Contacts of the strand formed by residues 424 - 430 (chain C) in PDB entry 2YWB
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 GLN 424 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C ARG* 4.9 1.2 + - - -
379C HIS* 3.6 15.9 - - - +
380C PRO* 2.9 39.1 + - + +
389C ARG* 4.3 4.3 + - - +
422C VAL* 3.3 5.6 - - - +
423C ALA* 1.3 82.3 - - + +
425C ALA* 1.3 86.6 + - - +
426C LEU* 4.1 15.5 - - + -
451C ARG 5.1 0.9 - - - +
452C ALA* 3.1 7.5 - - - +
453C VAL* 3.1 39.2 + - + +
500C ILE* 3.7 25.8 - - + +
501C GLU* 4.2 12.3 + - - -
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Residues in contact with ALA 425 (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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247C ARG* 3.0 21.7 + - - -
379C HIS* 3.7 17.9 + - + +
409C PHE* 4.0 10.0 - - + -
410C THR* 5.1 2.8 + - - +
413C LEU* 3.5 31.9 - - + -
419C TYR* 5.3 1.7 - - + -
422C VAL* 4.2 4.7 - - + -
424C GLN* 1.3 85.1 + - - +
426C LEU* 1.3 61.9 + - - +
451C ARG 3.4 6.1 - - - -
452C ALA* 4.3 2.9 - - + +
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Residues in contact with LEU 426 (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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247C ARG* 4.1 5.8 - - - +
389C ARG* 3.4 26.9 - - - +
406C ASP* 4.4 0.9 - - - -
409C PHE* 3.6 11.7 - - - -
424C GLN* 4.1 18.4 - - + +
425C ALA* 1.3 73.7 - - - +
427C ALA* 1.3 64.3 + - - +
428C VAL* 3.6 29.2 - - + -
450C LEU 3.7 0.2 - - - -
451C ARG* 2.8 52.2 + - + +
500C ILE* 4.1 18.6 - - + +
501C GLU* 3.7 30.5 - - - +
502C TRP* 5.0 1.1 - - + -
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Residues in contact with ALA 427 (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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389C ARG* 3.6 19.3 - - - +
402C LEU* 3.5 20.4 - - + +
405C ALA 5.1 0.4 - - - -
406C ASP* 4.1 22.5 + - - +
409C PHE* 4.7 2.7 - - + -
426C LEU* 1.3 76.7 - - - +
428C VAL* 1.3 65.7 + - - +
448C LEU* 4.0 28.9 - - + -
449C ALA 3.3 5.4 - - - +
450C LEU* 4.3 7.9 - - + -
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Residues in contact with VAL 428 (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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389C ARG* 3.3 20.2 - - + +
391C LEU* 4.2 16.6 - - + -
426C LEU* 3.6 21.3 - - + -
427C ALA* 1.3 78.5 - - - +
429C LEU* 1.3 68.1 + - - +
430C THR* 4.5 3.4 + - - +
447C VAL 3.7 0.7 - - - +
448C LEU* 3.3 8.4 - - - +
449C ALA* 2.8 38.7 + - + +
502C TRP* 3.8 52.9 - - + +
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Residues in contact with LEU 429 (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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389C ARG 2.9 14.4 + - - +
390C VAL* 3.7 6.0 - - + +
391C LEU* 2.9 29.6 + - - +
398C ARG* 3.5 38.6 - - + +
401C ILE* 4.1 21.3 - - + -
402C LEU* 4.4 12.5 - - + +
427C ALA 4.3 0.4 - - - -
428C VAL* 1.3 71.0 - - - +
430C THR* 1.3 60.8 + - - +
431C PRO* 3.7 3.2 - - + +
446C TYR* 3.6 50.3 - - + -
447C VAL 3.9 2.5 - - - +
448C LEU* 4.0 18.6 - - + +
485C ILE* 4.2 4.9 - - + -
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Residues in contact with THR 430 (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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391C LEU* 3.4 29.3 - - + +
428C VAL* 3.9 6.4 + - - +
429C LEU* 1.3 73.9 - - - +
431C PRO* 1.3 78.0 - - + +
432C VAL* 4.8 1.6 - - + +
446C TYR* 3.2 5.5 - - - -
447C VAL* 2.8 58.0 + - + -
449C ALA* 5.7 1.7 - - - +
502C TRP* 4.5 6.4 - - - -
391D LEU* 6.2 2.2 - - + -
430D THR* 4.9 16.6 - - + -
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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
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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