Contacts of the strand formed by residues 471 - 490 (chain B) in PDB entry 2W77
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 GLU 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B PRO* 3.8 25.9 - - + +
465B PHE* 3.6 21.7 + - - -
466B GLN* 3.1 29.2 + - - +
470B ARG* 1.3 72.2 - - - +
472B HIS* 1.3 61.7 + - - +
538B ASN* 3.4 21.1 + - - +
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Residues in contact with HIS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B PRO* 3.1 9.7 - - - +
465B PHE* 2.7 57.4 + - + +
467B PHE* 3.2 36.3 + + + +
468B LEU* 4.1 5.8 + - - +
470B ARG* 3.0 24.0 + - - +
471B GLU* 1.3 74.9 - - - +
473B GLU* 1.3 67.4 + - - +
536B ARG 3.6 11.0 - - - +
537B PHE* 3.9 16.0 - + + +
538B ASN* 2.9 45.3 + - + +
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Residues in contact with GLU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 3.8 37.8 - - + +
159B VAL 5.6 1.2 + - - +
160B LEU* 4.6 5.4 - - - +
463B GLY* 3.3 14.9 - - - +
464B PRO* 5.2 6.1 - - - +
465B PHE* 3.9 5.5 - - - -
472B HIS* 1.3 81.7 - - - +
474B LEU* 1.3 61.2 + - - +
534B THR 3.9 0.3 - - - +
535B ALA* 3.4 5.4 - - - +
536B ARG* 3.0 55.9 + - + +
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Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 4.5 0.3 - - - +
410B TRP* 4.1 23.8 - - + -
461B LEU 4.4 0.4 - - - -
462B THR* 3.1 27.9 + - - -
463B GLY 2.9 10.9 + - - -
465B PHE* 3.9 21.1 - - + -
473B GLU* 1.3 74.1 - - - +
475B VAL* 1.3 65.3 + - - +
476B VAL* 4.0 26.0 - - + -
533B MET* 5.0 5.2 - - + -
534B THR 3.4 23.1 - - - +
535B ALA* 4.1 11.4 - - + -
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B THR 4.2 8.7 - - - +
157B ARG* 4.0 27.4 - - + +
158B LEU* 3.6 32.3 - - + -
460B TYR* 4.7 4.9 - - + -
461B LEU 3.2 10.8 - - - +
462B THR* 4.1 9.2 - - - -
474B LEU* 1.3 80.0 - - - +
476B VAL* 1.3 66.2 + - - +
532B TYR* 3.7 14.5 - - + +
533B MET* 3.3 4.0 - - - -
534B THR* 2.8 44.5 + - - +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B TRP* 5.6 3.8 - - + -
459B ILE* 5.5 1.8 - - + +
460B TYR* 3.4 2.7 - - - -
461B LEU* 2.7 61.8 + - + +
474B LEU* 4.0 25.0 - - + +
475B VAL* 1.3 78.7 - - - +
477B GLY* 1.3 57.6 + - - +
532B TYR 3.4 4.7 - - - +
533B MET* 4.4 20.4 - - + -
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Residues in contact with GLY 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 3.3 17.3 - - - -
460B TYR* 3.9 3.1 - - - -
476B VAL* 1.3 76.6 - - - +
478B THR* 1.3 61.3 + - - -
531B SER* 3.4 3.5 - - - -
532B TYR* 3.0 51.0 + - - +
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Residues in contact with THR 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 6.0 2.9 - - + +
458B ASP* 3.6 2.6 - - - -
459B ILE* 3.1 50.7 + - + +
477B GLY* 1.3 73.5 - - - -
479B SER* 1.3 67.2 + - - +
530B GLY 2.8 16.9 + - - -
531B SER* 3.0 14.7 + - - -
532B TYR* 4.5 1.3 - - - -
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 3.2 10.1 - - - -
458B ASP* 3.0 26.7 - - - -
478B THR* 1.3 78.0 + - - +
480B ALA* 1.3 62.6 + - - +
481B SER* 5.8 1.0 - - - -
528B GLN* 5.1 2.6 + - - +
529B LEU* 3.3 6.4 - - - +
530B GLY 2.7 38.5 + - - +
532B TYR* 4.7 1.6 - - - -
550B ARG* 3.2 26.4 + - - -
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Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ASN 4.5 1.3 - - - -
456B SER* 3.4 3.1 - - - -
457B LEU* 2.9 50.1 + - + +
479B SER* 1.3 76.1 - - - +
481B SER* 1.3 65.2 + - - +
482B PHE* 4.1 15.3 - - + -
528B GLN 3.4 4.7 - - - -
529B LEU* 3.7 18.2 - - + -
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Residues in contact with SER 481 (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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223B PRO* 5.4 6.3 + - - +
225B THR* 3.8 23.7 - - - +
454B SER* 5.3 2.1 - - - -
455B ASN 3.7 5.5 - - - -
456B SER* 3.9 13.4 + - - -
479B SER* 5.8 1.3 - - - -
480B ALA* 1.3 78.0 - - - +
482B PHE* 1.3 65.6 + - - +
483B SER 4.0 0.3 + - - -
526B THR* 3.8 1.9 - - - +
527B ARG* 3.3 6.5 - - - +
528B GLN* 2.9 47.4 + - - -
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Residues in contact with PHE 482 (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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453B LYS 4.2 0.2 - - - +
