Contacts of the helix formed by residues 417 - 432 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 3.5 41.8 - + + +
59B ASP* 3.2 40.6 - - + -
63B ARG* 3.8 10.5 - - - -
387B GLU* 3.3 3.6 + - - +
407B ILE* 3.9 20.2 - - + -
408B SER* 5.7 0.2 - - - -
409B GLN* 3.4 48.9 - - + +
414B SER 3.0 19.8 + - - +
415B ILE 3.3 0.4 - - - -
416B GLY* 1.3 75.0 - - - +
418B THR* 1.3 69.6 + - + +
420B GLY 3.2 4.3 + - - -
421B ALA* 3.0 41.6 + - + -
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Residues in contact with THR 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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385B ILE* 3.3 25.4 - - + +
386B ALA 3.9 3.6 - - - +
387B GLU* 2.8 57.2 + - + +
407B ILE 5.4 0.9 - - - +
408B SER* 6.3 0.2 - - - -
409B GLN 6.2 0.7 - - - +
417B PHE* 1.3 86.4 - - + +
419B THR* 1.3 58.2 + - - +
421B ALA* 3.7 1.5 - - - -
422B THR* 2.5 36.8 + - - -
440B LEU* 3.7 14.1 - - - +
442B ILE* 3.3 14.4 - - - +
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Residues in contact with THR 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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416B GLY 3.3 1.8 + - - -
418B THR* 1.3 78.7 + - - +
420B GLY* 1.4 64.4 + - - +
422B THR* 4.2 3.4 - - - -
423B LEU* 3.5 2.8 + - - +
440B LEU* 5.2 6.0 - - + +
442B ILE* 3.1 23.3 - - - +
447B LEU* 4.4 6.0 - - + +
450B THR* 3.0 44.7 + - - +
451B VAL* 4.4 1.8 - - - +
453B GLU* 4.1 9.8 - - + +
454B ILE* 4.1 25.4 - - + -
457B MET* 3.2 29.2 - - + +
466B LEU* 6.4 0.4 - - + -
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Residues in contact with GLY 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASN* 3.7 21.8 - - - -
56B TYR* 3.9 3.3 - - - +
57B ALA* 3.4 10.7 - - - -
416B GLY 4.1 2.2 + - - -
417B PHE 3.2 8.0 + - - -
419B THR* 1.4 76.2 - - - +
421B ALA* 1.3 51.2 + - - +
423B LEU* 2.8 31.0 + - - +
424B GLY 3.3 4.3 + - - -
450B THR* 4.7 2.8 + - - -
453B GLU* 4.4 15.3 - - - +
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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
----------------------------------------------------------
56B TYR 3.6 20.8 - - - +
57B ALA* 4.2 0.4 - - - +
60B GLY* 3.7 14.6 - - - -
385B ILE* 4.2 10.1 - - + -
407B ILE* 5.1 3.1 - - + -
417B PHE* 3.0 37.8 + - + +
418B THR* 3.4 5.1 + - - +
420B GLY* 1.3 73.3 - - - +
422B THR* 1.3 49.5 + - - +
423B LEU 3.1 0.2 - - - -
424B GLY* 3.7 0.6 - - - -
425B ALA* 2.6 38.8 + - - +
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Residues in contact with THR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE* 3.8 14.2 - - - +
418B THR 2.5 25.1 + - - -
419B THR 3.6 0.2 - - - -
421B ALA* 1.3 68.5 - - - +
423B LEU* 1.3 65.5 + - - +
425B ALA* 4.2 0.3 - - - +
426B ALA* 3.0 27.9 + - - +
438B VAL* 4.1 12.7 - - + +
440B LEU* 3.1 25.3 - - + +
457B MET* 3.6 20.0 - - + -
464B PRO* 3.6 29.6 - - + -
466B LEU* 4.0 9.0 - - + -
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Residues in contact with LEU 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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23B PHE* 4.3 1.1 - - + -
48B ASN* 3.3 29.4 - - - +
57B ALA* 3.8 15.9 - - + -
419B THR 3.5 8.4 + - - +
420B GLY 2.8 10.6 + - - +
422B THR* 1.3 81.9 - - - +
424B GLY* 1.3 59.3 - - - +
426B ALA* 3.5 3.6 + - - +
427B PHE* 3.2 53.5 + - + -
453B GLU* 4.1 11.7 - - + +
456B THR* 3.9 18.2 - - + -
457B MET* 3.8 27.4 - - + +
462B LEU* 3.6 16.1 - - + +
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Residues in contact with GLY 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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23B PHE* 4.2 11.4 - - - -
57B ALA 3.5 22.4 - - - -
