Contacts of the strand formed by residues 473 - 480 (chain C) in PDB entry 2AYN
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 ILE 473 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ARG* 3.4 47.6 - - - +
341C LYS* 4.4 20.6 + - - +
343C LEU* 4.4 16.6 - - + +
424C THR* 3.2 16.8 - - - +
425C HIS 3.3 23.1 + - - +
426C GLN* 5.8 0.2 - - - -
465C LEU* 3.4 10.1 - - - +
467C GLY* 4.1 11.2 - - - -
469C GLY 4.3 13.9 - - - +
470C ASP* 5.7 0.4 - - - -
471C TRP 3.4 12.1 - - - +
472C HIS* 1.3 82.6 - - - +
474C ALA* 1.3 73.0 + - + +
475C TYR* 3.3 1.0 + - - +
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Residues in contact with ALA 474 (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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327C MET* 3.6 19.5 - - + +
329C ARG* 3.9 4.9 + - - -
348C PHE* 4.1 19.5 - - + -
422C VAL* 3.6 22.0 - - + -
423C LEU 3.8 0.4 - - - -
424C THR* 3.5 10.4 + - - -
465C LEU* 3.2 12.5 + - + +
473C ILE* 1.3 82.5 - - - +
475C TYR* 1.3 58.4 + - - +
477C LEU* 3.7 20.4 - - + -
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Residues in contact with TYR 475 (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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198C ASP* 3.0 39.5 + - - -
199C ALA* 4.8 1.3 - - + -
200C ASN* 3.1 20.1 - - + +
326C GLN* 3.6 26.8 + - + -
327C MET* 3.1 36.7 + - - -
328C VAL* 5.3 0.7 - - - -
329C ARG* 5.0 2.5 - - + +
330C PHE* 3.5 38.2 - + + -
341C LYS* 6.3 0.2 - - - +
423C LEU* 2.9 10.9 + - + +
425C HIS* 4.1 16.8 - - + +
435C TYR* 3.7 25.4 - + - -
473C ILE 3.3 0.8 + - - +
474C ALA* 1.3 74.9 - - - +
476C VAL* 1.3 70.7 + - + +
477C LEU 4.3 0.2 - - - -
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Residues in contact with VAL 476 (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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121C CYS* 5.3 0.2 - - - -
200C ASN* 3.4 30.7 - - + +
203C TRP* 3.5 37.5 - - + -
273C GLN* 5.5 0.2 - - - +
324C THR* 4.3 9.0 - - + -
325C ILE 3.6 7.4 - - - +
326C GLN* 4.9 1.3 - - - -
422C VAL* 3.4 6.1 - - - +
423C LEU* 2.9 48.2 + - + +
475C TYR* 1.3 97.5 - - + +
477C LEU* 1.3 73.0 + - - +
478C LEU* 5.3 0.3 - - - +
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Residues in contact with LEU 477 (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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285C LEU* 4.4 4.0 - - + -
323C LEU 3.8 0.4 - - - +
324C THR* 3.7 2.4 - - - -
325C ILE* 2.8 39.7 + - + +
327C MET* 3.6 33.7 - - + -
348C PHE* 4.0 26.7 - - + -
419C LEU* 3.9 5.8 - - + -
421C ALA 4.3 0.9 - - - -
422C VAL* 3.7 24.9 - - + -
474C ALA* 3.7 20.9 - - + -
476C VAL* 1.3 76.8 - - - +
478C LEU* 1.3 61.0 + - - +
479C TYR* 3.9 35.9 - - + +
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Residues in contact with LEU 478 (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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121C CYS* 4.1 11.4 - - + +
122C ILE* 5.9 0.2 - - - -
124C SER* 3.6 24.7 - - - +
125C VAL* 4.1 10.1 - - + -
203C TRP* 4.5 25.1 - - + -
246C PHE* 5.7 3.4 - - + -
322C TYR* 4.1 17.5 - - + -
323C LEU 3.8 7.9 - - - +
324C THR* 4.8 4.7 - - + +
419C LEU* 3.4 6.1 - - - +
420C GLN* 2.7 43.7 + - + +
421C ALA* 3.2 25.7 + - + +
476C VAL 5.3 0.7 - - - +
477C LEU* 1.3 75.5 - - - +
479C TYR* 1.3 69.3 + - - +
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Residues in contact with TYR 479 (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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285C LEU* 3.9 3.9 - - + +
322C TYR* 3.3 3.6 - - - -
323C LEU* 2.8 43.6 + - + +
325C ILE* 4.0 15.0 - - + -
348C PHE* 3.7 22.7 - - - +
349C PRO* 2.7 36.2 + - - +
350C LEU 4.3 2.0 - - - -
352C LEU* 3.8 41.7 - - + -
417C TYR* 3.4 22.9 - - + -
418C ASP* 4.0 2.7 - - - -
419C LEU* 3.1 45.5 - - + +
477C LEU* 3.9 18.8 - - + -
478C LEU* 1.3 73.9 - - - +
480C GLY* 1.3 60.9 + - - +
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Residues in contact with GLY 480 (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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321C ALA 3.8 3.6 - - - -
322C TYR* 3.7 13.2 - - - -
417C TYR* 3.2 6.2 - - - -
418C ASP 2.4 43.1 + - - -
420C GLN* 3.9 14.9 - - - +
479C TYR* 1.3 75.8 - - - +
481C PRO* 1.3 70.5 - - - +
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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