Contacts of the helix formed by residues 529 - 540 (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 ASP 529 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446C PHE* 3.0 45.4 - - + +
447C PRO* 2.8 27.5 - - - +
448C GLN* 5.0 1.3 - - - +
526C ASP* 5.4 7.7 - - - +
527C TYR 2.8 12.6 + - - -
528C VAL* 1.3 76.3 + - - +
530C LEU* 1.3 61.4 + - + +
531C PHE* 2.6 14.0 + - - +
532C ARG* 3.0 17.2 + - - +
533C HIS* 3.8 4.3 + - - +
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Residues in contact with LEU 530 (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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444C ASP* 3.1 39.5 - - + +
446C PHE 5.8 0.7 - - - +
487C LEU* 3.4 41.5 - - + +
490C ILE* 3.5 36.3 - - + -
526C ASP 5.6 0.2 - - - +
527C TYR* 3.2 22.9 - - + +
528C VAL 2.7 3.6 + - - +
529C ASP* 1.3 83.8 - - + +
531C PHE* 1.3 71.1 + - + +
533C HIS* 2.9 5.0 + - - +
534C LEU* 2.8 34.2 + - + +
619C ASP* 5.4 0.4 - - - +
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Residues in contact with PHE 531 (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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527C TYR* 3.2 51.6 - + - -
528C VAL* 2.8 49.1 - - + +
529C ASP 2.6 4.0 + - - -
530C LEU* 1.3 77.1 - - + +
532C ARG* 1.3 53.2 + - + +
534C LEU* 2.9 9.9 + - - +
535C LEU* 2.6 44.6 + - + +
618C LYS* 5.1 2.5 - - - -
619C ASP* 3.2 33.2 - - - +
623C PHE* 4.3 4.8 - - + -
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Residues in contact with ARG 532 (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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454C GLN* 5.8 4.5 - - - +
455C LEU* 6.0 3.4 - - - +
529C ASP 3.0 7.8 + - - +
531C PHE* 1.3 80.5 - - + +
533C HIS* 1.3 52.3 + - - +
535C LEU* 2.9 44.3 - - + +
536C SER* 2.2 56.2 + - - +
539C GLN* 4.8 11.9 - - - +
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Residues in contact with HIS 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C GLN* 5.2 0.4 - - - -
443C ILE* 3.0 38.2 + - + +
444C ASP* 2.4 34.3 + - - +
446C PHE* 4.7 6.3 - - + -
449C TYR* 3.1 24.3 + + - -
454C GLN* 4.1 12.1 + - + -
457C CYS* 3.3 26.9 - - + +
458C CYS* 4.7 2.5 - - - -
461C ILE* 4.2 7.8 - - + +
529C ASP 3.8 1.6 + - - +
530C LEU* 2.9 7.8 + - - +
532C ARG* 1.3 77.3 - - - +
534C LEU* 1.3 53.3 + - + +
536C SER* 3.2 13.4 - - - -
537C SER* 2.3 40.6 + - - -
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Residues in contact with LEU 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ILE* 6.2 3.1 - - + -
444C ASP* 3.8 13.9 - - - +
483C VAL* 6.5 1.1 - - + -
487C LEU* 3.6 23.3 - - + -
530C LEU* 2.8 26.4 + - + +
531C PHE* 3.0 5.6 - - - +
533C HIS* 1.3 72.6 - - - +
535C LEU* 1.3 61.8 + - - +
537C SER* 2.0 32.8 + - - +
538C ASP* 2.6 12.5 - - - +
619C ASP* 3.4 30.3 - - - +
620C PHE* 3.7 11.9 - - + -
623C PHE* 3.3 17.9 - - + -
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Residues in contact with LEU 535 (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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531C PHE* 2.6 20.8 + - + +
532C ARG* 2.9 53.6 - - + +
534C LEU* 1.3 72.4 - - - +
536C SER* 1.3 65.1 + - - +
538C ASP* 2.9 18.6 + - - +
539C GLN* 3.0 19.5 - - - +
622C ALA 5.6 1.3 - - - +
623C PHE* 3.1 28.8 - - + -
626C LEU* 5.7 3.1 - - + -
627C VAL* 4.4 12.1 - - + -
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Residues in contact with SER 536 (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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454C GLN* 4.2 5.6 + - - +
455C LEU* 3.6 14.2 - - - +
458C CYS* 2.3 43.9 - - - +
532C ARG* 2.2 46.6 + - - +
533C HIS* 3.2 13.9 - - - -
535C LEU* 1.3 66.5 - - - +
537C SER* 1.3 64.8 + - - +
538C ASP 2.8 2.1 + - - -
539C GLN* 2.9 19.8 + - - +
540C MET* 4.3 3.3 + - - +
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Residues in contact with SER 537 (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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443C ILE* 6.4 1.6 - - - -
458C CYS* 4.7 10.9 - - - +
461C ILE* 6.2 5.2 - - - -
462C VAL* 5.4 6.6 - - - +
533C HIS* 2.3 28.9 + - - -
534C LEU* 2.0 37.8 + - - +
536C SER* 1.3 68.7 - - - +
538C ASP* 1.3 72.9 + - - +
539C GLN 3.6 0.2 + - - -
540C MET 5.1 0.5 + - - -
545C LEU* 4.3 8.3 - - - +
548C GLU* 4.7 4.2 - - - +
623C PHE* 4.9 0.2 - - - -
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Residues in contact with ASP 538 (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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534C LEU 2.6 13.0 - - - +
535C LEU* 2.9 7.4 + - - +
536C SER 2.8 0.2 + - - -
537C SER* 1.3 102.2 + - - +
539C GLN* 1.3 79.8 + - - +
545C LEU* 3.0 34.8 - - - +
548C GLU* 5.7 0.7 - - - -
549C ALA* 5.1 16.8 - - + +
623C PHE* 3.0 28.2 - - - -
627C VAL* 3.8 11.9 - - + +
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Residues in contact with GLN 539 (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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455C LEU* 6.5 1.3 - - + -
532C ARG* 4.8 12.8 - - - +
535C LEU* 3.0 25.7 + - + +
536C SER* 2.9 11.5 + - - +
538C ASP* 1.3 106.5 + - - +
540C MET* 1.3 67.2 + - + +
545C LEU* 3.9 6.3 - - - +
626C LEU* 5.7 2.8 - - - +
627C VAL* 4.5 13.7 - - - +
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Residues in contact with MET 540 (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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455C LEU* 3.6 44.6 - - + +
458C CYS* 4.5 19.1 - - + -
459C ARG* 4.7 9.0 - - + +
462C VAL* 5.8 2.4 - - + +
536C SER 4.3 2.4 + - - +
537C SER 5.1 0.6 + - - -
538C ASP 3.7 1.6 - - - -
539C GLN* 1.3 83.9 - - + +
541C MET* 1.3 105.7 + - + +
542C ASP 3.5 0.2 + - - -
545C LEU* 3.2 25.3 - - - +
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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