487D LEU* 1.3 75.4 - - + +
489D VAL* 1.3 59.3 + - + +
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Residues in contact with VAL 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 3.3 24.2 - - - +
35C GLN* 3.9 16.8 - - + +
484D PHE* 4.3 9.4 - - + +
485D GLN* 3.0 18.6 + - - +
488D ALA* 1.3 83.6 - - + +
490D GLY* 1.3 58.3 + - - +
493D ARG* 3.7 28.6 - - + +
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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