Contacts of the helix formed by residues 606 - 621 (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 SER 606 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567C GLU* 2.3 35.6 + - - -
571C SER* 4.4 0.6 - - - -
605C THR* 1.3 78.7 - - - +
607C ASP* 1.3 55.1 + - - +
608C PRO* 3.9 12.1 - - - +
609C ALA* 3.1 10.4 + - - +
610C ALA* 2.6 30.9 + - - +
1798C LEU* 5.5 10.5 - - - -
1800C SER* 4.6 0.9 + - - -
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Residues in contact with ASP 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C PRO* 4.0 12.1 - - - +
605C THR 3.7 4.7 + - - +
606C SER* 1.3 71.2 - - - +
608C PRO* 1.3 68.3 - - + +
610C ALA* 3.3 13.1 - - - +
611C ASN* 2.8 51.0 + - - +
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Residues in contact with PRO 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LEU* 4.2 0.2 - - - +
606C SER* 3.3 13.7 - - - +
607C ASP* 1.3 90.2 - - + +
609C ALA* 1.3 61.9 + - - +
612C LEU* 3.0 41.8 + - + +
1800C SER* 3.9 10.1 - - - -
1801C VAL* 3.6 31.9 - - + -
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Residues in contact with ALA 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LEU* 3.7 4.5 - - + -
567C GLU* 3.5 21.3 - - + -
568C PHE* 3.7 15.3 - - + +
571C SER* 5.0 0.2 - - - -
606C SER* 2.9 21.0 + - - +
608C PRO* 1.3 76.2 - - - +
610C ALA* 1.3 50.8 - - - +
611C ASN 2.6 3.0 + - - -
613C HIS* 2.2 42.2 + - - +
1800C SER* 3.1 24.3 + - - +
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Residues in contact with ALA 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C PHE* 3.2 16.6 - - - -
604C PRO* 3.2 32.9 - - + +
606C SER 2.6 10.7 + - - +
607C ASP* 2.9 29.1 + - - +
609C ALA* 1.3 72.1 - - - +
611C ASN* 1.3 67.4 + - - +
613C HIS* 3.4 7.0 - - - -
614C PRO* 2.9 15.4 - - - +
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Residues in contact with ASN 611 (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 CYS* 4.6 5.5 - - - -
494C PRO* 4.9 16.1 - - + +
497C LEU* 4.4 22.5 - - + +
604C PRO* 5.3 1.0 - - - +
607C ASP* 2.8 48.4 + - - +
608C PRO* 5.1 0.2 - - + -
609C ALA 2.6 6.9 + - - -
610C ALA* 1.3 94.4 - - - +
612C LEU* 1.3 55.2 + - + +
613C HIS 2.8 0.9 - - - -
614C PRO* 2.7 18.6 - - + +
615C ALA* 2.7 29.5 + - - +
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Residues in contact with LEU 612 (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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488C ILE* 3.6 40.2 - - + +
489C ARG* 3.8 10.8 - - + -
491C CYS* 4.9 4.2 - - + -
492C SER* 3.7 23.1 - - - +
494C PRO* 6.3 0.7 - - + -
560C LEU* 4.1 6.8 - - - +
563C LEU* 3.5 21.3 - - + +
607C ASP 4.9 0.4 - - - +
608C PRO* 3.0 31.1 + - + +
611C ASN* 1.3 77.3 - - + +
613C HIS* 1.3 56.0 + - - +
615C ALA* 2.5 32.4 + - + +
616C LYS 3.7 3.3 + - - -
1801C VAL* 3.5 29.2 - - + -
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Residues in contact with HIS 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C LEU* 3.8 4.8 - - - +
563C LEU* 4.0 10.1 - - + +
564C LEU* 4.9 7.7 - - + +
568C PHE* 3.1 54.1 - + + +
609C ALA 2.2 32.3 + - - +
610C ALA 3.4 3.1 - - - -
612C LEU* 1.3 75.1 - - - +
614C PRO* 1.3 81.5 - - + +
617C PRO* 3.2 6.2 - - - +
653C LEU* 3.2 37.2 - - + +
654C ILE* 4.9 5.3 + - + +
655C LEU* 3.1 44.2 - - + +
