Contacts of the helix formed by residues 473 - 494 (chain C) in PDB entry 2Y0N
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 473 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C SER 3.9 1.4 + - - -
472C PHE* 1.3 76.8 - - - +
474C GLU* 1.3 66.2 + - - +
475C LYS* 4.1 2.5 + - - +
476C ASN* 3.2 32.9 + - - +
477C LEU* 3.0 22.6 + - - +
579G ARG* 5.0 1.4 - - - +
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Residues in contact with GLU 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C PHE 3.9 1.3 + - - +
473C SER* 1.3 75.2 - - - +
475C LYS* 1.3 66.5 + - + +
477C LEU* 3.3 11.8 + - - +
478C LYS* 3.3 33.4 + - - +
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Residues in contact with LYS 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C SER* 3.4 3.0 + - - +
474C GLU* 1.3 83.4 - - + +
476C ASN* 1.3 70.4 + - - +
478C LYS* 3.9 4.2 + - - +
479C ALA* 3.6 20.3 + - - +
553F VAL* 4.5 11.2 - - + +
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Residues in contact with ASN 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C PHE* 4.9 9.8 - - + -
473C SER* 3.2 24.3 + - - +
474C GLU 3.3 0.6 - - - -
475C LYS* 1.3 83.3 - - - +
477C LEU* 1.3 64.1 + - - +
479C ALA* 3.6 3.4 + - - +
480C LEU* 3.1 23.4 + - - +
553F VAL* 4.1 19.0 - - - +
555F SER 3.5 8.0 - - - +
556F PHE* 3.4 47.0 - - + +
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Residues in contact with LEU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ILE* 3.8 36.6 - - + -
467C LEU* 4.9 3.8 - - + -
472C PHE* 3.8 34.0 - - + +
473C SER 3.0 18.1 + - - +
474C GLU* 3.3 12.3 + - - +
476C ASN* 1.3 75.4 - - - +
478C LYS* 1.3 57.2 + - + +
480C LEU* 3.1 15.7 + - + +
481C LEU* 2.8 65.4 + - + +
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Residues in contact with LYS 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C GLU* 3.3 22.2 + - - +
475C LYS* 4.3 4.5 - - - +
477C LEU* 1.3 78.8 - - + +
479C ALA* 1.3 63.2 + - - +
481C LEU* 3.3 12.2 + - + +
482C LYS* 3.0 40.1 + - - +
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Residues in contact with ALA 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ALA* 4.5 10.1 - - + -
253C LEU* 4.4 9.2 - - + -
475C LYS 3.6 15.6 + - - +
476C ASN 3.8 4.9 - - - +
477C LEU 3.3 0.6 - - - -
478C LYS* 1.3 78.5 - - - +
480C LEU* 1.3 59.9 + - - +
482C LYS* 3.7 8.9 - - - +
483C HIS* 3.0 31.1 + - - -
553F VAL* 4.2 20.0 - - + -
556F PHE* 4.3 8.1 - - + -
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Residues in contact with LEU 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C MET* 4.4 6.5 - - + -
467C LEU* 4.0 9.4 - - + -
472C PHE* 3.8 33.4 - - + -
476C ASN 3.1 13.9 + - - +
477C LEU* 3.1 17.6 + - + +
479C ALA* 1.3 75.4 - - - +
481C LEU* 1.3 64.1 + - - +
483C HIS* 2.9 16.2 + - - +
484C PHE* 3.1 50.0 + - + -
556F PHE* 4.0 27.5 - - + -
577G PHE* 3.8 23.8 - - + -
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Residues in contact with LEU 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ILE* 4.0 20.0 - - + -
173C THR 4.5 7.4 - - - +
174C ILE* 3.8 33.1 - - + +
467C LEU* 4.4 3.8 - - + -
477C LEU* 2.8 54.3 + - + +
478C LYS* 3.8 11.2 - - + +
480C LEU* 1.3 73.0 - - - +
482C LYS* 1.3 62.8 + - + +
484C PHE* 3.1 13.6 + - + +
485C ASP* 3.0 29.3 + - - +
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Residues in contact with LYS 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLU* 3.6 36.8 + - + +
478C LYS* 3.0 30.3 + - - +
479C ALA* 3.7 9.0 - - - +
481C LEU* 1.3 76.5 - - + +
483C HIS* 1.3 58.0 + - + +
485C ASP* 3.2 11.6 + - - +
486C LEU* 3.0 33.8 + - + +
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Residues in contact with HIS 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TYR* 4.0 4.7 + - - -
217C PHE* 3.9 14.9 - + - -
247C ALA* 3.1 27.1 + - + -
248C GLU* 3.7 18.0 + - - -
250C ASN 4.0 0.8 + - - -
253C LEU* 3.7 21.9 - - + +
254C CYS* 3.8 33.2 + - + -
257C MET* 3.4 31.7 - - + +
479C ALA* 3.0 20.7 + - - +
480C LEU* 2.9 11.9 + - - +
482C LYS* 1.3 77.2 - - + +
484C PHE* 1.3 62.3 + - - +
486C LEU* 4.0 8.6 - - + +
487C PHE* 3.3 16.6 + - - +
556F PHE* 4.8 1.9 - + + -
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Residues in contact with PHE 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 4.2 20.4 - - + -
257C MET* 3.5 30.5 - - + -
261C LEU* 4.4 6.7 - - + -
460C PHE* 3.9 23.3 - + + -
463C LEU* 3.6 29.4 - - + -
467C LEU* 4.0 8.3 - - + -
480C LEU* 3.1 49.4 + - + -
