Contacts of the helix formed by residues 486 - 507 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451C TYR* 4.6 1.7 + - - -
484C GLY 3.4 3.4 + - - -
485C ALA* 1.3 74.5 - - - +
487C GLU* 1.3 67.8 + - - +
488C GLU* 3.1 11.8 + - - +
489C GLU* 3.2 21.4 + - - +
490C ILE* 2.9 27.2 + - - +
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Residues in contact with GLU 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C SER* 1.3 74.4 - - - +
488C GLU* 1.3 61.4 + - + +
490C ILE* 3.6 11.8 + - - +
491C ARG* 3.0 50.3 + - - +
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Residues in contact with GLU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C TYR* 3.5 33.2 + - + +
486C SER* 3.1 8.4 + - - +
487C GLU* 1.3 82.4 - - + +
489C GLU* 1.3 60.1 + - - +
491C ARG* 3.3 21.2 + - - +
492C LEU* 2.9 25.8 + - - +
531C ALA* 3.8 23.2 - - - +
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Residues in contact with GLU 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C TYR* 3.5 27.8 + - + +
453C PRO* 3.4 6.6 - - - +
454C SER* 2.8 47.4 + - - -
455C PHE* 3.0 23.9 - - - -
473C PHE* 5.5 0.2 - - - +
474C SER* 5.3 1.7 + - - +
479C PRO* 3.9 9.6 - - + +
485C ALA* 3.3 15.1 - - + -
486C SER* 3.2 15.8 + - - +
488C GLU* 1.3 76.2 - - - +
490C ILE* 1.3 66.6 + - - +
492C LEU* 3.2 7.6 + - + +
493C SER* 2.9 24.8 + - - -
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Residues in contact with ILE 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C PRO* 4.0 16.4 - - + +
480C PHE* 3.7 24.9 - - + -
485C ALA* 3.9 22.7 - - + +
486C SER 2.9 27.1 + - - +
487C GLU* 3.7 9.4 - - - +
489C GLU* 1.3 79.6 - - - +
491C ARG* 1.3 62.8 + - - +
493C SER* 3.3 2.1 + - - -
494C LYS* 3.1 34.5 + - + +
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Residues in contact with ARG 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C GLU* 3.0 38.4 + - - +
488C GLU* 3.5 25.9 + - - +
489C GLU 3.2 0.2 - - - -
490C ILE* 1.3 79.2 - - - +
492C LEU* 1.3 61.9 + - - +
494C LYS* 3.5 8.9 + - - +
495C MET* 3.1 36.7 + - + +
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Residues in contact with LEU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C PHE* 3.9 7.9 - - + -
451C TYR* 3.6 46.0 - - + -
474C SER* 3.5 19.5 - - - +
488C GLU 2.9 14.7 + - - +
489C GLU* 3.5 9.4 - - + +
491C ARG* 1.3 76.3 - - - +
493C SER* 1.3 64.2 + - - +
495C MET* 3.1 16.3 + - + +
496C VAL* 3.0 24.5 + - + +
529C ILE* 4.0 21.1 - - + -
530C GLY 3.4 26.7 - - - +
531C ALA* 6.3 0.7 - - - -
533C THR* 4.5 3.1 - - - +
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Residues in contact with SER 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C SER* 3.0 32.5 + - - -
477C GLY* 3.2 20.3 - - - -
479C PRO* 3.8 19.1 - - - -
480C PHE* 3.9 4.0 - - - -
489C GLU 2.9 15.4 + - - -
490C ILE 3.7 4.7 - - - -
492C LEU* 1.3 78.1 - - - +
494C LYS* 1.3 62.0 + - - +
496C VAL* 3.3 1.7 + - - +
497C MET* 2.9 30.6 + - - +
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Residues in contact with LYS 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C HIS* 4.6 14.4 - - - -
