Contacts of the strand formed by residues 561 - 564 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A ASP* 4.9 4.0 - - - -
433A LEU 3.9 1.0 - - - +
434A ASN* 2.9 15.5 - - - +
435A PHE 3.3 19.2 + - - +
543A HIS* 3.8 15.7 - + - +
546A GLU* 4.3 15.5 + - - -
547A HIS* 3.3 45.3 - + + +
550A GLU* 2.6 32.4 + - - -
559A VAL* 4.7 1.8 - - + -
560A GLU* 1.3 84.8 + - - +
562A TRP* 1.3 65.0 + - - +
563A HIS* 3.9 9.4 - - - +
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Residues in contact with TRP 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A LYS* 5.2 3.4 - - + -
400A VAL* 3.9 37.6 + - + +
402A ASP* 4.2 24.6 - - - +
418A ARG* 6.0 6.1 - - - -
421A LEU* 3.1 21.5 - - + +
432A GLU* 3.5 41.3 - - + -
433A LEU 3.6 14.4 - - - -
434A ASN* 3.7 36.9 - - + +
452A LYS* 3.9 20.9 - - + -
453A ALA 4.5 0.4 - - - -
454A SER* 4.1 21.1 - - - -
543A HIS* 2.7 33.0 + - - -
560A GLU* 5.0 2.3 + - + -
561A HIS* 1.3 76.3 + - - +
563A HIS* 1.3 58.7 + - - +
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Residues in contact with HIS 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 3.9 9.0 - - - -
432A GLU* 3.4 5.0 - - - +
433A LEU* 3.0 33.3 + - - +
435A PHE* 3.1 32.0 - + - -
533A CYS* 4.1 24.2 - - + -
534A ARG 4.7 4.1 + - - -
535A VAL* 4.2 4.2 - - + +
543A HIS* 3.4 41.2 - + - -
544A GLY* 4.1 11.8 - - - -
547A HIS* 2.7 34.1 + + + -
561A HIS* 3.9 8.2 - - - +
562A TRP* 1.3 76.0 - - - +
564A GLN* 1.3 61.5 + - - +
565A LEU 3.6 0.2 + - - -
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Residues in contact with GLN 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A GLN* 3.3 22.3 - - - +
421A LEU* 4.0 23.0 - - + +
422A GLU 3.9 15.7 - - - +
423A GLY* 3.7 33.6 - - - +
424A GLY 4.4 1.1 + - - -
425A SER* 5.0 0.2 - - - -
429A ASP* 3.0 26.2 + - - +
431A GLY 3.2 16.1 + - - -
432A GLU* 3.1 19.8 + - - +
532A VAL 3.7 4.0 - - - +
533A CYS* 3.8 7.8 - - - +
543A HIS* 5.6 0.6 - - - -
563A HIS* 1.3 73.0 - - - +
565A LEU* 1.3 73.4 + - - +
566A VAL* 3.2 13.7 - - + +
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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