Contacts of the strand formed by residues 554 - 562 (chain C) in PDB entry 1NYE
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 GLU 554 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516C THR 3.1 13.9 + - - +
517C LYS* 3.2 21.6 + - + +
518C ILE 2.8 25.8 + - - -
553C ALA* 1.3 75.2 - - - +
555C ILE* 1.3 66.4 + - - +
556C THR* 3.8 18.0 - - + +
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Residues in contact with ILE 555 (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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476C HIS* 3.8 35.0 - - + +
518C ILE* 3.1 15.0 - - + +
520C LEU* 3.9 18.2 - - + -
542C LYS* 3.7 28.8 + - + +
543C ALA* 6.2 0.9 - - - -
548C SER* 3.8 30.7 - - - +
551C LEU* 4.3 10.1 - - + +
553C ALA 3.3 18.1 + - - +
554C GLU* 1.3 79.0 - - - +
556C THR* 1.3 68.2 + - - +
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Residues in contact with THR 556 (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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517C LYS* 3.8 16.7 + - - +
518C ILE 3.0 5.3 + - - +
519C ALA* 3.4 23.7 - - - +
520C LEU* 2.7 37.8 + - - +
542C LYS* 5.0 2.9 - - - +
554C GLU* 3.8 21.5 - - + +
555C ILE* 1.3 80.6 - - - +
557C LEU* 1.3 58.2 + - - +
558C ASP* 4.6 8.8 + - - -
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Residues in contact with LEU 557 (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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480C PHE* 4.6 9.4 - - + -
520C LEU* 3.2 13.9 - - + +
522C SER* 4.6 8.3 - - - +
538C ILE* 3.8 39.7 - - + -
539C GLN* 4.3 10.5 - - - +
542C LYS* 3.8 36.2 - - + +
556C THR* 1.3 77.1 - - - +
558C ASP* 1.3 103.6 + - - +
559C TYR* 4.0 18.0 - - + -
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Residues in contact with ASP 558 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519C ALA* 5.9 1.6 - - - +
520C LEU 2.7 10.8 + - - +
521C LYS* 3.1 17.5 - - + -
522C SER 2.6 32.7 + - - -
556C THR* 4.6 8.1 + - - -
557C LEU* 1.3 83.8 + - - +
559C TYR* 1.3 56.8 + - - +
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Residues in contact with TYR 559 (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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521C LYS* 5.8 0.4 - - - -
522C SER* 2.9 20.9 - - - +
524C VAL* 5.4 3.6 - - + -
531C ALA* 4.5 3.5 + - - +
534C PHE* 3.6 30.6 - + - -
535C ASP* 2.6 40.8 + - - +
538C ILE* 3.9 15.9 - - + -
539C GLN* 5.2 1.8 - - - -
557C LEU* 4.0 24.7 - - + -
558C ASP* 1.3 77.2 - - - +
560C GLN* 1.3 73.6 + - - +
561C LEU* 4.3 9.2 - - + -
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Residues in contact with GLN 560 (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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522C SER 2.9 6.4 + - - +
523C GLU* 3.4 37.3 - - + +
524C VAL* 3.0 27.2 + - - +
559C TYR* 1.3 80.2 - - - +
561C LEU* 1.3 60.2 + - - +
562C LYS* 4.0 6.6 + - + +
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Residues in contact with LEU 561 (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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524C VAL 3.8 9.9 - - - +
526C VAL* 4.1 12.3 - - + +
529C ILE* 4.3 14.4 - - + +
531C ALA* 5.1 14.4 - - + -
534C PHE* 3.5 44.6 - - + -
559C TYR* 4.3 17.5 + - + -
560C GLN* 1.3 70.8 - - - +
562C LYS* 1.3 67.6 + - - +
563C SER 2.7 31.9 + - - +
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Residues in contact with LYS 562 (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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499C ASP* 5.9 0.6 + - - -
523C GLU* 4.2 33.4 + - - +
524C VAL 3.2 17.6 + - - +
525C ALA* 4.1 14.0 - - + +
526C VAL 3.4 18.4 + - - +
560C GLN* 5.0 6.4 + - + +
561C LEU* 1.3 69.0 - - - +
563C SER* 1.3 76.3 + - - +
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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