Contacts of the helix formed by residues 474 - 490 (chain C) in PDB entry 5Y3R
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 VAL 474 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C GLU* 5.5 6.5 - - - +
471C LYS* 2.6 31.5 - - + +
472C GLY 2.7 14.0 + - - +
473C PRO* 1.3 71.4 - - - +
475C LEU* 1.3 75.5 + - + +
476C ARG* 3.2 15.3 + - - +
477C ASN* 3.8 9.4 + - - +
478C CYS* 4.6 5.5 + - - -
1560C TYR* 5.1 7.9 - - + -
1561C SER* 3.1 30.1 - - - +
1564C SER* 6.5 0.4 - - - -
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Residues in contact with LEU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C THR* 3.4 36.1 - - + +
435C LEU* 3.4 37.7 - - + -
436C GLU* 3.2 25.1 - - - +
468C LEU* 5.0 2.5 - - + -
471C LYS* 3.1 18.2 - - + +
474C VAL* 1.3 80.5 - - + +
476C ARG* 1.3 68.7 + - - +
478C CYS* 3.2 14.5 + - + -
479C ILE* 3.1 31.5 + - + +
1811C ARG* 5.8 1.6 - - - +
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Residues in contact with ARG 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C PHE* 5.4 5.1 - - + -
468C LEU* 3.5 40.0 - - + +
471C LYS* 3.6 12.8 - - - +
473C PRO* 2.5 54.5 + - - +
474C VAL* 3.2 10.2 + - - +
475C LEU* 1.3 74.4 - - - +
477C ASN* 1.3 79.9 + - - +
479C ILE* 3.0 5.3 + - - +
480C SER* 3.0 18.5 + - - -
551C PHE* 5.2 14.8 - - - -
1491C ILE* 5.3 10.7 - - - +
1565C GLU* 4.3 15.6 + - - +
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Residues in contact with ASN 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C VAL 4.2 8.1 - - - +
475C LEU 3.4 0.4 - - - -
476C ARG* 1.3 86.0 - - + +
478C CYS* 1.3 76.6 + - - +
480C SER* 2.8 20.4 + - - -
481C THR* 2.9 14.8 + - - -
551C PHE* 5.4 15.2 - - + +
555C SER* 3.1 24.8 + - - -
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Residues in contact with CYS 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLU* 3.4 11.4 - - - +
474C VAL 4.8 7.6 - - - -
475C LEU* 3.2 18.7 + - + +
477C ASN* 1.3 89.1 - - - +
479C ILE* 1.3 64.9 + - - +
481C THR* 2.9 17.9 + - - +
482C VAL* 2.9 15.9 + - + +
1811C ARG* 4.6 20.6 - - - +
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Residues in contact with ILE 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C LEU* 3.5 32.3 - - + +
436C GLU* 3.1 37.5 - - + -
439C VAL* 4.3 22.4 - - + -
440C VAL* 4.2 10.5 - - + -
464C VAL* 5.7 4.7 - - + -
465C PHE* 6.0 5.8 - - + -
468C LEU* 5.5 8.3 - - + -
475C LEU* 3.1 23.6 - - + +
476C ARG* 3.0 8.4 + - - +
478C CYS* 1.3 76.0 - - - +
480C SER* 1.3 65.5 + - - +
482C VAL* 2.7 14.9 + - - +
483C VAL* 3.0 15.7 + - + +
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Residues in contact with SER 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C PHE* 5.9 7.5 - - - -
476C ARG 3.0 10.2 + - - -
477C ASN* 2.8 19.9 + - - -
479C ILE* 1.3 71.4 - - - +
481C THR* 1.3 59.9 + - - -
483C VAL* 2.8 21.0 - - - +
484C HIS* 2.7 49.2 + - - -
551C PHE* 4.1 5.1 + - - -
552C SER* 3.4 21.2 + - - -
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Residues in contact with THR 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C ASN* 2.9 12.4 + - - -
478C CYS* 2.9 11.4 + - - -
480C SER* 1.3 77.0 - - - +
482C VAL* 1.3 64.5 + - - +
484C HIS* 2.8 25.0 - - - +
485C GLN* 2.8 14.8 + - + +
555C SER* 3.1 23.8 + - - +
559C SER* 3.2 25.6 - - - +
562C HIS* 5.5 7.2 - - + +
1807C LYS* 6.4 1.8 - - + -
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Residues in contact with VAL 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLU* 3.1 21.8 - - - +
440C VAL* 3.4 33.9 - - + -
478C CYS* 2.9 16.4 + - - +
479C ILE 2.7 7.1 + - - +
481C THR* 1.3 77.1 - - - +
483C VAL* 1.3 55.5 + - - +
485C GLN* 2.5 60.6 + - - +
486C GLY* 3.0 5.0 + - - -
1804C MET* 4.5 5.3 - - + +
1808C ASP* 5.2 2.9 - - + +
1811C ARG* 5.2 7.9 - - - +
1812C LEU* 4.8 12.1 - - + -
