Contacts of the strand formed by residues 516 - 521 (chain B) in PDB entry 1Y8Q
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 ARG 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B GLU* 2.6 38.2 + - - -
482B ILE* 4.1 2.1 - - - +
483B GLU* 2.9 72.9 + - + +
514B GLY 3.7 3.8 + - - +
515B SER* 1.3 75.6 - - - +
517B LEU* 1.3 70.0 + - - +
529B LEU* 3.6 23.4 - - + +
530B ILE 3.4 7.0 - - - +
531B ASN* 3.2 18.9 + - - +
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Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B LEU* 4.2 28.7 - - + -
480B VAL* 4.3 10.1 - - + -
481B GLN 3.6 4.3 - - - +
482B ILE* 3.7 34.5 - - + -
483B GLU* 5.4 0.9 - - - -
490B LEU* 4.2 6.5 - - + -
506B LEU* 5.9 0.9 - - + -
511B ILE* 4.0 17.3 - - + -
515B SER* 5.2 1.1 - - - -
516B ARG* 1.3 85.2 - - - +
518B GLN* 1.3 61.5 + - - +
519B ALA 3.9 0.4 - - - -
528B LEU 3.7 0.5 - - - +
529B LEU* 3.4 5.7 - - - +
530B ILE* 2.5 57.7 + - + +
532B ILE* 4.0 28.7 - - + -
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Residues in contact with GLN 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B ASP 3.6 2.6 - - - +
480B VAL* 3.4 3.5 - - - -
481B GLN* 2.9 57.5 + - + +
482B ILE 6.1 0.2 - - - -
483B GLU* 4.5 12.8 - - + +
516B ARG 4.4 0.2 + - - -
517B LEU* 1.3 73.0 - - - +
519B ALA* 1.3 58.8 + - - +
520B ASP* 2.9 27.6 + - - +
527B THR* 4.0 20.3 - - + +
528B LEU 3.7 2.5 - - - -
529B LEU* 3.8 20.7 - - + +
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B VAL* 4.5 3.4 - - + -
475B MET* 3.6 20.7 - - + +
479B ASP 3.6 4.3 - - - -
480B VAL* 3.9 20.6 - - + -
517B LEU 3.9 0.6 + - - -
518B GLN* 1.3 72.9 - - - +
520B ASP* 1.3 61.3 + - - +
527B THR* 3.4 2.8 - - - +
528B LEU* 2.7 47.5 + - + +
530B ILE* 4.0 20.6 - - + -
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Residues in contact with ASP 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B MET* 4.2 2.9 - - - -
477B ALA 3.9 0.5 - - - +
478B PRO* 3.3 4.5 - - - +
479B ASP* 2.8 43.8 + - + +
481B GLN* 4.4 6.8 + - - -
518B GLN* 2.9 32.8 + - - +
519B ALA* 1.3 76.2 - - - +
521B ASP* 1.3 61.2 + - - +
522B PHE* 3.9 34.4 + - + -
526B TYR 3.4 3.1 - - - +
527B THR* 2.5 33.6 + - - +
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Residues in contact with ASP 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B MET* 3.6 22.4 - - + +
476B VAL* 2.8 33.5 + - - +
477B ALA 3.1 17.5 + - - +
520B ASP* 1.3 73.8 - - - +
522B PHE* 1.3 56.9 + - - +
523B LEU* 3.1 12.0 + - - +
524B GLN* 2.8 43.5 + - + +
525B ASP 2.9 22.5 + - - -
526B TYR* 2.9 19.6 + - + +
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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