Contacts of the strand formed by residues 436 - 457 (chain B) in PDB entry 1PO3
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 TYR 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B MET* 5.6 3.4 - - + -
419B ARG 2.9 25.6 - - - +
420B TYR* 3.9 18.2 - - + +
421B TYR* 3.1 12.3 + - - -
434B SER 3.3 2.4 + - - -
435B PRO* 1.3 75.2 - - - +
437B ASP* 1.3 64.6 + - - +
438B ARG 4.5 5.4 - - - +
439B ASP* 5.9 3.4 - - + -
479B ILE* 6.6 0.2 - - + -
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Residues in contact with ASP 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ARG* 2.8 21.7 + - - +
419B ARG* 3.0 39.0 + - - +
421B TYR* 2.9 29.9 - - + +
436B TYR* 1.3 77.2 - - - +
438B ARG* 1.3 65.3 + - - +
479B ILE* 5.1 12.0 - - - +
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Residues in contact with ARG 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLN* 5.5 0.4 - - - +
378B SER* 5.8 0.2 + - - -
380B ARG* 3.3 16.3 - - - +
417B GLU* 5.0 12.1 - - - +
418B MET* 3.0 9.6 - - - +
419B ARG* 2.5 86.5 + - + +
436B TYR* 4.5 2.0 - - - +
437B ASP* 1.3 83.4 - - - +
439B ASP* 1.3 61.8 + - - +
440B THR* 4.6 15.5 - - + +
479B ILE* 4.7 4.7 - - - +
573B ASP* 3.0 34.0 + - - +
742B FLC 3.2 36.4 + - - +
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Residues in contact with ASP 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B HIS* 3.0 30.7 + - - -
417B GLU 3.6 2.9 - - - -
418B MET* 3.3 13.2 - - + +
436B TYR* 5.9 4.0 - - + -
438B ARG* 1.3 74.7 - - - +
440B THR* 1.3 65.6 + - - +
441B ARG* 3.8 11.8 + - - -
477B ASN* 3.9 2.6 - - - +
478B ALA* 3.1 44.9 + - - +
479B ILE* 3.9 22.3 + - + +
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Residues in contact with THR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B HIS* 3.4 4.3 - - - -
417B GLU* 3.0 58.1 + - - +
438B ARG* 4.6 11.1 - - + +
439B ASP* 1.3 85.0 + - - +
441B ARG* 1.3 64.6 + - - +
475B GLN* 3.4 24.0 + - - +
476B ASN 3.5 8.5 - - - -
477B ASN* 3.7 26.9 - - - +
478B ALA* 4.8 0.4 - - - +
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 3.7 11.0 - - - +
416B HIS* 3.5 42.3 + - + +
439B ASP* 3.8 21.8 + - - -
440B THR* 1.3 75.4 - - - +
442B SER* 1.3 57.2 + - - +
474B TYR* 3.5 11.9 - - + +
476B ASN* 2.7 45.7 + - + +
478B ALA* 4.6 8.7 - - - +
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Residues in contact with SER 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B SER* 3.5 1.7 - - - -
415B THR* 2.8 39.6 + - - +
417B GLU* 4.3 1.4 + - - -
441B ARG* 1.3 72.0 - - - +
443B GLY* 1.3 57.7 + - - +
474B TYR* 2.9 31.8 + - - -
475B GLN* 2.7 41.7 + - - +
520B TYR* 3.9 20.0 - - - -
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Residues in contact with GLY 443 (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 GLU 3.0 13.2 - - - -
414B SER* 4.0 2.0 - - - -
442B SER* 1.3 77.0 - - - +
444B THR* 1.3 69.7 + - - -
473B SER* 3.0 1.8 - - - -
474B TYR* 2.9 46.3 + - - -
520B TYR* 3.1 9.4 + - - -
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Residues in contact with THR 444 (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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174B TYR* 4.2 15.1 - - + +
411B LEU 3.9 0.6 - - - +
412B ASN* 3.5 7.7 - - - +
413B GLU* 2.7 45.0 + - + +
443B GLY* 1.3 77.0 + - - -
445B GLU* 1.3 77.0 + - - +
446B ALA* 4.2 2.0 - - + +
471B ILE* 3.6 20.6 - - + -
472B GLU 3.0 9.2 - - - +
473B SER* 2.5 30.6 + - - +
474B TYR* 5.0 0.4 - - - -
520B TYR* 2.7 19.2 + - - -
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Residues in contact with GLU 445 (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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410B TYR* 3.7 31.1 + - + -
411B LEU 3.6 2.5 - - - -
412B ASN* 3.6 13.9 - - - +
444B THR* 1.3 75.5 - - - +
446B ALA* 1.3 59.2 + - - +
447B HIS* 4.1 18.6 + - + +
470B HIS 3.5 3.5 - - - +
472B GLU* 2.6 49.0 + - + +
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Residues in contact with ALA 446 (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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174B TYR* 3.3 49.0 + - + +
409B ARG 3.5 4.2 - - - +
410B TYR* 3.8 1.6 - - - -
411B LEU* 3.1 32.1 + - - +
444B THR* 4.1 1.3 - - + +
445B GLU* 1.3 76.2 - - - +
447B HIS* 1.3 63.0 + - - +
469B GLU* 4.2 1.8 - - - +
470B HIS 3.2 3.8 - - - -
471B ILE* 3.6 16.2 - - + -
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Residues in contact with HIS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TYR* 2.8 31.3 + + + -
409B ARG 3.9 1.6 - - - -
410B TYR* 3.2 32.5 - + - -
445B GLU* 4.1 20.6 + - + +
446B ALA* 1.3 73.9 - - - +
448B ALA* 1.3 58.9 + - - +
449B TRP* 4.2 13.2 + + - +
468B PHE 3.5 1.4 - - - +
469B GLU* 3.3 6.6 - - - -