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Residues in contact with VAL 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL 4.6 4.0 - - - +
440C VAL* 4.0 31.6 - - + +
443C ILE* 4.7 20.6 - - + -
479C ILE* 3.0 17.8 + - + +
480C SER* 2.8 29.6 - - - +
482C VAL* 1.3 72.5 - - - +
484C HIS* 1.3 60.3 + - + +
486C GLY* 4.6 1.6 - - - +
487C LEU* 2.3 41.2 + - + +
534C LEU* 6.5 1.3 - - + -
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Residues in contact with HIS 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C SER* 2.7 42.6 + - - -
481C THR* 2.8 19.9 - - - +
483C VAL* 1.3 83.2 - - + +
485C GLN* 1.3 64.5 + - - +
487C LEU* 2.9 28.1 - - + +
488C ILE* 2.9 14.5 + - + +
552C SER* 2.9 19.3 + - - -
555C SER* 3.1 17.2 + - - -
556C SER* 2.9 45.3 + - - -
559C SER* 3.5 14.6 + - - +
620C PHE* 6.2 0.2 - + - -
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Residues in contact with GLN 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C THR* 2.8 22.4 + - + +
482C VAL* 2.5 41.4 + - - +
484C HIS* 1.3 74.5 - - - +
486C GLY* 1.3 68.0 + - - +
488C ILE* 3.0 11.0 - - - +
489C ARG* 2.9 17.2 + - - +
559C SER* 6.2 2.2 - - - -
1803C GLU* 4.2 5.7 + - + +
1804C MET* 2.8 57.5 + - + +
1807C LYS* 4.8 8.7 - - - +
1808C ASP* 3.8 15.2 + - - +
1811C ARG* 5.8 0.4 - - - +
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Residues in contact with GLY 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C VAL 3.0 8.1 + - - -
483C VAL* 4.4 1.3 - - - -
485C GLN* 1.3 76.7 - - - +
487C LEU* 1.3 53.5 + - - +
489C ARG* 2.7 5.7 + - - -
490C ILE* 2.3 51.5 + - - +
1804C MET* 3.4 24.4 - - - +
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Residues in contact with LEU 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ASP* 4.6 1.3 - - - +
483C VAL* 2.3 32.7 + - + +
484C HIS* 2.9 30.3 - - + +
486C GLY* 1.3 76.5 - - - +
488C ILE* 1.3 69.8 + - + +
490C ILE* 3.0 27.0 - - - +
491C CYS* 3.5 2.8 + - - -
527C TYR* 5.4 1.9 - - - -
530C LEU* 3.4 26.9 - - + +
534C LEU* 3.6 33.2 - - + -
556C SER* 5.4 1.3 - - - -
619C ASP* 3.6 8.3 - - - +
620C PHE* 3.6 26.7 - - + -
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Residues in contact with ILE 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C HIS* 3.0 12.6 - - + +
485C GLN* 3.0 16.2 - - - +
487C LEU* 1.3 88.1 - - + +
489C ARG* 1.3 72.4 + - + +
490C ILE 3.0 1.6 - - - -
491C CYS* 2.5 35.3 + - - +
527C TYR* 6.3 0.2 - - - -
559C SER* 6.2 2.7 - - - -
560C LEU* 6.5 0.2 - - + -
563C LEU* 4.7 8.5 - - + -
612C LEU* 3.6 27.6 - - + +
615C ALA* 3.8 13.8 - - + +
616C LYS* 3.6 38.8 - - + +
619C ASP* 5.3 2.0 - - + +
620C PHE* 4.8 0.9 - - + -
1803C GLU* 5.5 3.8 - - + +
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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
----------------------------------------------------------
485C GLN 2.9 12.8 + - - +
486C GLY* 2.7 14.3 + - - +
488C ILE* 1.3 74.6 - - + +
490C ILE* 1.3 61.6 + - + +
492C SER* 3.0 28.2 + - - +
612C LEU* 3.8 20.0 - - + -
1801C VAL* 3.9 28.6 + - + +
1804C MET* 3.4 45.8 - - + +
1805C PHE* 5.1 2.4 - - - +
1818C SER* 4.8 12.8 + - - -
1819C PHE* 5.2 13.1 - - - +
1822C ARG* 5.4 13.1 - - - +
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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
----------------------------------------------------------
440C VAL 6.1 1.1 - - - +
444C ASP* 4.7 17.3 - - + +
445C SER* 5.4 4.3 - - - +
486C GLY* 2.3 49.9 + - - +
487C LEU* 3.0 16.8 - - - +
489C ARG* 1.3 65.9 - - + +
491C CYS* 1.3 59.8 + - - +
492C SER 2.6 20.5 - - - +
525C LYS* 6.6 0.4 - - - -
526C ASP 4.6 7.6 - - - +
527C TYR* 3.5 11.4 - - - +
530C LEU* 3.5 35.4 - - + -
1821C ASP* 6.1 0.7 - - - +
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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