161C GLU* 4.1 1.9 - - - +
480C PHE* 3.2 30.5 - - + -
490C ILE* 3.1 25.0 + - + +
491C ARG* 3.8 7.4 - - - +
493C SER* 1.3 75.6 - - - +
495C MET* 1.3 63.4 + - - +
497C MET* 3.4 11.8 + - + +
498C LYS* 3.1 31.8 + - + +
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Residues in contact with MET 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C ARG* 3.1 29.8 + - + +
492C LEU* 3.1 17.5 + - + +
494C LYS* 1.3 78.8 - - - +
496C VAL* 1.3 64.7 + - + +
498C LYS* 3.0 15.9 + - - +
499C PHE* 3.1 26.6 + - + -
514C LEU* 3.8 25.1 - - + +
515C PRO* 4.5 13.9 - - + -
529C ILE* 5.9 1.8 - - - -
530C GLY 5.6 1.1 - - - +
531C ALA 6.1 1.1 - - - +
533C THR* 3.7 31.6 - - - +
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Residues in contact with VAL 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C PHE* 4.5 3.8 - - + -
471C GLU* 6.4 0.4 - - + -
474C SER* 3.8 17.0 - - - -
475C VAL* 3.9 33.2 - - + +
492C LEU* 3.0 20.1 + - + +
493C SER 3.7 6.5 - - - +
495C MET* 1.3 75.8 - - + +
497C MET* 1.3 63.6 + - - +
499C PHE* 3.1 12.6 + - + +
500C TRP* 2.9 41.7 + - + +
529C ILE* 4.0 31.0 - - + -
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Residues in contact with MET 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C ALA 4.6 0.9 - - - -
157C LEU* 4.1 30.1 - - + +
160C HIS* 4.3 18.2 - - + -
161C GLU* 3.2 15.4 - - + +
474C SER 3.5 4.3 - - - +
475C VAL 3.4 20.9 - - - +
477C GLY* 3.9 17.5 - - - -
480C PHE* 3.6 23.8 - - + -
493C SER* 2.9 38.2 + - - +
494C LYS* 3.7 9.4 - - - +
496C VAL* 1.3 76.1 - - - +
498C LYS* 1.3 57.4 + - - +
500C TRP* 3.6 5.5 + - - +
501C ALA* 3.0 30.8 + - - +
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Residues in contact with LYS 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C HIS 4.9 4.2 + - - -
161C GLU* 3.1 33.6 + - - +
494C LYS* 3.1 18.6 + - + +
495C MET* 3.0 11.0 + - - +
497C MET* 1.3 73.4 - - - +
499C PHE* 1.3 55.0 + - - +
501C ALA* 3.2 1.4 + - - +
502C ASN* 2.7 51.5 + - - +
505C ARG* 4.9 0.9 - - - +
512C GLU 5.5 6.7 - - - -
514C LEU* 3.6 26.2 - - + -
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Residues in contact with PHE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C MET* 3.1 40.7 + - + -
496C VAL* 3.4 10.8 - - + +
498C LYS* 1.3 79.2 - - - +
500C TRP* 1.3 67.2 + - + +
502C ASN 3.2 0.7 + - - -
503C PHE* 3.0 23.6 + - - +
509C PRO* 3.1 29.9 - - - +
510C ASN* 4.7 1.8 - - - -
514C LEU* 3.7 19.5 - - + -
515C PRO* 3.6 37.0 - - + -
517C TRP* 3.5 38.6 - + + -
527C LEU* 3.9 19.7 - - + -
529C ILE* 5.2 5.8 - - + -
533C THR* 4.9 3.6 - - + -
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Residues in contact with TRP 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C MET* 3.8 13.9 - - + +
157C LEU* 5.6 3.8 - - + -
218C PHE* 4.1 11.7 - + - -
244C ILE* 3.7 21.7 - - + +
246C GLU* 3.2 21.5 + - + -
347C MET* 3.8 13.5 - - + -
447C TYR* 3.4 46.2 - + - -
449C PHE* 6.6 0.2 - + - -
471C GLU* 5.5 1.8 - - + -
475C VAL* 3.6 35.7 - - + +
496C VAL* 2.9 34.5 + - + +
497C MET* 4.0 6.7 - - - +
499C PHE* 1.3 81.8 - - + +
501C ALA* 1.3 58.8 + - - +
503C PHE* 3.4 7.8 + - - +
