Contacts of the strand formed by residues 404 - 410 (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 VAL 404 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356C ARG* 3.1 18.1 + - - -
374C ILE* 3.7 24.1 - - + +
382C ARG 3.1 10.3 + - - +
383C HIS* 4.1 6.7 - - - +
384C ILE* 3.9 20.2 - - + -
398C THR* 3.8 18.6 - - - +
402C TRP* 3.6 21.7 - - + -
403C GLU* 1.3 70.3 - - - +
405C ILE* 1.3 64.8 + - - +
406C GLY 3.7 9.0 - - - +
417C TYR* 3.7 26.5 - - + -
418C ILE 3.5 12.3 - - - +
419C SER* 3.9 0.9 - - - -
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Residues in contact with ILE 405 (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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356C ARG* 3.3 21.4 + - - +
374C ILE* 4.1 2.0 - - - +
403C GLU 4.1 9.9 - - - +
404C VAL* 1.3 73.8 - - - +
406C GLY* 1.3 55.5 + - - +
418C ILE* 2.6 24.6 + - + +
419C SER* 3.8 10.1 - - - -
420C ASN* 4.1 14.6 - - - +
429C ARG* 3.6 52.0 - - - +
585C TYR* 3.6 32.5 - - + -
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Residues in contact with GLY 406 (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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361C GLU* 5.6 1.6 - - - -
374C ILE* 3.5 10.8 - - - -
404C VAL* 3.4 3.4 - - - -
405C ILE* 1.3 83.1 - - - +
407C ILE* 1.3 63.6 + - - -
408C GLU* 3.5 14.1 + - - +
417C TYR* 3.3 3.6 - - - +
418C ILE* 2.9 27.4 + - - +
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Residues in contact with ILE 407 (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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361C GLU* 4.2 8.5 + - - +
363C HIS* 3.4 53.9 + - + +
372C TYR* 3.9 7.6 - - + +
373C LYS* 3.9 18.4 - - - -
374C ILE* 3.9 18.8 - - + +
384C ILE* 3.8 38.4 - - + -
406C GLY* 1.3 73.0 - - - -
408C GLU* 1.3 64.9 + - - +
409C ALA 4.2 4.3 - - - +
415C LEU* 3.6 26.9 - - + -
416C TYR 3.8 5.4 - - - +
417C TYR* 4.2 1.1 - - - -
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Residues in contact with GLU 408 (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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363C HIS* 5.2 3.6 - - - -
406C GLY* 3.5 25.9 - - - +
407C ILE* 1.3 77.2 - - - +
409C ALA* 1.3 59.9 + - - +
416C TYR 2.8 14.2 + - - +
417C TYR* 4.3 0.9 - - - -
418C ILE* 3.9 29.3 - - + +
431C LEU* 4.8 0.4 - - + -
459C VAL* 3.6 39.5 + - + +
461C PHE* 3.9 13.4 - - + +
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Residues in contact with ALA 409 (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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363C HIS* 5.4 2.0 - - - -
407C ILE* 3.8 3.0 - - - +
408C GLU* 1.3 80.5 - - - +
410C LEU* 1.3 60.9 + - - +
415C LEU* 3.5 7.0 - - - +
416C TYR* 2.9 46.6 + - + +
461C PHE* 3.8 29.4 - - + -
465C ALA* 4.2 11.0 - - + -
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Residues in contact with LEU 410 (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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363C HIS* 3.4 31.8 + - + +
364C PHE 3.4 27.1 - - - +
365C THR* 4.3 6.7 - - + +
372C TYR* 3.8 14.8 - - + -
409C ALA* 1.3 75.0 - - - +
411C THR* 1.3 91.4 + - - +
414C TYR 3.8 8.7 - - - +
415C LEU* 3.6 22.4 - - + -
436C LEU* 3.8 14.1 - - + -
465C ALA* 5.3 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
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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