Contacts of the helix formed by residues 486 - 507 (chain B) in PDB entry 1YA8
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 SER 486 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B TYR* 4.4 1.6 + - - -
454B SER* 5.9 0.2 - - - -
484B GLY 3.2 6.6 + - - -
485B ALA* 1.3 76.0 - - - +
487B GLU* 1.3 65.7 + - - +
488B GLU* 3.6 15.3 + - - +
489B GLU* 3.1 22.6 + - - +
490B ILE* 2.8 20.6 + - - +
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Residues in contact with GLU 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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486B SER* 1.3 74.5 - - - +
488B GLU* 1.3 61.7 + - - +
490B ILE* 3.6 20.5 - - - +
491B ARG* 3.0 58.4 + - + +
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Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B TYR* 3.3 26.3 + - + +
486B SER* 3.1 10.5 + - - +
487B GLU* 1.3 78.4 - - - +
489B GLU* 1.3 57.6 + - - +
491B ARG* 3.2 4.4 + - - +
492B LEU* 2.8 29.5 + - + +
531B ALA* 3.5 33.2 - - - +
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Residues in contact with GLU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B TYR* 3.6 26.0 + - + +
453B PRO* 3.5 9.5 - - - +
454B SER* 2.9 40.0 + - - -
455B PHE* 3.0 28.6 - - - -
473B PHE* 5.5 0.2 - - - +
474B SER* 5.4 4.4 + - - +
479B PRO* 4.2 10.3 - - + -
485B ALA* 3.2 16.9 - - + -
486B SER* 3.1 15.5 + - - +
488B GLU* 1.3 79.5 - - - +
490B ILE* 1.3 65.6 + - - +
492B LEU* 3.0 7.9 + - + +
493B SER* 3.0 24.3 + - - -
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Residues in contact with ILE 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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479B PRO* 4.0 16.6 - - + +
480B PHE* 3.6 28.3 - - + -
485B ALA* 3.3 33.0 - - + +
486B SER 2.8 17.7 + - - +
487B GLU* 3.6 28.7 - - - +
489B GLU* 1.3 75.7 - - - +
491B ARG* 1.3 60.5 + - + +
493B SER* 3.6 1.4 + - - -
494B LYS* 3.3 31.3 + - - +
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Residues in contact with ARG 491 (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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487B GLU* 3.0 44.8 + - - +
488B GLU* 3.8 4.2 - - - +
490B ILE* 1.3 76.6 - - + +
492B LEU* 1.3 65.4 + - - +
493B SER 3.2 2.0 - - - -
494B LYS* 3.7 17.7 - - + +
495B MET* 3.0 41.0 + - + +
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Residues in contact with LEU 492 (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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449B PHE* 4.3 3.1 - - + -
451B TYR* 3.4 54.7 - - + -
474B SER* 3.8 16.2 - - - +
488B GLU* 2.8 14.5 + - + +
489B GLU* 3.4 9.4 - - + +
491B ARG* 1.3 76.2 - - - +
493B SER* 1.3 63.1 + - - +
495B MET* 3.3 12.7 - - + +
496B VAL* 3.0 24.8 + - + +
529B ILE* 3.7 28.0 - - + -
530B GLY* 4.0 16.6 - - - +
533B THR* 4.7 3.6 - - - +
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Residues in contact with SER 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B SER* 3.1 32.4 + - - +
477B GLY* 3.3 12.1 - - - -
479B PRO* 3.8 17.3 - - - -
480B PHE* 3.6 2.9 - - - -
489B GLU 3.0 10.8 + - - -
490B ILE 3.6 9.4 - - - -
492B LEU* 1.3 74.8 - - - +
494B LYS* 1.3 67.4 + - - +
496B VAL 3.0 2.1 + - - -
497B MET* 3.0 40.3 + - - +
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Residues in contact with LYS 494 (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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160B HIS* 4.6 12.1 - - - +
161B GLU* 4.5 2.3 - - - +