504C ALA* 3.0 25.1 + - - +
517C TRP* 3.7 23.6 - + - -
529C ILE* 4.3 11.9 - - + -
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Residues in contact with ALA 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C MET* 4.6 6.0 - - - -
157C LEU* 5.1 1.8 - - + +
161C GLU* 3.4 23.8 - - + +
163C VAL* 4.4 5.6 - - + -
497C MET 3.0 19.1 + - - +
498C LYS 3.8 0.4 - - - +
500C TRP* 1.3 73.8 - - - +
502C ASN* 1.3 59.8 + - - +
503C PHE 3.1 0.2 - - - -
504C ALA* 3.5 8.8 - - - +
505C ARG* 2.9 56.5 + - - +
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Residues in contact with ASN 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C LYS* 2.7 25.9 + - - +
499C PHE 3.6 0.4 - - - +
501C ALA* 1.3 73.6 - - - +
503C PHE* 1.3 57.3 + - - +
505C ARG* 3.0 26.8 + - - +
506C ASN* 2.9 33.4 + - - +
508C ASN 3.1 12.0 - - - +
509C PRO 2.9 33.3 + - - +
510C ASN 3.1 15.0 + - - +
511C GLY* 3.5 6.2 - - - -
514C LEU* 3.4 24.5 - - - +
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Residues in contact with PHE 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C THR* 4.5 5.2 - - + -
242C ARG* 2.9 11.5 - - + -
243C ALA 3.5 23.8 - - - -
244C ILE* 3.6 26.9 - - + -
345C PRO* 3.4 45.1 - - + -
347C MET* 3.5 28.9 - - + -
445C TYR* 4.1 14.8 - + - -
499C PHE 3.0 13.1 + - - +
500C TRP 3.4 7.9 - - - +
502C ASN* 1.3 75.1 - - - +
504C ALA* 1.3 64.5 + - - +
507C GLY* 2.6 31.3 + - - -
508C ASN 3.6 19.5 + - - +
509C PRO* 4.1 12.3 - - + -
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Residues in contact with ALA 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PRO* 4.2 13.3 - - + +
135C VAL 5.2 0.2 - - - +
136C MET* 3.7 28.3 - - + -
163C VAL* 5.1 2.0 - - + -
214C SER* 3.5 11.4 + - - -
216C THR* 3.2 27.4 + - - +
242C ARG* 2.7 20.5 + - - +
500C TRP 3.0 13.6 + - - +
501C ALA* 3.3 9.6 + - - +
503C PHE* 1.3 76.1 - - - +
505C ARG* 1.3 56.5 + - - +
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Residues in contact with ARG 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PRO* 4.0 22.7 - - + +
161C GLU* 3.1 37.2 + - - -
162C ASN* 4.7 1.6 + - - +
163C VAL* 3.8 8.1 - - - +
214C SER* 4.4 3.5 + - - -
242C ARG* 3.1 14.9 + - - -
498C LYS* 4.2 1.6 + - - +
501C ALA* 2.9 39.4 + - - +
502C ASN* 3.0 30.8 + - - +
503C PHE 3.0 0.2 - - - -
504C ALA* 1.3 78.3 - - - +
506C ASN* 1.3 75.2 + - - +
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Residues in contact with ASN 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ARG* 3.8 10.2 + - - +
345C PRO* 5.3 0.3 - - - +
502C ASN* 2.9 22.7 + - - +
505C ARG* 1.3 92.9 - - - +
507C GLY* 1.3 66.8 + - - +
508C ASN* 3.1 16.7 + - + +
510C ASN 5.0 4.2 + - - -
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Residues in contact with GLY 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ARG* 3.5 17.1 - - - +
345C PRO* 3.7 21.2 - - - +
443C PRO* 4.5 4.9 - - - +
445C TYR* 3.7 14.6 + - - -
503C PHE* 2.6 37.5 + - - -
506C ASN* 1.3 73.1 - - - +
508C ASN* 1.3 58.0 + - - +
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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