Contacts of the strand formed by residues 561 - 564 (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 HIS 561 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419C ASP* 4.9 3.8 - - - -
433C LEU 3.9 0.9 - - - +
434C ASN* 2.9 15.0 - - - +
435C PHE 3.3 19.4 + - - +
543C HIS* 3.8 15.6 - + - +
546C GLU* 4.3 16.0 + - - -
547C HIS* 3.3 43.1 - + + +
550C GLU* 2.6 34.6 + - - -
559C VAL* 4.7 1.8 - - + -
560C GLU* 1.3 84.6 + - - +
562C TRP* 1.3 64.3 + - - +
563C HIS* 3.9 10.0 - - - +
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Residues in contact with TRP 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C LYS* 5.2 3.6 - - + -
400C VAL* 3.9 38.9 + - + +
402C ASP* 4.2 24.3 - - - +
418C ARG* 6.0 6.3 - - - -
421C LEU* 3.1 21.8 - - + +
432C GLU* 3.5 42.4 - - + -
433C LEU 3.6 14.1 - - - -
434C ASN* 3.7 36.4 - - + +
452C LYS* 3.9 21.1 - - + -
453C ALA 4.5 0.2 - - - -
454C SER* 4.1 20.9 - - - -
543C HIS* 2.7 33.0 + - - -
560C GLU* 5.0 2.6 + - + -
561C HIS* 1.3 75.8 + - - +
563C HIS* 1.3 58.8 + - - +
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Residues in contact with HIS 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU* 3.9 8.5 - - - -
432C GLU* 3.4 5.7 - - - +
433C LEU* 3.0 33.8 + - - +
435C PHE* 3.1 30.7 - + - -
533C CYS* 4.1 24.2 - - + +
534C ARG 4.7 4.3 + - - -
535C VAL* 4.2 4.2 - - + +
543C HIS* 3.4 41.1 + + - -
544C GLY* 4.0 12.5 + - - -
547C HIS* 2.7 33.7 + - + -
561C HIS* 3.9 7.6 - - - +
562C TRP* 1.3 76.9 - - - +
564C GLN* 1.3 61.7 + - - +
565C LEU 3.6 0.2 + - - -
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Residues in contact with GLN 564 (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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398C GLN* 3.3 21.8 - - - +
421C LEU* 4.0 23.7 - - + +
422C GLU 3.9 16.4 - - - +
423C GLY* 3.7 34.0 - - - +
424C GLY 4.4 0.9 - - - -
425C SER* 5.0 0.3 - - - -
429C ASP* 3.0 25.8 + - - -
431C GLY 3.2 16.9 + - - -
432C GLU* 3.1 20.4 + - - +
532C VAL 3.7 3.5 - - - +
533C CYS* 3.8 8.1 - - - +
541C ASP* 6.0 0.2 - - - +
563C HIS* 1.3 73.5 - - - +
565C LEU* 1.3 74.4 + - - +
566C VAL* 3.2 14.1 - - + +
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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