Contacts of the helix formed by residues 558 - 564 (chain B) in PDB entry 1QCO
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 558 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554B ALA 3.4 20.7 + - - +
555B LEU* 2.9 10.7 + - - +
557B LYS* 1.3 98.1 + - + +
559B GLN* 1.3 56.6 + - - +
560B HIS* 2.9 13.7 + - - +
561B VAL* 3.1 28.3 + - + +
573B LEU* 4.0 39.8 - - + +
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Residues in contact with GLN 559 (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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547B LYS* 3.5 41.0 + - + +
548B HIS* 3.9 20.8 + - - +
550B PHE* 2.8 28.9 + - + +
551B THR* 4.7 4.4 - - - +
555B LEU 3.1 13.4 + - - +
556B SER* 3.6 16.3 + - - +
557B LYS 3.7 1.4 - - - -
558B HIS* 1.3 75.9 - - - +
560B HIS* 1.3 61.6 + - - +
561B VAL 3.2 1.5 + - - -
562B PHE* 3.3 27.2 + - - +
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Residues in contact with HIS 560 (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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547B LYS* 5.5 1.5 + - - +
558B HIS* 2.9 3.2 + - - +
559B GLN* 1.3 73.3 - - - +
561B VAL* 1.3 56.4 + - + +
562B PHE 3.0 5.4 - - - -
563B ASP* 2.9 48.3 + - + +
564B GLU* 3.2 27.6 + - - +
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Residues in contact with VAL 561 (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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532B ILE* 3.3 19.4 - - - +
555B LEU* 5.0 0.9 - - + -
558B HIS* 3.2 22.9 - - + +
560B HIS* 1.3 77.4 - - + +
562B PHE* 1.3 85.8 + - + +
563B ASP 3.2 0.9 - - - -
564B GLU* 3.3 19.2 - - - +
566B THR 4.7 0.7 - - - +
569B ASN* 3.9 22.4 - - + +
570B PHE* 4.2 18.1 + - + +
573B LEU* 3.9 32.3 - - + -
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Residues in contact with PHE 562 (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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531B ARG* 5.6 0.2 - - - +
532B ILE* 4.2 21.7 + - + +
543B LEU* 3.9 46.2 - - + +
544B SER* 3.3 22.9 + - - -
547B LYS* 4.1 5.8 - - + -
550B PHE* 3.5 43.1 - + + -
555B LEU* 4.3 17.5 - - + -
559B GLN* 3.3 18.1 + - - +
560B HIS 3.0 1.0 - - - -
561B VAL* 1.3 87.8 - - + +
563B ASP* 1.3 61.0 + - - +
564B GLU 3.4 1.8 - - - +
570B PHE* 3.8 44.0 - + - -
581B ALA* 4.5 3.4 - - + -
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Residues in contact with ASP 563 (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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529B LYS* 3.2 23.1 + - - +
544B SER* 3.7 18.0 - - - +
547B LYS* 2.7 43.7 + - - +
559B GLN 4.4 0.2 + - - -
560B HIS* 2.9 39.3 + - + +
562B PHE* 1.3 75.7 - - - +
564B GLU* 1.3 66.2 + - - +
565B THR* 5.0 0.5 - - - +
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Residues in contact with GLU 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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529B LYS* 4.1 1.4 + - - -
530B PRO 4.1 5.5 - - - +
531B ARG* 4.2 3.5 - - - -
532B ILE* 3.8 15.2 + - - +
560B HIS* 3.2 34.2 + - - +
561B VAL* 3.3 21.2 - - - +
562B PHE 3.4 1.2 - - - -
563B ASP* 1.3 82.7 - - - +
565B THR* 1.3 64.2 + - - +
566B THR* 3.3 23.4 + - - +
569B ASN* 3.1 32.7 + - + +
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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