Contacts of the strand formed by residues 443 - 447 (chain C) in PDB entry 1N8Z
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 LEU 443 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C MET* 3.7 36.3 - - + +
26C HIS* 4.3 10.1 - - + -
27C LEU* 5.5 5.6 - - + +
418C ALA 2.9 18.2 + - - +
419C TYR* 3.3 17.9 - - + +
420C SER* 2.9 23.9 + - - -
421C LEU 3.4 4.2 + - - +
442C GLY* 1.3 75.4 - - - +
444C ALA* 1.3 63.0 + - - +
464C PHE* 5.1 1.6 - - - -
468C HIS 3.4 11.0 - - - +
469C GLN* 3.1 17.3 - - - -
470C ALA 2.9 34.1 - - - +
472C LEU* 4.1 11.7 - - + -
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Residues in contact with ALA 444 (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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419C TYR* 4.5 0.4 - - - -
421C LEU* 3.2 16.6 - - + +
439C LEU* 4.5 3.8 - - + -
443C LEU* 1.3 76.0 - - - +
445C LEU* 1.3 59.5 + - - +
446C ILE* 5.0 2.5 - - + -
460C TRP* 4.4 15.9 - - + -
464C PHE* 4.3 11.8 - - + -
470C ALA 3.1 11.2 + - - +
471C LEU* 3.6 19.5 - - + -
472C LEU* 2.8 30.7 + - - +
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Residues in contact with LEU 445 (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* 5.3 4.5 - - + +
16C SER* 5.0 2.5 - - - +
19C THR* 3.3 39.5 - - + +
419C TYR* 3.5 42.0 - - + +
421C LEU 2.9 10.2 + - - +
422C THR* 3.4 15.5 - - + +
423C LEU 2.8 26.5 + - - +
424C GLN* 4.4 2.7 - - - +
444C ALA* 1.3 75.5 - - - +
446C ILE* 1.3 62.3 + - - +
447C HIS* 3.6 33.7 - - + +
472C LEU* 3.4 7.0 - - + +
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Residues in contact with ILE 446 (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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421C LEU* 4.9 4.0 - - + -
423C LEU* 3.2 31.6 - - + +
431C LEU* 4.4 2.2 - - + -
444C ALA* 4.9 1.8 - - + -
445C LEU* 1.3 80.6 - - - +
447C HIS* 1.3 55.8 + - - +
449C ASN* 3.6 8.3 - - - +
452C LEU* 3.5 31.2 - - + -
455C VAL* 4.0 16.8 - - + -
460C TRP* 3.7 35.2 - - + -
471C LEU* 3.9 14.4 - - + -
472C LEU 2.8 11.0 + - - +
473C HIS* 3.3 15.8 - - + -
476C ASN* 2.7 26.4 - - - +
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Residues in contact with HIS 447 (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* 3.3 25.2 + - + +
16C SER* 4.2 13.2 - - - -
423C LEU 2.9 6.3 + - - -
424C GLN* 3.0 61.2 + - + +
445C LEU* 3.6 28.8 - - + +
446C ILE* 1.3 75.6 - - - +
448C HIS* 1.3 94.9 + + + +
449C ASN* 2.8 14.6 + - - -
474C THR* 3.1 24.9 - - + +
476C ASN* 3.2 4.5 - - - -
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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