481C LEU* 3.1 16.6 + - + +
483C HIS* 1.3 78.0 - - - +
485C ASP* 1.3 54.7 + - - +
487C PHE* 3.2 4.7 + - - +
488C LEU* 2.7 40.4 + - - +
577G PHE* 4.1 16.4 - + - -
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Residues in contact with ASP 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 4.6 11.1 - - - +
175C GLU* 4.9 14.1 + - - +
177C PRO* 5.6 0.2 - - - +
481C LEU* 3.0 16.0 + - - +
482C LYS* 3.2 13.4 + - - +
484C PHE* 1.3 76.5 - - - +
486C LEU* 1.3 59.0 + - + +
488C LEU* 3.1 8.0 + - - +
489C ARG* 2.8 40.8 + - + +
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TYR* 3.4 14.6 - - + +
217C PHE* 4.1 23.8 - - + -
248C GLU* 4.5 24.0 - - + +
482C LYS* 3.0 20.2 + - + +
483C HIS* 4.0 11.0 - - + +
484C PHE 3.3 0.2 - - - -
485C ASP* 1.3 77.6 - - + +
487C PHE* 1.3 57.8 + - - +
489C ARG* 3.4 17.2 + - + +
490C PHE* 2.9 28.4 + - - +
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Residues in contact with PHE 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ILE* 4.5 4.7 - - + -
210C LEU* 3.8 20.6 - - + -
213C TYR* 3.5 49.8 + + + -
257C MET* 4.5 10.1 - - + -
261C LEU* 4.6 4.9 - - + -
456C LEU* 3.8 24.2 - - + -
460C PHE* 3.4 36.8 - + - -
483C HIS 3.3 15.4 + - - +
484C PHE* 3.2 7.0 + - - +
486C LEU* 1.3 78.2 - - - +
488C LEU* 1.3 58.1 + - - +
490C PHE* 3.3 11.2 + + - +
491C LEU* 2.8 52.5 + - + +
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Residues in contact with LEU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 3.9 15.3 - - + -
175C GLU 3.7 22.4 - - - +
176C ILE* 4.7 5.2 - - + -
177C PRO* 3.8 16.4 - - + -
180C LEU* 3.3 27.4 - - + +
457C LEU* 4.1 12.8 - - + -
460C PHE* 3.9 43.1 - - + -
484C PHE 2.7 24.8 + - - +
485C ASP* 3.6 6.7 - - - +
487C PHE* 1.3 71.2 - - - +
489C ARG* 1.3 60.0 + - - +
491C LEU* 3.2 8.3 + - + -
492C ALA* 2.8 26.0 + - - +
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Residues in contact with ARG 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PRO* 4.4 7.6 - - + +
485C ASP* 2.8 29.1 + - - +
486C LEU* 3.5 18.1 - - + +
488C LEU* 1.3 68.6 - - - +
490C PHE* 1.3 55.9 - - - +
492C ALA* 3.1 7.1 + - - +
493C GLU* 2.7 41.3 + - - +
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Residues in contact with PHE 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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209C ILE* 4.6 3.6 - - + -
212C SER* 4.4 7.0 - - - -
213C TYR* 3.3 49.6 - + + -
216C HIS* 3.2 45.8 - + + -
486C LEU 2.9 14.5 + - - +
487C PHE* 3.3 15.5 - + - +
488C LEU 3.3 0.2 - - - -
489C ARG* 1.3 74.5 - - - +
491C LEU* 1.3 70.9 + - + +
493C GLU* 4.4 8.1 - - - -
494C TYR* 3.3 42.2 + + - +
498C PHE* 3.6 33.4 - + - -
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Residues in contact with LEU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 3.9 10.5 - - + +
209C ILE* 4.4 10.8 - - + -
453C ALA* 5.7 3.6 - - + +
456C LEU* 5.0 6.3 - - + -
457C LEU* 4.4 17.0 - - + +
460C PHE* 4.9 3.6 - - + -
487C PHE* 2.8 52.0 + - + +
488C LEU* 3.2 20.2 + - + +
490C PHE* 1.3 81.7 - - + +
492C ALA* 1.3 60.5 + - - +
494C TYR 3.7 1.6 - - - -
495C HIS* 3.2 22.5 + - - +
498C PHE* 4.1 28.0 - - + -
499C PHE* 4.3 17.8 - - + -
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Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PRO* 3.9 24.0 - - + -
179C VAL* 4.5 18.6 - - + +
180C LEU* 3.9 13.4 - - + +
488C LEU 2.8 17.0 + - - +
489C ARG* 3.6 5.8 - - - +
491C LEU* 1.3 76.1 - - - +
493C GLU* 1.3 64.8 + - - +
495C HIS* 3.2 17.6 + - - +
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Residues in contact with GLU 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C HIS* 4.6 7.0 + - - -
489C ARG* 2.7 22.4 + - - +
490C PHE* 3.4 9.9 + - - +
492C ALA* 1.3 73.6 - - - +
494C TYR* 1.3 90.9 + - + +
495C HIS 3.5 0.7 + - - -
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Residues in contact with TYR 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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216C HIS* 3.2 26.3 + + - -
490C PHE* 3.3 40.3 + + - +
491C LEU 3.7 3.4 - - - -
492C ALA 3.2 0.4 - - - -
493C GLU* 1.3 110.9 + - + +
495C HIS* 1.3 63.8 + - - +
496C ASP* 3.2 2.9 - - - -
497C ASP* 3.1 33.0 + - + +
498C PHE* 3.1 31.1 + + + -
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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
------------------------------------------------------------
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