Contacts of the helix formed by residues 823 - 827 (chain A) in PDB entry 1QXP
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 PHE 823 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A PRO 5.0 5.8 - - - -
821A GLY* 2.9 10.9 - - - -
822A ALA* 1.3 77.5 - - + +
824A GLU* 1.3 49.8 + - - +
825A ALA 2.9 3.8 - - - -
826A ALA* 2.5 27.4 + - - +
827A GLY 2.9 1.2 + - - -
828A PHE* 2.8 32.5 + + + +
830A LEU* 4.0 23.3 - - + -
849A MET* 4.2 11.4 - - - -
854A PHE* 3.2 39.7 - + - -
857A CYS* 3.5 30.5 - - + -
858A LEU* 5.4 5.4 - - + -
861A LEU* 3.7 31.2 - - + -
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Residues in contact with GLU 824 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821A GLY* 3.6 9.7 + - - +
823A PHE* 1.3 65.7 - - - +
825A ALA* 1.3 56.0 - - - +
826A ALA 2.6 15.8 + - - -
827A GLY* 3.0 10.2 + - - -
828A PHE 2.4 22.4 + - - -
829A HIS* 3.3 46.4 - - + +
830A LEU 4.6 0.9 - - - +
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Residues in contact with ALA 825 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802A ILE* 5.7 2.1 - - - +
803A TYR 4.3 15.5 - - - +
821A GLY 3.5 5.9 + - - +
822A ALA* 2.9 36.7 - - + +
824A GLU* 1.3 80.9 - - - +
826A ALA* 1.3 56.5 + - - +
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Residues in contact with ALA 826 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798A LYS* 3.9 23.6 + - - +
799A TRP* 3.7 35.2 + - + +
802A ILE* 5.2 4.9 - - + -
822A ALA 3.1 19.1 - - - +
823A PHE* 2.5 20.4 + - - +
824A GLU 2.6 2.8 + - - -
825A ALA* 1.3 75.1 - - - +
827A GLY* 1.3 55.5 + - - -
828A PHE* 4.2 6.6 - - + -
854A PHE* 5.5 2.5 - - + -
858A LEU* 5.6 2.2 - - + -
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Residues in contact with GLY 827 (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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824A GLU* 3.0 8.0 + - - -
826A ALA* 1.3 83.4 - - - +
828A PHE* 1.3 70.2 - - - +
829A HIS* 3.5 4.2 + - - +
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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