Contacts of the helix formed by residues 417 - 432 (chain A) in PDB entry 1PYD
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 PHE 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TYR* 3.5 48.6 - + + +
59A ASP* 3.3 37.5 - - + -
60A GLY 4.7 0.7 - - - -
63A ARG* 4.0 10.1 - - - -
387A GLU* 4.4 3.4 - - - +
407A ILE* 4.0 18.2 - - + -
409A GLN* 3.5 40.2 - - + +
414A SER* 3.1 18.4 + - - +
415A ILE 3.3 0.6 - - - -
416A GLY* 1.3 74.3 - - - +
418A THR* 1.3 67.3 + - + +
420A GLY* 3.1 9.4 + - - -
421A ALA* 3.0 41.9 + - + -
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Residues in contact with THR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A ILE* 3.6 22.2 - - + -
386A ALA 3.7 9.4 - - - +
387A GLU* 2.5 53.1 + - - +
407A ILE* 5.7 0.9 - - + +
408A SER* 6.3 0.2 - - - -
409A GLN* 6.1 1.1 - - + +
416A GLY 3.0 1.8 + - - -
417A PHE* 1.3 77.8 - - + +
419A THR* 1.3 58.4 + - - +
420A GLY 3.2 1.1 - - - -
421A ALA* 3.6 7.6 - - - +
422A THR* 2.7 36.0 + - - -
440A LEU* 3.6 10.1 - - - +
442A ILE* 3.3 14.2 - - - +
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Residues in contact with THR 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A GLY 3.2 3.2 + - - -
418A THR* 1.3 77.4 + - - +
420A GLY* 1.3 63.5 + - - +
422A THR* 3.5 3.3 + - - -
423A LEU* 3.5 1.4 + - - +
440A LEU* 4.9 7.8 - - + +
442A ILE* 3.4 19.8 - - - +
447A LEU* 3.8 15.0 - - + +
450A THR* 2.9 40.6 + - - +
453A GLU* 4.1 8.3 - - + +
454A ILE* 4.1 19.3 - - + -
457A MET* 3.3 38.6 - - + +
466A LEU* 5.7 0.7 - - + -
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Residues in contact with GLY 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN* 3.9 21.8 - - - -
56A TYR* 4.1 5.6 - - - -
57A ALA* 3.1 26.6 - - - +
416A GLY 4.2 1.6 + - - -
417A PHE 3.1 7.7 + - - -
419A THR* 1.3 76.7 - - - +
421A ALA* 1.3 66.0 + - - +
423A LEU* 3.0 11.1 + - - +
424A GLY 3.2 0.2 + - - -
450A THR* 4.8 3.0 + - - -
453A GLU* 4.4 10.7 - - - +
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TYR 3.6 11.1 + - - +
60A GLY* 4.0 11.0 - - - -
385A ILE* 4.3 12.1 - - + -
407A ILE* 4.9 4.0 - - + -
417A PHE* 3.0 43.3 + - + -
418A THR* 3.9 10.8 - - - -
419A THR 3.4 0.2 - - - -
420A GLY* 1.3 75.7 - - - +
422A THR* 1.3 57.7 + - - +
424A GLY* 3.4 1.2 + - - -
425A ALA* 3.0 32.0 + - - +
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Residues in contact with THR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A ILE* 3.4 17.8 - - - +
418A THR 2.7 22.1 + - - -
419A THR 3.8 5.4 - - - -
420A GLY 3.1 0.4 - - - -
421A ALA* 1.3 76.4 - - - +
423A LEU* 1.3 60.3 - - - +
425A ALA* 3.6 0.9 - - - +
426A ALA* 2.9 26.5 + - - +
438A VAL* 3.9 12.2 - - + +
440A LEU* 3.3 22.8 - - + +
457A MET* 4.1 13.2 - - + -
464A PRO* 3.8 29.6 - - + -
466A LEU* 4.2 6.3 - - + -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.9 3.4 - - + -
48A ASN* 3.6 27.4 - - - +
57A ALA* 3.7 14.1 - - + -
419A THR 3.5 8.1 + - - +
420A GLY 3.0 8.5 + - - +
422A THR* 1.3 76.7 - - - +
424A GLY* 1.4 64.2 + - - +
426A ALA* 3.1 5.4 + - - +
427A PHE* 3.0 53.6 + - + -
453A GLU* 4.4 6.7 - - + +
456A THR* 3.7 22.7 - - + -
457A MET* 3.9 25.7 - - + +
462A LEU* 3.4 27.8 - - + -
