Contacts of the strand formed by residues 420 - 425 (chain C) in PDB entry 1N8Y
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 TYR 420 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C MET* 5.2 3.4 - - + -
15C ALA* 6.5 0.9 - - + -
16C SER* 5.9 1.0 - - - -
19C THR* 5.1 2.9 - - - +
20C HIS* 5.4 2.4 - - - -
23C MET* 3.1 37.3 - - + +
388C TYR* 3.6 3.5 - - - +
389C LEU 5.4 0.2 - - - +
415C LEU* 3.7 4.4 - - - +
416C HIS* 3.0 52.6 + - + +
417C ASP* 4.7 10.1 - - + -
419C ALA* 1.3 85.7 - - + +
421C SER* 1.3 61.1 + - - +
422C LEU 4.4 1.1 - - - +
423C THR* 3.5 22.2 + - - +
444C LEU* 3.3 21.3 - - + +
446C LEU* 3.6 39.3 - - + +
473C LEU* 3.9 19.2 - - + +
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Residues in contact with SER 421 (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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388C TYR* 3.8 7.4 - - - -
389C LEU 3.0 22.6 + - - -
410C ILE* 3.4 17.0 - - - +
412C GLY* 4.0 10.5 - - - -
415C LEU* 3.4 14.1 - - - +
420C TYR* 1.3 73.9 - - - +
422C LEU* 1.3 59.1 + - - +
440C LEU* 3.8 20.4 - - - +
442C SER 3.0 28.5 + - - -
443C GLY 4.2 1.0 + - - -
444C LEU 2.8 13.4 + - - +
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Residues in contact with LEU 422 (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 LEU* 3.3 28.0 - - + -
410C ILE* 4.3 4.3 - - + -
420C TYR* 3.3 0.7 - - - +
421C SER* 1.3 81.1 + - - +
423C THR* 1.3 59.7 + - - +
424C LEU* 3.9 29.2 - - + -
434C LEU* 4.7 9.6 - - + -
437C LEU* 4.5 12.1 - - + -
440C LEU* 4.3 16.6 - - + -
444C LEU 3.5 2.0 + - - +
445C ALA* 3.2 16.8 - - + -
446C LEU* 2.8 31.5 + - - +
447C ILE* 4.7 5.8 - - + -
461C TRP* 4.0 32.3 - - + -
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Residues in contact with THR 423 (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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15C ALA* 6.3 0.4 - - + -
389C LEU 3.0 7.8 + - - +
390C TYR* 3.5 38.6 - - + -
391C ILE 2.8 26.3 + - - +
416C HIS* 4.5 3.2 + - - +
420C TYR* 3.5 24.1 + - - +
422C LEU* 1.3 75.4 + - - +
424C LEU* 1.3 73.8 + - - +
425C GLN* 4.3 18.6 - - + +
446C LEU* 3.3 24.7 - - + +
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Residues in contact with LEU 424 (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 ILE* 3.4 33.9 - - + -
401C LEU* 3.7 16.8 - - + -
422C LEU* 3.9 22.4 - - + -
423C THR* 1.3 88.4 - - - +
425C GLN* 1.3 60.6 + - - +
427C LEU* 4.0 12.3 - - + -
429C ILE* 4.9 2.2 - - + -
432C LEU* 3.6 31.2 - - + -
434C LEU* 5.2 2.0 - - + -
446C LEU 2.9 7.1 + - - +
447C ILE* 3.3 24.8 - - + -
448C HIS* 3.0 25.1 + - - -
450C ASN* 3.2 12.5 + - - +
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Residues in contact with GLN 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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15C ALA* 3.5 20.1 - - - +
390C TYR* 4.1 15.5 + - - +
391C ILE 3.0 9.9 + - - +
392C SER* 3.5 27.6 + - - +
423C THR* 4.3 12.1 - - + +
424C LEU* 1.3 75.1 - - - +
426C GLY* 1.3 69.7 + - - +
427C LEU* 3.2 15.8 + - - +
448C HIS* 2.9 34.0 + - + +
449C ARG* 3.5 23.2 - - - +
450C ASN* 3.5 1.0 + - - -
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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