480B PHE* 3.5 33.9 - - + -
490B ILE* 3.3 13.7 + - - +
491B ARG* 3.7 20.8 - - + +
493B SER* 1.3 80.0 + - - +
495B MET* 1.3 64.7 + - - +
497B MET* 3.3 12.8 + - + +
498B LYS* 3.1 25.6 + - + +
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Residues in contact with MET 495 (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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491B ARG* 3.0 39.3 + - + +
492B LEU* 3.3 15.9 - - + +
493B SER 3.1 0.2 - - - -
494B LYS* 1.3 76.2 - - - +
496B VAL* 1.3 64.3 + - + +
498B LYS* 3.2 19.8 - - - +
499B PHE* 3.2 14.1 + - + -
514B LEU* 3.7 28.7 - - + +
515B PRO* 4.3 15.7 - - + -
529B ILE* 5.9 0.7 - - - -
530B GLY 5.6 1.8 - - - +
531B ALA 6.0 1.6 - - - +
533B THR* 3.6 34.5 - - - +
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Residues in contact with VAL 496 (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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449B PHE* 4.8 4.3 - - + -
471B GLU* 6.4 0.2 - - + -
474B SER* 3.9 16.6 - - - +
475B VAL* 3.8 29.4 - - + +
492B LEU* 3.0 31.6 + - + +
493B SER 3.0 5.6 + - - +
495B MET* 1.3 73.3 - - + +
497B MET* 1.3 67.7 + - - +
499B PHE* 3.1 10.4 + - + +
500B TRP* 2.9 45.1 + - + +
529B ILE* 4.2 17.5 - - + -
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Residues in contact with MET 497 (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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156B ALA* 4.6 1.1 - - - -
157B LEU* 3.7 33.6 - - + +
160B HIS* 4.3 18.2 - - + -
161B GLU* 3.7 15.9 - - + +
474B SER 3.7 4.0 - - - +
475B VAL* 3.4 23.1 - - - +
477B GLY* 4.1 9.9 - - - -
480B PHE* 3.5 23.8 - - + -
493B SER* 3.0 41.4 + - - +
494B LYS* 3.7 9.0 - - - +
496B VAL* 1.3 74.4 - - - +
498B LYS* 1.3 54.1 + - - +
500B TRP* 3.8 4.7 - - - +
501B ALA* 2.7 38.3 + - - +
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Residues in contact with LYS 498 (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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160B HIS 5.3 1.2 + - - -
161B GLU* 3.5 31.1 + - - +
494B LYS* 3.1 14.7 + - + +
495B MET* 3.2 11.0 - - - +
497B MET* 1.3 76.4 - - - +
499B PHE* 1.3 54.3 + - - +
501B ALA 3.5 0.2 - - - -
502B ASN* 2.5 51.5 + - - +
505B ARG* 5.1 0.7 - - - +
511B GLY* 6.1 0.4 - - - -
512B GLU 4.9 12.6 - - - +
513B GLY 6.5 0.2 - - - -
514B LEU* 3.4 30.5 - - + -
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Residues in contact with PHE 499 (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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347B MET* 5.1 0.2 - - - -
495B MET* 3.2 27.0 + - + -
496B VAL* 3.1 10.7 + - + +
498B LYS* 1.3 79.9 - - - +
500B TRP* 1.3 75.2 + - + +
502B ASN* 3.1 2.1 + - - +
503B PHE* 2.8 24.5 + - - +
509B PRO* 2.9 34.3 - - - +
510B ASN* 4.8 1.3 - - - -
514B LEU* 3.9 14.4 - - + -
515B PRO* 3.6 38.1 - - + -
517B TRP* 3.7 29.8 - + + -
527B LEU* 3.6 26.2 - - + -
529B ILE* 4.8 8.3 - - + -
533B THR* 4.5 10.8 - - + -
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Residues in contact with TRP 500 (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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136B MET* 4.1 13.8 - - + +
157B LEU* 5.7 2.7 - - + -
218B PHE* 3.9 11.7 - + - -
244B ILE* 3.8 20.5 - - + +
246B GLU* 3.0 25.7 + - + -
347B MET* 4.0 13.9 - - - -
447B TYR* 3.5 41.3 - + - -
449B PHE* 6.4 0.9 - + - -
471B GLU* 5.3 2.5 - - + -
475B VAL* 3.6 35.7 - - + +
496B VAL* 2.9 36.8 + - + +
497B MET* 3.8 6.3 - - - +
499B PHE* 1.3 77.9 - - + +
