Contacts of the strand formed by residues 432 - 435 (chain C) in PDB entry 3HN8
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 432 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381C HIS* 3.7 10.7 + - - -
398C GLN* 3.1 14.9 - - + +
400C VAL* 3.6 25.6 - - + +
421C LEU* 4.1 15.3 - - + -
429C ASP* 2.9 25.4 - - - +
431C GLY* 1.3 73.9 - - - +
433C LEU* 1.3 61.6 + - - +
453C ALA* 3.1 6.4 - - - +
454C SER* 2.8 45.4 + - - +
455C ASN* 4.2 3.6 - - - +
456C LEU* 4.4 0.2 - - - +
562C TRP* 3.5 22.3 - - + -
563C HIS 3.4 11.2 - - - +
564C GLN* 3.1 15.3 + - - +
565C LEU* 4.5 1.8 - - - -
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Residues in contact with LEU 433 (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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431C GLY 4.4 0.2 + - - -
432C GLU* 1.3 73.6 - - - +
434C ASN* 1.3 61.0 + - - +
435C PHE* 3.6 24.2 + - + -
450C ILE* 3.9 23.3 - - + -
452C LYS 3.4 15.5 - - - +
453C ALA* 4.3 6.3 - - + -
469C VAL* 4.4 6.1 - - + -
496C TYR* 5.4 0.2 - - + -
516C ILE* 3.6 34.1 - - + -
518C VAL* 3.9 22.9 - - + -
533C CYS* 4.2 7.2 - - - -
561C HIS 3.9 1.4 - - - +
562C TRP* 3.6 3.8 - - - -
563C HIS* 3.0 33.4 + - - +
565C LEU* 4.0 18.1 - - + +
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Residues in contact with ASN 434 (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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402C ASP* 3.7 13.5 + - - -
433C LEU* 1.3 75.1 - - - +
435C PHE* 1.3 67.5 + - - +
450C ILE* 4.2 0.7 - - - -
451C ILE* 2.9 39.8 + - - +
452C LYS* 2.7 24.6 + - + +
560C GLU* 2.9 34.5 + - - +
561C HIS 2.9 25.6 - - - +
562C TRP* 3.7 31.9 + - + +
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Residues in contact with PHE 435 (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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433C LEU* 3.6 33.9 - - + -
434C ASN* 1.3 78.5 + - - +
436C SER* 1.3 79.1 + - - +
437C LEU* 3.9 13.7 - - + -
448C VAL* 4.3 4.5 - - + +
449C THR 3.3 15.3 - - - +
450C ILE* 4.0 16.6 - - + -
451C ILE* 3.8 8.1 - - - -
516C ILE* 4.1 18.2 - - + -
533C CYS* 4.0 11.7 - - - -
535C VAL* 4.6 11.0 - - + -
547C HIS* 3.2 23.6 - + - -
559C VAL 3.7 1.4 - - - +
561C HIS 3.3 22.6 + - - +
563C HIS* 3.1 32.5 - + - -
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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