Contacts of the strand formed by residues 430 - 435 (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 ASN 430 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C ILE* 3.3 8.6 - - - +
419C SER 3.1 30.5 + - - +
422C TYR* 3.4 33.7 - - + +
428C GLY* 5.2 1.8 - - - -
429C ARG* 1.3 78.9 + - - +
431C LEU* 1.3 60.7 + - - +
432C TYR* 3.4 14.5 - - + +
444C CYS* 3.8 14.1 - - - -
446C SER* 2.8 29.4 + - - +
447C CYS* 3.4 9.9 + - - -
454C CYS 5.1 1.4 - - - +
455C GLN* 4.2 11.1 + - - +
457C TYR* 3.3 15.6 - - - -
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Residues in contact with LEU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C GLU* 4.8 0.2 - - + -
416C TYR* 4.4 1.3 - - + -
417C TYR 3.2 26.5 - - - +
418C ILE* 4.2 13.2 - - + +
430C ASN* 1.3 72.7 - - - +
432C TYR* 1.3 67.0 + - - +
444C CYS* 3.4 10.0 - - - -
445C LEU* 2.9 54.8 + - + -
446C SER* 2.9 12.8 + - - +
457C TYR* 4.6 1.8 - - + +
459C VAL* 3.9 15.3 - - + -
461C PHE* 4.0 20.0 - - + -
468C TYR* 3.8 13.0 - - + -
470C LEU* 3.7 29.6 - - + -
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Residues in contact with TYR 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C TYR* 3.3 5.3 - - - +
417C TYR* 2.7 61.0 + + + +
419C SER* 3.1 29.4 - - - -
421C GLU* 3.9 17.6 + - + +
422C TYR* 3.3 26.3 + - - +
430C ASN* 3.4 27.6 - - + -
431C LEU* 1.3 77.4 - - - +
433C LYS* 1.3 59.7 + - - +
442C VAL* 4.2 12.8 - - + -
443C THR 3.3 9.0 - - - +
444C CYS* 3.3 33.4 - - + -
445C LEU* 4.6 1.8 - - - +
447C CYS* 3.5 12.9 - - - -
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Residues in contact with LYS 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C TYR* 3.5 44.8 + - + -
415C LEU 3.4 6.1 - - - +
416C TYR* 3.6 29.8 + - + -
417C TYR* 4.8 0.7 - - - -
432C TYR* 1.3 74.9 - - - +
434C ILE* 1.3 61.2 + - - +
441C LYS 3.9 1.2 - - - +
442C VAL* 3.4 5.2 - - - +
443C THR* 2.8 52.9 + - - +
445C LEU* 3.4 26.9 - - + -
485C SER 4.0 6.9 + - - -
486C VAL 5.5 1.8 + - - -
488C ASP* 3.2 26.2 + - - +
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Residues in contact with ILE 434 (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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397C ILE* 3.2 54.5 - - + +
398C THR* 4.2 4.5 - - + -
414C TYR* 3.5 4.2 - - - -
415C LEU* 3.1 46.4 + - + +
417C TYR* 4.1 15.0 - - + -
433C LYS* 1.3 74.3 - - - +
435C GLN* 1.3 74.2 + - - +
436C LEU* 3.3 3.5 - - + +
439C TYR* 3.9 21.8 - - + +
441C LYS 3.8 3.1 - - - +
442C VAL* 3.9 20.2 - - + +
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Residues in contact with GLN 435 (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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413C ASP* 3.5 12.8 - - + +
414C TYR* 3.6 29.2 + - + -
434C ILE* 1.3 71.4 - - - +
436C LEU* 1.3 63.8 + - - +
437C SER* 2.7 27.8 + - - +
438C ASP* 3.1 42.6 - - - +
439C TYR* 3.5 8.5 - - - -
441C LYS* 3.3 45.6 + - + +
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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
------------------------------------------------------------
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