Contacts of the helix formed by residues 416 - 427 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412D ALA 3.0 13.5 + - - -
413D VAL 3.7 4.3 - - - -
415D ILE* 1.3 78.4 - - - +
417D LEU* 1.3 59.6 + - - -
418D PRO* 3.7 1.6 - - - -
419D PHE* 3.7 24.5 + - - +
420D LEU* 3.3 30.6 + - - +
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Residues in contact with LEU 417 (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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413D VAL* 3.3 34.8 + - + +
414D ALA 4.4 0.7 - - - +
415D ILE 3.3 1.6 + - - -
416D GLY* 1.3 72.2 - - - +
418D PRO* 1.4 70.0 - - + +
419D PHE 3.2 2.2 - - - -
420D LEU* 3.4 6.7 + - + +
421D ALA* 3.0 26.5 + - - +
445D ALA* 4.5 8.3 - - + +
448D ALA* 4.8 1.6 - - + -
449D SER* 4.1 22.4 - - - +
452D ILE* 3.8 27.8 - - + -
501D TRP* 5.3 2.0 - - + -
761D PRO* 4.3 18.8 - - + -
763D PRO* 5.0 3.4 - - + -
764D PHE* 3.6 24.9 - - + -
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Residues in contact with PRO 418 (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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415D ILE 4.3 7.2 - - - +
416D GLY* 4.0 1.6 - - - -
417D LEU* 1.4 92.3 - - + +
419D PHE* 1.3 66.4 + - + +
421D ALA* 3.5 2.7 - - + +
422D LEU* 2.9 33.9 + - + +
425D TRP* 5.5 0.5 - - - -
764D PHE* 3.9 23.6 - - + -
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Residues in contact with PHE 419 (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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415D ILE* 4.8 5.8 - - + -
416D GLY* 3.7 28.3 - - - +
417D LEU 3.2 1.6 - - - -
418D PRO* 1.3 87.0 - - + +
420D LEU* 1.3 58.5 + - + +
422D LEU* 3.2 13.4 + - + +
423D ILE* 2.9 36.0 + - + +
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Residues in contact with LEU 420 (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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412D ALA 5.6 0.2 - - - +
413D VAL* 3.8 35.0 - - + -
416D GLY 3.3 20.4 + - - +
417D LEU* 3.4 7.4 + - + +
419D PHE* 1.3 75.3 - - + +
421D ALA* 1.3 59.5 + - - +
423D ILE* 3.5 15.7 - - + +
424D TYR* 2.9 23.9 + - - +
432D MET* 4.0 21.5 - - + -
436D MET* 3.4 40.9 - - + +
441D MET* 5.9 2.9 - - + -
760D LEU* 5.0 0.7 - - - -
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Residues in contact with ALA 421 (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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417D LEU 3.0 18.1 + - - +
418D PRO 3.5 5.8 - - - +
420D LEU* 1.3 77.4 - - - +
422D LEU* 1.3 57.0 + - - +
424D TYR* 3.4 2.8 + - - +
425D TRP* 2.9 40.1 + - + +
760D LEU* 3.8 18.2 - - + +
764D PHE* 3.7 38.8 - - + -
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Residues in contact with LEU 422 (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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418D PRO* 2.9 20.3 + - + +
419D PHE* 3.2 13.0 + - + +
421D ALA* 1.3 73.2 - - - +
423D ILE* 1.3 61.3 + - + +
425D TRP* 3.6 22.8 - - + +
426D PHE* 2.9 69.6 + - + +
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Residues in contact with ILE 423 (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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419D PHE* 2.9 19.3 + - + +
420D LEU* 3.5 26.7 - - + +
421D ALA 3.3 0.2 - - - -
422D LEU* 1.3 77.6 - - + +
424D TYR* 1.3 62.9 + - - +
427D ALA* 2.9 43.4 + - + +
430D SER* 6.1 1.1 - - - -
432D MET* 4.1 29.6 - - + -
433D GLY* 4.7 6.1 - - - +
436D MET* 4.7 6.3 - - + -
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Residues in contact with TYR 424 (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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420D LEU 2.9 16.2 + - - +
421D ALA 3.9 3.1 - - - +
423D ILE* 1.3 79.1 - - - +
425D TRP* 1.3 64.7 + + - +
427D ALA 4.9 1.3 - - - -
428D PRO* 3.4 23.7 - - + +
433D GLY* 4.7 13.0 - - - -
436D MET* 3.7 18.2 - - + -
437D ARG* 3.4 43.1 + - + -
757D GLY 5.2 0.7 + - - -
759D THR* 3.4 40.7 + - + -
760D LEU* 3.7 31.6 - - + -
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Residues in contact with TRP 425 (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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418D PRO 5.5 0.4 - - - -
421D ALA* 2.9 24.5 + - + +
422D LEU* 3.6 27.4 - - + +
423D ILE 3.3 0.4 - - - -
424D TYR* 1.3 82.8 - + - +
426D PHE* 1.3 76.5 + + + +
428D PRO* 4.3 4.3 - - - +
760D LEU* 3.5 22.7 - - + +
764D PHE* 3.6 42.9 + + + -
767D VAL* 3.6 48.0 - - + +
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Residues in contact with PHE 426 (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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422D LEU* 2.9 41.5 + - + +
425D TRP* 1.3 89.7 - + + +
427D ALA* 1.3 61.3 + - + +
428D PRO* 3.4 8.6 - - - +
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Residues in contact with ALA 427 (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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423D ILE* 2.9 28.8 + - + +
426D PHE* 1.3 80.8 - - + +
428D PRO* 1.3 64.1 - - - +
430D SER* 3.5 17.6 + - - +
433D GLY* 4.9 1.4 - - - -
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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