501B ALA* 1.3 57.7 + - - +
503B PHE* 3.1 10.9 + - - +
504B ALA* 2.8 27.4 + - - +
517B TRP* 3.9 22.4 - + - -
529B ILE* 4.3 12.1 - - + -
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Residues in contact with ALA 501 (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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136B MET* 4.3 6.9 - - - -
157B LEU* 5.6 1.3 - - + +
161B GLU* 3.3 32.1 - - + +
163B VAL* 4.3 5.7 - - + +
497B MET 2.7 22.8 + - - +
500B TRP* 1.3 73.0 - - - +
502B ASN* 1.3 56.6 + - - +
504B ALA* 3.1 10.4 + - - +
505B ARG* 2.8 49.2 + - - +
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Residues in contact with ASN 502 (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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498B LYS* 2.5 30.4 + - - +
499B PHE 3.4 4.3 - - - +
501B ALA* 1.3 70.5 - - - +
503B PHE* 1.3 54.8 + - - +
505B ARG* 2.7 36.5 + - - +
506B ASN* 2.8 37.1 + - - +
508B ASN 3.6 6.5 - - - +
509B PRO 3.2 15.4 + - - +
510B ASN 3.3 19.2 + - - +
511B GLY* 3.7 4.8 - - - -
514B LEU* 3.2 33.1 - - - +
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Residues in contact with PHE 503 (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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216B THR* 4.8 2.2 - - + -
242B ARG* 3.1 21.4 - - + -
243B ALA 3.4 17.7 - - - -
244B ILE* 3.5 26.9 - - + -
345B PRO* 3.6 45.8 - - + -
347B MET* 3.6 30.5 - - + -
445B TYR* 4.0 15.3 - + - -
499B PHE 2.8 11.8 + - - +
500B TRP 3.3 7.9 - - - +
502B ASN* 1.3 74.2 - - - +
504B ALA* 1.3 61.0 + - - +
507B GLY* 2.5 45.3 + - - -
508B ASN 3.6 10.0 + - - +
509B PRO* 4.0 12.6 - - + -
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Residues in contact with ALA 504 (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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134B PRO* 4.3 11.2 - - + +
135B VAL 5.2 0.4 - - - +
136B MET* 3.8 30.3 - - + -
163B VAL* 5.2 1.6 - - + -
214B SER* 3.5 11.1 + - - +
216B THR* 3.4 24.0 + - + +
242B ARG* 2.8 22.0 + - - -
500B TRP 2.8 12.1 + - - +
501B ALA* 3.2 9.6 - - - +
503B PHE* 1.3 76.7 - - - +
505B ARG* 1.3 58.3 + - - +
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Residues in contact with ARG 505 (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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134B PRO* 3.7 25.5 - - + +
161B GLU* 3.1 46.5 + - - -
162B ASN* 4.8 1.2 + - - +
163B VAL* 4.1 4.9 - - - +
214B SER* 4.4 4.1 + - - -
242B ARG* 3.5 12.2 + - - -
498B LYS* 5.1 1.4 - - - +
501B ALA* 2.8 20.3 + - - +
502B ASN* 2.7 45.1 + - - +
504B ALA* 1.3 80.3 - - - +
506B ASN* 1.3 75.0 + - - +
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Residues in contact with ASN 506 (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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242B ARG* 3.8 10.8 + - - +
345B PRO* 5.3 0.2 - - - +
502B ASN* 2.8 22.7 + - - +
505B ARG* 1.3 90.3 - - - +
507B GLY* 1.3 63.6 + - - +
508B ASN* 3.0 17.8 + - + +
510B ASN 5.1 4.8 + - - -
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Residues in contact with GLY 507 (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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242B ARG* 3.4 19.3 - - - +
345B PRO* 3.7 18.9 - - - +
443B PRO* 4.8 4.0 - - - +
445B TYR* 3.5 15.9 + - - -
503B PHE* 2.5 39.1 + - - -
506B ASN* 1.3 73.1 - - - +
508B ASN* 1.3 56.1 + - - +
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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