Contacts of the strand formed by residues 460 - 477 (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 TRP 460 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ILE 4.3 0.2 - - - -
456B ASP* 3.5 5.2 - - - +
457B ILE* 2.9 45.0 + - + +
458B GLY 4.7 1.4 - - - +
459B ASN* 1.3 87.2 - - + +
461B THR* 1.3 66.9 + - - +
462B ILE* 4.0 14.6 - - + -
497B VAL* 3.7 31.2 - - + -
498B LEU 4.0 2.7 - - - -
499B TYR* 3.4 42.6 - + + -
500B HIS* 4.4 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 4.9 2.2 + - - +
101B ALA* 5.8 0.2 - - - +
454B LYS* 5.2 6.1 - - + -
455B ILE 3.2 9.9 - - - +
456B ASP* 3.2 25.2 + - - +
460B TRP* 1.3 71.9 - - - +
462B ILE* 1.3 62.6 + - - +
463B THR* 4.1 10.5 + - - +
496B ASN 3.3 5.0 - - - +
497B VAL* 3.6 0.3 - - - -
498B LEU* 3.1 43.4 + - + +
500B HIS* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ASP 3.4 2.3 - - - +
454B LYS* 3.9 0.3 - - - -
455B ILE* 2.9 45.9 + - + +
457B ILE* 5.5 5.8 - - + -
460B TRP* 4.0 22.7 - - + -
461B THR* 1.3 75.5 - - - +
463B THR* 1.3 62.6 + - - +
464B PRO* 3.7 9.2 - - + -
495B LEU* 3.6 24.7 - - + -
496B ASN 3.3 1.3 - - - +
497B VAL* 3.3 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 5.0 2.6 - - - +
452B ASP* 4.7 11.2 - - + -
453B ASP 3.5 20.4 - - - +
454B LYS* 4.3 9.6 - - + +
461B THR* 4.1 11.4 + - - +
462B ILE* 1.3 76.6 + - - +
464B PRO* 1.3 64.1 - - - +
465B GLY* 3.6 1.3 + - - -
495B LEU* 3.4 3.9 - - - -
496B ASN* 2.6 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU 4.2 0.2 - - - +
452B ASP* 3.4 3.2 - - - -
453B ASP* 3.1 42.6 + - + +
455B ILE* 4.0 17.9 - - + -
462B ILE* 3.6 10.8 - - + +
463B THR* 1.3 87.2 - - - +
465B GLY* 1.3 56.5 + - - +
494B ALA 3.5 5.6 - - - +
495B LEU* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 4.4 5.2 - - - -
451B LEU 3.2 9.4 - - - -
452B ASP* 4.1 8.1 - - - -
463B THR* 3.6 2.1 + - - -
464B PRO* 1.3 75.2 - - - +
466B MET* 1.3 55.3 + - - -
493B PRO* 3.7 1.4 - - - +
494B ALA* 2.5 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.1 7.6 - - - +
449B TRP 4.1 0.2 - - - +
450B TYR* 3.1 2.4 - - - -
451B LEU* 2.8 43.6 + - - +
465B GLY* 1.3 73.9 - - - -
467B ARG* 1.3 59.5 + - - +
492B LEU 3.6 9.4 - - - -
493B PRO* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.1 20.3 - - + +
202B ARG* 3.0 38.4 + - - +
203B TYR 3.8 13.7 - - - -
204B GLY* 3.3 20.2 + - - +
409B ARG* 3.5 24.4 - - - +
448B ALA* 3.5 17.4 - - - +
449B TRP 3.2 11.7 - - - +
450B TYR* 3.7 12.0 - - + +
466B MET* 1.3 72.9 - - - +
468B PHE* 1.3 65.5 + - - +
469B GLU* 2.9 28.1 + - - -
491B PRO* 4.2 0.2 - - - +
492B LEU* 3.0 58.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B HIS 3.5 0.9 - - - +
448B ALA* 3.3 1.0 - - - -
449B TRP* 2.6 56.9 + + + +
467B ARG* 1.3 73.7 - - - +
469B GLU* 1.3 87.3 + - - +
470B HIS* 4.3 5.8 - - + -
489B ASN* 3.2 44.0 - - + -
490B ALA 3.5 19.1 - - - -
491B PRO* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 3.0 36.2 + - - -
205B PRO* 3.0 27.1 - - - +
446B ALA* 4.2 1.9 - - - +
447B HIS 3.3 2.7 - - - +
448B ALA* 3.7 14.8 - - + -
467B ARG* 2.9 32.4 + - + +
468B PHE* 1.3 86.5 - - - +
