Contacts of the strand formed by residues 561 - 564 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419B ASP* 4.9 4.5 - - - -
433B LEU 3.9 1.0 - - - +
434B ASN* 2.9 15.0 - - - +
435B PHE 3.3 19.6 + - - +
543B HIS* 3.8 16.1 - + - +
546B GLU* 4.3 14.3 + - - -
547B HIS* 3.2 45.5 - + + +
550B GLU* 2.6 32.4 + - - -
559B VAL* 4.7 1.6 - - + -
560B GLU* 1.3 85.5 + - - +
562B TRP* 1.3 64.8 + - - +
563B HIS* 3.9 9.6 - - - +
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Residues in contact with TRP 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LYS* 5.2 4.0 - - + -
400B VAL* 3.9 39.2 + - + +
402B ASP* 4.2 24.3 - - - +
418B ARG* 6.0 5.8 - - - -
421B LEU* 3.1 22.7 - - + +
432B GLU* 3.5 43.5 - - + -
433B LEU 3.6 13.7 - - - -
434B ASN* 3.7 36.3 - - + +
452B LYS* 3.9 20.6 - - + -
453B ALA 4.5 0.2 - - - -
454B SER* 4.1 20.2 - - - -
543B HIS* 2.7 33.1 + - - -
560B GLU* 5.0 3.0 + - + -
561B HIS* 1.3 76.1 + - - +
563B HIS* 1.3 57.7 + - - +
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Residues in contact with HIS 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU* 3.9 9.2 - - - -
432B GLU* 3.3 5.4 - - - +
433B LEU* 3.0 34.8 + - - +
435B PHE* 3.1 30.9 - + - -
533B CYS* 4.1 23.3 - - + -
534B ARG 4.7 3.9 + - - -
535B VAL* 4.2 4.2 - - + +
543B HIS* 3.4 41.3 - + - -
544B GLY* 4.0 12.2 + - - -
547B HIS* 2.7 34.0 + - + -
561B HIS* 3.9 7.6 - - - +
562B TRP* 1.3 73.9 - - - +
564B GLN* 1.3 62.6 + - - +
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Residues in contact with GLN 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B GLN* 3.3 22.3 - - - +
421B LEU* 4.0 23.2 - - + +
422B GLU 3.9 16.2 - - - +
423B GLY* 3.7 33.6 - - - +
424B GLY 4.4 0.9 - - - -
425B SER* 5.0 0.3 - - - -
429B ASP* 3.0 26.8 + - - +
431B GLY 3.2 16.3 + - - -
432B GLU* 3.1 20.1 + - - +
532B VAL 3.7 3.3 - - - +
533B CYS* 3.8 8.5 - - - +
543B HIS* 5.6 0.2 - - - -
563B HIS* 1.3 72.8 - - - +
565B LEU* 1.3 74.1 + - - +
566B VAL* 3.2 13.9 - - + +
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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