Contacts of the strand formed by residues 467 - 472 (chain C) in PDB entry 5Y7K
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 TYR 467 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C TRP* 3.6 19.5 - + + -
65C ASP 3.5 13.0 - - - -
66C HIS* 3.5 21.7 - - + +
81C ALA* 3.8 24.7 - - + -
82C GLU* 3.0 36.7 + - + +
461C PHE* 3.3 6.6 - - - -
462C SER* 2.8 27.9 + - - -
466C LYS* 1.3 114.1 - - + +
468C TYR* 1.3 67.8 + - - +
482C LEU* 4.4 2.0 - - + -
483C HIS 3.2 21.3 - - - +
484C SER* 3.8 18.4 - - - -
485C SER* 3.9 2.7 - - - -
491C LEU* 3.9 12.3 - - + -
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Residues in contact with TYR 468 (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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62C TRP* 4.5 0.9 - - - -
416C TYR* 5.2 1.1 - + - -
431C LEU* 3.8 14.6 - - + -
445C LEU* 3.6 31.4 + - + +
459C VAL* 3.6 22.2 - - + -
460C SER 3.3 6.5 - - - -
461C PHE* 3.4 32.8 - + + -
467C TYR* 1.3 78.8 - - - +
469C GLN* 1.3 60.3 + - - +
470C LEU* 3.9 16.2 - - + -
482C LEU* 4.1 4.0 - - - -
483C HIS* 3.2 58.9 + + + +
484C SER 4.1 10.1 - - - -
485C SER* 3.6 19.3 - - - -
488C ASP* 3.7 17.5 + - - +
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Residues in contact with GLN 469 (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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58C TYR* 2.8 37.4 + - - +
60C LEU* 3.4 36.0 + - + +
62C TRP* 4.4 2.0 - - + -
459C VAL* 3.2 5.1 - - - -
460C SER* 2.9 45.8 + - - +
468C TYR* 1.3 70.9 - - - +
470C LEU* 1.3 66.1 + - - +
471C ARG* 3.4 32.5 + - - -
480C TYR* 3.9 10.5 - - - -
481C THR 3.3 14.8 - - - +
482C LEU* 4.3 7.8 - - + +
494C LEU* 3.7 8.6 - - + +
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Residues in contact with LEU 470 (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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431C LEU* 3.7 33.9 - - + -
445C LEU 4.3 4.7 - - - +
446C SER* 4.0 10.3 - - - -
449C LEU* 3.4 32.8 - - + -
457C TYR* 4.0 19.1 - - + -
458C SER 3.5 10.8 - - - +
459C VAL* 4.1 6.7 - - + -
468C TYR* 3.8 17.8 + - + -
469C GLN* 1.3 72.4 - - - +
471C ARG* 1.3 61.3 - - - +
472C CYS 4.0 0.4 - - - -
479C LEU 3.6 1.2 - - - +
480C TYR* 3.5 6.6 - - - -
481C THR* 3.1 37.9 + - - +
483C HIS* 3.5 13.9 - - + +
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Residues in contact with ARG 471 (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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58C TYR 5.8 1.0 + - - -
59C SER* 6.2 2.0 - - - +
456C TYR 3.5 1.4 - - - +
457C TYR* 3.2 7.7 - - - -
458C SER* 2.7 75.2 + - - +
459C VAL 3.6 18.1 + - - +
460C SER* 4.4 5.7 - - - -
469C GLN* 3.4 35.3 + - - +
470C LEU* 1.3 70.3 - - - +
472C CYS* 1.3 60.0 + - - +
473C SER* 4.0 3.1 + - - -
479C LEU 3.8 3.1 - - - -
480C TYR* 3.5 33.3 - - + -
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Residues in contact with CYS 472 (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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453C ARG 3.9 5.8 - - - -
454C CYS* 2.0 55.0 - - + -
456C TYR 3.4 5.6 - - - +
457C TYR* 3.8 16.6 - - + -
470C LEU 4.0 0.6 - - - -
471C ARG* 1.3 72.3 - - - +
473C SER* 1.3 61.6 + - - +
474C GLY 3.9 5.6 - - - -
477C LEU 4.3 5.4 - - - -
478C PRO* 3.0 8.3 - - - +
479C LEU* 2.8 46.8 + - + +
480C TYR* 5.1 2.3 - - - -
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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