61B TYR* 3.4 22.4 - - - -
420B GLY 3.3 6.7 + - - -
421B ALA 3.7 0.9 - - - -
423B LEU* 1.3 76.6 - - - +
425B ALA* 1.3 63.0 + - - +
426B ALA 3.1 1.6 - - - -
427B PHE 3.1 1.2 + - - -
428B ALA* 3.0 19.6 + - - +
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLY 3.9 6.5 - - - +
64B ILE* 3.7 29.0 - - + +
383B VAL* 4.1 10.1 - - + -
385B ILE* 3.8 21.1 - - + -
407B ILE* 4.4 2.0 - - + -
421B ALA 2.6 21.0 + - - +
422B THR 4.2 1.8 - - - +
424B GLY* 1.3 72.7 - - - +
426B ALA* 1.3 50.9 + - - +
428B ALA* 3.5 1.4 - - - +
429B ALA* 2.5 38.1 + - - +
438B VAL* 4.4 3.6 - - + -
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B THR 3.0 19.7 + - - +
423B LEU* 3.7 4.7 - - - +
424B GLY 3.1 0.4 - - - -
425B ALA* 1.3 75.7 - - - +
427B PHE* 1.3 57.0 + - - +
429B ALA* 4.1 0.3 - - - +
430B GLU* 2.9 29.8 + - - +
438B VAL* 4.0 22.4 - - + +
457B MET* 6.3 0.2 - - + -
462B LEU* 4.0 24.4 - - + +
463B LYS 5.7 0.2 - - - +
464B PRO* 5.0 11.0 - - + -
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Residues in contact with PHE 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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21B THR* 3.8 15.3 - - + -
23B PHE* 3.7 19.1 - + - -
44B ARG* 3.5 33.5 + - - +
46B ALA* 3.7 26.7 - - + -
61B TYR* 4.0 5.4 - - + -
423B LEU* 3.2 43.0 + - + -
424B GLY 3.1 6.0 + - - +
426B ALA* 1.3 72.4 - - - +
428B ALA* 1.3 66.3 + - - +
430B GLU* 3.5 4.4 + - - +
431B GLU* 3.0 29.5 + - - +
460B TRP* 3.4 51.1 - + + -
462B LEU* 4.1 8.3 - - + -
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 3.6 29.8 - - + +
64B ILE* 3.7 31.0 - - + -
65B LYS* 3.8 16.4 - - + -
424B GLY 3.0 10.8 + - - +
425B ALA 3.8 0.2 - - - +
427B PHE* 1.3 77.7 - - - +
429B ALA* 1.3 64.6 + - - +
431B GLU* 2.9 15.0 + - - +
432B ILE* 3.1 15.6 + - - +
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Residues in contact with ALA 429 (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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64B ILE* 4.2 1.0 - - + +
383B VAL* 4.8 4.5 - - + -
425B ALA 2.5 28.6 + - - +
426B ALA 4.1 2.2 - - - +
428B ALA* 1.3 74.0 - - - +
430B GLU* 1.3 55.7 + - - +
432B ILE* 3.5 1.4 + - - +
433B ASP 2.8 33.8 + - - +
436B LYS* 4.0 38.7 - - + +
438B VAL* 3.9 21.5 - - + -
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Residues in contact with GLU 430 (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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44B ARG* 2.8 39.1 + - - -
426B ALA 2.9 17.3 + - - +
427B PHE* 3.7 4.0 - - - +
429B ALA* 1.3 77.2 - - - +
431B GLU* 1.3 62.2 + - - +
432B ILE 3.6 0.2 + - - -
433B ASP 3.7 11.8 + - - -
434B PRO* 3.8 24.2 - - + +
460B TRP 5.1 4.2 - - - +
461B GLY 5.3 1.9 - - - +
462B LEU* 3.9 18.9 - - + +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASN* 4.0 14.6 - - + +
21B THR* 2.7 14.9 - - - +
44B ARG* 2.7 28.8 + - - +
61B TYR* 2.3 34.1 + - - -
65B LYS* 3.0 27.7 + - - +
427B PHE 3.0 13.9 + - - +
428B ALA 2.9 8.6 + - - +
430B GLU* 1.3 75.8 - - - +
432B ILE* 1.3 66.6 + - - +
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Residues in contact with ILE 432 (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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64B ILE* 4.4 9.6 - - + +
65B LYS* 3.2 41.5 - - + -
428B ALA 3.1 15.6 + - - +
429B ALA 4.0 1.6 - - - +
431B GLU* 1.3 80.2 - - - +
433B ASP* 1.3 63.1 - - + +
434B PRO* 4.8 0.4 - - - +
436B LYS* 4.0 33.4 - - + +
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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
------------------------------------------------------------
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