454B SER* 3.3 1.1 - - - -
455B ASN* 2.8 48.0 + - + +
480B ALA* 4.1 22.2 - - + -
481B SER* 1.3 77.0 - - - +
483B SER* 1.3 59.9 + - - +
526B THR 3.9 3.8 - - - -
527B ARG* 3.7 35.0 - - + -
529B LEU* 5.1 3.8 - - + -
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Residues in contact with SER 483 (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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225B THR* 2.9 34.7 + - - +
452B THR* 4.5 6.1 - - - +
453B LYS 3.3 12.3 - - - -
454B SER* 3.5 10.1 - - - -
481B SER* 4.0 1.4 + - - -
482B PHE* 1.3 74.3 - - - +
484B HIS* 1.3 59.3 + - - +
485B TRP 4.3 0.4 - - - -
525B LYS* 3.4 4.3 - - - +
526B THR* 2.9 50.1 + - - +
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Residues in contact with HIS 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B GLU 4.0 0.2 - - - +
452B THR* 3.4 3.8 - - - -
453B LYS* 3.0 40.4 + - + +
483B SER* 1.3 71.6 - - - +
485B TRP* 1.3 60.3 + - - +
486B GLU* 3.4 34.8 + - + +
523B ASP* 2.7 29.5 + - - -
524B ASP 3.5 13.0 - - - -
525B LYS* 3.9 26.2 - - + +
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Residues in contact with TRP 485 (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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228B ASN* 4.2 18.6 - - + -
231B TYR* 3.6 38.8 - + + -
423B TYR* 3.1 26.9 + + - -
451B GLU 3.5 6.7 - - - -
452B THR* 3.4 26.5 - - + +
483B SER 4.3 0.6 - - - -
484B HIS* 1.3 72.0 - - - +
486B GLU* 1.3 77.5 + - - +
487B GLY* 4.4 0.4 - - - +
522B ILE* 3.5 39.6 - - + +
523B ASP* 3.6 2.8 + - - -
524B ASP* 2.9 56.0 + - + +
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Residues in contact with GLU 486 (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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450B GLY* 3.3 1.4 - - - -
451B GLU* 3.0 34.0 + - + +
453B LYS* 5.5 7.3 - - - -
484B HIS* 3.4 40.6 + - + +
485B TRP* 1.3 76.8 - - - +
487B GLY* 1.3 58.7 + - - +
522B ILE 3.3 8.5 - - - +
523B ASP* 3.8 12.9 - - - +
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Residues in contact with GLY 487 (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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423B TYR* 4.2 7.9 - - - -
449B THR 3.3 10.5 - - - -
450B GLY* 3.9 3.1 - - - -
486B GLU* 1.3 75.1 - - - +
488B LYS* 1.3 66.5 + - - +
520B GLN 3.9 0.3 - - - +
521B TYR* 3.5 6.1 - - - -
522B ILE* 2.8 49.6 + - - +
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Residues in contact with LYS 488 (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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231B TYR* 6.1 0.2 - - - -
423B TYR* 5.1 0.7 + - - -
447B LYS 4.0 0.5 - - - +
448B TYR* 3.5 2.9 - - - +
449B THR* 2.7 45.1 + - - +
487B GLY* 1.3 77.9 - - - +
489B SER* 1.3 63.3 + - - +
490B TYR* 4.0 24.0 + - + +
518B PRO* 3.7 22.9 - - + +
520B GLN 3.7 5.4 - - - +
521B TYR* 4.2 24.7 - - + -
522B ILE* 6.0 0.2 - - - -
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Residues in contact with SER 489 (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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231B TYR* 4.3 8.8 + - - -
447B LYS 3.5 4.5 - - - -
448B TYR* 3.5 23.5 - - - -
488B LYS* 1.3 77.5 + - - +
490B TYR* 1.3 57.4 + - - +
491B TRP* 3.4 29.2 - - - -
518B PRO* 3.5 2.4 - - - +
519B SER 2.7 31.2 + - - -
520B GLN* 3.3 25.5 + - - +
522B ILE* 4.5 4.7 - - - +
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Residues in contact with TYR 490 (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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446B GLN* 3.7 5.9 - - - +
447B LYS* 3.0 63.3 + - + +
449B THR* 4.7 7.0 - - + -
488B LYS* 4.0 29.6 + - + +
489B SER* 1.3 80.4 - - - +
491B TRP* 1.3 65.5 + - - +
515B TRP* 3.8 27.5 - - + +
516B GLY 3.2 28.7 - - - -
517B THR 3.9 2.2 - - - -
518B PRO* 3.5 33.1 - - + +
519B SER* 4.0 4.3 - - - +
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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
------------------------------------------------------------
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