470B HIS* 2.9 58.9 + + + +
472B GLU* 5.5 2.0 + - - -
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 4.6 1.6 - - - +
408B TYR* 3.1 8.4 - - - -
409B ARG* 2.7 55.6 + - + +
447B HIS* 1.3 75.0 - - - +
449B TRP* 1.3 61.3 - - - +
450B TYR* 3.8 2.7 - - + -
467B ARG* 3.5 30.1 - - - +
468B PHE 3.3 3.1 - - - -
469B GLU* 3.7 15.3 - - + -
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Residues in contact with TRP 449 (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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406B VAL* 6.1 5.2 - - + -
407B GLY 3.3 6.3 - - - +
408B TYR* 3.6 46.2 - + + -
447B HIS* 4.3 14.7 - + + +
448B ALA* 1.3 75.3 - - - +
450B TYR* 1.3 62.6 + - - +
467B ARG* 3.2 5.0 - - - +
468B PHE* 2.6 62.5 + + + +
470B HIS* 6.0 1.0 - - - +
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Residues in contact with TYR 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA 5.7 0.2 - - - -
201B VAL* 2.6 32.1 - - + +
202B ARG* 3.4 25.1 - - + -
388B GLU* 2.4 44.5 + - - +
390B ARG* 3.8 11.7 - - + -
405B GLY 5.6 0.9 - - - -
406B VAL* 3.3 11.7 - - - +
407B GLY* 2.9 65.7 + - - -
408B TYR* 3.6 5.9 + - - -
409B ARG* 4.1 1.8 - - + -
448B ALA 3.8 11.2 - - - -
449B TRP* 1.3 81.6 - - - +
451B LEU* 1.3 60.0 + - - +
452B ASP* 5.8 2.5 - - - -
466B MET 3.1 9.6 - - - +
467B ARG* 3.7 19.3 - - + -
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Residues in contact with LEU 451 (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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201B VAL* 4.6 1.9 + - - +
404B VAL* 4.2 17.3 - - + -
405B GLY 3.3 9.9 - - - +
406B VAL* 3.7 30.1 - - + -
450B TYR* 1.3 75.6 - - - +
452B ASP* 1.3 64.2 + - - +
465B GLY* 3.2 2.6 - - - -
466B MET* 2.8 40.0 + - - +
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Residues in contact with ASP 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA* 2.7 30.4 - - - +
201B VAL* 4.9 1.4 - - + +
202B ARG* 5.5 2.1 - - - +
403B GLU 4.1 4.5 - - - +
404B VAL* 3.1 5.6 - - - +
405B GLY* 2.7 45.6 + - - +
450B TYR* 5.8 2.1 - - - -
451B LEU* 1.3 79.4 - - - +
453B ASP* 1.3 60.5 + - - +
454B LYS 5.0 0.5 + - - -
463B THR* 4.7 12.1 - - + -
464B PRO 3.4 12.8 - - - +
465B GLY* 4.1 6.5 - - - -
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Residues in contact with ASP 453 (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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402B HIS* 3.4 21.7 + - - +
403B GLU 3.0 21.2 + - - -
404B VAL* 3.3 22.5 - - + +
452B ASP* 1.3 76.5 - - - +
454B LYS* 1.3 62.0 + - - +
455B ILE* 2.8 32.5 + - - +
462B ILE 3.4 1.2 - - - +
463B THR* 3.5 5.3 - - - -
464B PRO* 3.1 36.1 + - + +
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Residues in contact with LYS 454 (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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401B ALA 2.9 14.6 - - - +
403B GLU* 2.7 45.1 + - + +
452B ASP* 5.0 0.6 + - - -
453B ASP* 1.3 70.9 + - - +
455B ILE* 1.3 61.2 + - - +
456B ASP* 3.7 11.5 + - - +
461B THR* 5.2 7.2 - - + -
462B ILE 3.9 3.4 - - - -
463B THR* 4.3 12.8 - - + +
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Residues in contact with ILE 455 (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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400B SER* 3.7 9.2 - - - +
401B ALA 3.2 2.9 - - - -
402B HIS* 3.0 37.5 - - + +
453B ASP* 2.8 31.9 - - - +
454B LYS* 1.3 71.4 - - - +
456B ASP* 1.3 61.5 + - - +
457B ILE* 3.9 8.4 + - + +
460B TRP 3.8 0.9 - - - +
461B THR* 3.2 7.1 - - - +
462B ILE* 2.9 47.1 + - + +
464B PRO* 4.0 18.6 - - + -
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Residues in contact with ASP 456 (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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399B PRO 3.9 1.9 - - - +
400B SER* 3.1 6.4 - - - -
401B ALA* 2.8 42.3 + - + +
403B GLU* 5.9 0.5 - - - +
454B LYS* 3.9 14.7 - - - +
455B ILE* 1.3 74.5 - - - +
457B ILE* 1.3 60.0 + - - +
458B GLY 4.0 2.8 + - - -
460B TRP 3.5 3.9 - - - +
461B THR* 3.2 32.2 + - - +
500B HIS* 5.0 2.8 + - - -
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Residues in contact with ILE 457 (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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399B PRO* 4.0 35.2 - - + +
400B SER* 3.7 13.7 - - - -
455B ILE* 5.2 8.5 - - + +
456B ASP* 1.3 74.0 - - - +
458B GLY* 1.3 60.9 + - - +
459B ASN 3.0 0.9 + - - -
460B TRP* 2.9 46.4 + - + +
462B ILE* 5.5 5.6 - - + -
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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
------------------------------------------------------------
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