470B HIS* 1.3 60.9 + - - +
471B ILE* 3.2 17.2 - - + +
488B TYR 3.5 2.3 - - - +
489B ASN* 3.2 4.5 - - - -
490B ALA* 2.7 44.6 + - + +
492B LEU* 5.2 3.6 - - + -
515B PHE* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU 3.5 2.9 - - - +
446B ALA* 3.2 2.9 - - - -
447B HIS* 2.9 56.9 + + + +
449B TRP* 6.0 1.3 - - - +
468B PHE* 4.3 6.0 - - + -
469B GLU* 1.3 70.8 - - - +
471B ILE* 1.3 60.7 + - - +
472B GLU* 2.8 39.9 + - + -
487B SER* 4.3 14.8 - - - -
488B TYR 3.6 4.4 + - - -
489B ASN* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 3.7 12.8 - - + -
444B THR* 3.6 23.1 - - + -
445B GLU 3.6 2.2 - - - -
446B ALA* 3.6 15.7 - - + -
469B GLU* 3.2 45.8 - - + +
470B HIS* 1.3 73.6 - - - +
472B GLU* 1.3 64.2 + - - +
473B SER* 3.9 5.6 - - - +
486B VAL 3.7 0.3 - - - +
487B SER* 3.1 5.2 - - - -
488B TYR* 3.0 44.7 + - + +
515B PHE* 3.7 23.3 - - + -
517B THR* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B THR* 3.0 2.3 - - - -
445B GLU* 2.6 53.9 + - + +
447B HIS* 5.5 2.1 - - - -
470B HIS* 2.8 32.5 + - + +
471B ILE* 1.3 77.8 - - - +
473B SER* 1.3 61.8 + - - +
474B TYR* 5.9 0.7 - - - -
486B VAL 3.3 6.1 - - - +
487B SER* 3.6 21.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 5.3 1.0 - - - +
175B GLY* 5.7 0.2 - - - -
443B GLY 3.0 7.2 - - - -
444B THR* 2.5 31.9 + - - +
471B ILE* 3.9 8.3 - - - +
472B GLU* 1.3 71.5 - - - +
474B TYR* 1.3 65.1 + - - +
485B GLU* 3.4 1.9 - - - +
486B VAL* 3.0 45.7 + - - +
488B TYR* 5.1 0.4 - - - -
517B THR* 4.6 4.9 + - - -
518B VAL 4.7 4.4 + - - -
520B TYR* 4.0 10.6 - - - -
523B ILE* 5.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B SER* 5.6 3.9 - - - -
415B THR 5.7 0.2 + - - -
441B ARG* 3.5 24.6 + - + +
442B SER* 2.9 20.7 + - - -
443B GLY* 2.9 48.7 + - - +
444B THR* 5.6 0.2 - - - -
472B GLU 5.9 0.2 - - - -
473B SER* 1.3 78.3 - - - +
475B GLN* 1.3 66.3 + - - +
476B ASN* 3.8 11.9 - - + -
483B HIS* 3.9 23.6 - + + +
484B GLU 3.2 12.3 - - - +
485B GLU* 4.5 4.0 - - + -
520B TYR* 4.5 1.4 - - - -
523B ILE* 5.2 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B GLU* 4.0 6.7 + - - -
440B THR* 3.4 33.8 + - + +
441B ARG 3.5 2.2 - - - +
442B SER* 2.7 26.8 + - - +
474B TYR* 1.3 77.0 - - - +
476B ASN* 1.3 63.5 + - - +
477B ASN* 3.9 5.1 + - + +
482B THR 4.8 0.2 - - - -
483B HIS* 3.6 5.7 - - - -
484B GLU* 2.9 29.5 + - - +
520B TYR* 3.5 26.7 + - - +
523B ILE* 4.2 24.3 - - + +
524B GLY 5.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B THR* 3.5 3.1 - - - -
441B ARG* 2.7 42.3 + - + +
474B TYR* 3.8 9.9 - - + -
475B GLN* 1.3 72.4 - - - +
477B ASN* 1.3 72.6 + - - +
478B ALA* 3.7 6.2 + - - +
481B GLY* 5.2 3.6 + - - -
482B THR 3.9 9.0 + - - -
483B HIS* 4.1 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ASP 3.9 2.3 - - - +
440B THR* 3.7 21.4 - - + +
475B GLN* 3.9 6.5 + - + +
476B ASN* 1.3 74.9 + - - +
478B ALA* 1.3 54.8 + - - +
479B ILE* 2.7 37.6 + - - +
480B THR* 3.0 35.8 + - - +
481B GLY* 2.6 36.4 + - - -
482B THR* 3.4 14.3 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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