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Residues in contact with PRO 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C LEU* 6.6 0.4 - - + -
610C ALA 2.9 28.9 - - - +
611C ASN* 2.7 21.8 - - - +
613C HIS* 1.3 88.7 - - + +
615C ALA* 1.3 51.4 + - - +
617C PRO* 2.8 7.3 - - + +
618C LYS* 2.1 51.2 + - + +
655C LEU* 4.3 9.2 - - + -
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Residues in contact with ALA 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C ILE* 3.8 15.9 - - + -
491C CYS* 3.5 28.9 - - + -
527C TYR* 5.1 0.9 - - + +
611C ASN 2.7 5.7 + - - -
612C LEU* 2.5 34.3 + - - +
614C PRO* 1.3 68.1 - - - +
616C LYS* 1.3 57.3 + - - +
618C LYS* 2.6 8.1 + - - -
619C ASP* 2.2 41.0 + - + -
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Residues in contact with LYS 616 (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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488C ILE* 3.6 21.0 - - + +
556C SER* 3.3 26.2 - - - +
557C SER* 3.1 28.0 + - - +
560C LEU* 3.1 41.0 - - + +
612C LEU 3.7 2.0 + - - -
615C ALA* 1.3 74.8 - - - +
617C PRO* 1.3 76.0 - - + +
619C ASP* 4.1 0.4 - - - -
620C PHE* 2.8 54.7 + - + +
645C TRP* 3.3 13.5 - - - -
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Residues in contact with PRO 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C LEU* 3.5 16.4 - - + -
613C HIS 3.2 18.4 - - - +
614C PRO* 2.8 15.5 - - + +
616C LYS* 1.3 93.7 - - + +
618C LYS* 1.3 54.2 + - - +
620C PHE* 5.2 1.6 - - + -
621C SER* 2.5 37.7 + - - -
655C LEU* 3.5 30.5 - - + +
658C THR* 5.3 11.3 - - + +
659C ARG* 5.1 0.4 + - - +
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Residues in contact with LYS 618 (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 CYS* 5.3 4.9 - - - -
496C VAL* 4.1 35.4 - - + +
527C TYR* 3.7 24.4 + - + +
531C PHE* 5.1 2.8 - - - -
614C PRO* 2.1 49.7 + - + +
615C ALA* 2.6 7.0 + - - +
617C PRO* 1.3 66.8 - - - +
619C ASP* 1.3 61.3 + - - +
621C SER* 2.4 22.2 + - - +
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Residues in contact with ASP 619 (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 LEU* 3.6 10.3 - - - +
488C ILE* 5.3 2.9 - - + -
527C TYR* 3.3 18.2 + - + +
530C LEU* 5.7 0.4 - - - -
531C PHE* 3.2 34.2 - - - +
534C LEU* 3.4 14.3 - - - +
615C ALA* 2.2 32.3 + - + +
616C LYS* 3.3 5.2 - - - +
618C LYS* 1.3 69.5 - - - +
620C PHE* 1.3 93.3 + - + +
621C SER* 2.7 14.2 + - - -
622C ALA 4.3 1.9 + - - -
623C PHE* 4.6 3.6 + - - +
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Residues in contact with PHE 620 (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 LEU* 3.6 26.0 - - + -
488C ILE* 4.8 0.2 - - + -
534C LEU* 3.7 15.5 - - + -
556C SER* 5.0 10.3 - - - -
616C LYS* 2.8 56.7 + - + +
617C PRO* 3.8 1.8 - - + +
619C ASP* 1.3 98.6 - - + +
621C SER* 1.3 52.1 - - - +
623C PHE* 2.1 64.3 + + + -
624C ILE* 3.8 9.9 - - + -
659C ARG* 2.0 36.2 + - - +
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Residues in contact with SER 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C PRO 2.5 16.4 + - - -
618C LYS* 2.4 35.1 + - - +
619C ASP 2.7 3.4 + - - -
620C PHE* 1.3 72.5 - - - +
622C ALA* 1.3 54.5 + - - -
625C ASN* 4.1 1.0 + - - +
658C THR* 5.8 9.8 - - - +
659C ARG* 2.2 32.3 + - - +
662C LEU* 5.2 6.4 - - - +
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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