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Residues in contact with GLY 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.1 7.4 - - - -
57A ALA* 3.2 29.7 - - - +
61A TYR* 3.4 24.2 - - - +
420A GLY 3.2 7.1 + - - -
421A ALA 3.4 1.1 + - - -
422A THR 3.3 0.2 - - - -
423A LEU* 1.4 80.9 - - - +
425A ALA* 1.3 54.1 + - - +
427A PHE* 3.4 0.5 + - - +
428A ALA 3.1 22.0 + - - -
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLY 4.0 4.0 - - - +
61A TYR 3.8 2.2 - - - +
64A ILE* 4.0 27.8 - - + +
383A VAL* 4.3 8.9 - - + +
385A ILE* 3.8 19.3 - - + -
407A ILE* 4.5 3.1 - - + -
421A ALA 3.0 18.8 + - - +
422A THR 3.6 4.5 - - - +
424A GLY* 1.3 70.1 - - - +
426A ALA* 1.3 61.9 + - - +
428A ALA* 3.8 1.4 - - - +
429A ALA* 2.8 29.8 + - - +
438A VAL* 4.1 4.9 - - + +
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A THR 2.9 21.3 + - - +
423A LEU* 3.1 4.9 + - - +
425A ALA* 1.3 75.3 - - - +
427A PHE* 1.3 61.4 + - - +
429A ALA* 3.6 1.6 - - - +
430A GLU* 2.9 30.3 + - - +
438A VAL* 3.7 22.9 - - + +
462A LEU* 3.9 27.8 - - + +
463A LYS 5.7 0.4 - - - +
464A PRO* 4.9 9.2 - - + -
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Residues in contact with PHE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 3.9 15.5 - - + +
23A PHE* 3.8 16.8 - + - -
44A ARG* 3.2 40.0 + - - -
46A ALA* 3.7 18.8 - - + -
61A TYR* 4.1 3.8 - - + -
423A LEU* 3.0 44.3 + - + +
424A GLY 3.6 5.6 - - - +
426A ALA* 1.3 76.5 - - - +
428A ALA* 1.4 66.3 + - - +
430A GLU* 3.4 6.4 - - - +
431A GLU* 3.1 28.8 + - - +
460A TRP* 3.3 49.4 - + + -
462A LEU* 3.8 11.0 - - + -
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 3.8 19.9 - - + +
64A ILE* 3.6 28.5 - - + -
65A LYS* 3.6 18.5 - - + +
424A GLY 3.1 11.0 + - - +
425A ALA 4.1 0.4 - - - +
427A PHE* 1.4 75.2 - - - +
429A ALA* 1.3 65.2 + - - +
431A GLU* 3.0 20.6 + - - +
432A ILE* 3.0 17.2 + - - +
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.1 5.3 - - - +
383A VAL* 4.7 5.6 - - + -
425A ALA 2.8 20.0 + - - +
426A ALA 3.6 5.2 - - - +
428A ALA* 1.3 75.3 - - - +
430A GLU* 1.3 56.4 + - - +
432A ILE* 2.9 3.0 + - - +
433A ASP 2.6 39.1 + - - +
436A LYS* 4.1 30.7 - - + +
438A VAL* 3.9 19.3 - - + -
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Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 2.7 40.8 + - - -
426A ALA 2.9 17.4 + - - +
427A PHE* 3.4 6.5 - - - +
429A ALA* 1.3 78.9 - - - +
431A GLU* 1.3 61.4 + - + +
434A PRO* 3.4 37.3 - - + +
460A TRP 4.9 4.5 - - - +
461A GLY 5.1 3.1 - - - +
462A LEU* 3.8 17.9 - - + +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.3 29.1 - - - +
21A THR* 3.0 22.8 + - - -
44A ARG* 3.0 16.3 + - - +
61A TYR* 2.8 27.8 + - - -
65A LYS* 3.0 22.4 + - - +
427A PHE 3.1 15.3 - - - +
428A ALA 3.0 6.7 + - - +
430A GLU* 1.3 78.4 - - - +
432A ILE* 1.3 60.1 + - - +
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Residues in contact with ILE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.5 34.5 - - + +
65A LYS* 4.4 14.8 - - + -
405A TYR* 3.5 22.0 - - - +
428A ALA 3.3 9.2 - - - +
429A ALA* 2.9 6.6 + - - +
430A GLU 4.4 0.2 - - - -
431A GLU* 1.3 79.1 - - - +
433A ASP* 1.3 67.1 + - + +
434A PRO* 4.5 0.7 - - - -
436A LYS* 4.2 19.7 - - + +
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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