Contacts of the helix formed by residues 907 - 911 (chain C) in PDB entry 2QFD
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 LYS 907 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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889C ILE* 3.9 5.2 - - - -
905C TYR* 3.5 6.4 - - - +
906C SER* 1.3 97.1 + - - +
908C TRP* 1.3 66.1 + - - +
909C LYS* 3.0 29.9 + - + +
910C ASP* 3.1 29.8 + - - +
911C PHE 4.0 2.1 + - - -
827E GLU* 2.9 38.6 + - + +
855E SER* 5.0 1.6 - - - +
879E TYR* 4.2 8.9 + - - -
880E LYS* 5.0 5.3 - - - +
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Residues in contact with TRP 908 (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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808C LEU* 4.4 11.9 - - + -
820C THR* 6.3 0.2 - - + -
823C VAL* 4.7 5.6 - - + -
829C CYS 5.0 2.9 - - - -
831C TYR* 3.3 70.3 - + + +
887C ILE* 3.1 49.2 + - + -
888C LYS* 4.3 1.3 - - - +
889C ILE* 3.4 35.0 - - + +
907C LYS* 1.3 72.0 - - - +
909C LYS* 1.3 62.9 + - - +
910C ASP 3.0 1.6 + - - -
911C PHE* 3.1 31.6 + + - +
913C PHE* 3.7 26.2 - + - -
915C LYS* 3.1 15.4 + - - -
828E GLU* 3.7 4.9 - - - +
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Residues in contact with LYS 909 (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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907C LYS* 3.0 24.0 - - + +
908C TRP* 1.3 80.8 - - - +
910C ASP* 1.3 87.5 + - - +
911C PHE 3.8 0.2 + - - -
912C HIS* 3.9 11.4 + - - -
915C LYS* 4.4 5.0 + - - -
827E GLU* 4.2 28.3 - - + +
828E GLU* 3.9 26.0 + - + +
879E TYR* 3.7 19.2 + - - -
880E LYS* 4.1 13.1 - - - +
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Residues in contact with ASP 910 (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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905C TYR* 3.5 21.1 + - + -
906C SER* 5.5 1.2 + - - -
907C LYS* 3.1 21.4 + - - +
908C TRP 3.1 1.0 - - - -
909C LYS* 1.3 111.1 - - - +
911C PHE* 1.3 57.2 + - - +
912C HIS* 2.8 25.4 + - + -
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Residues in contact with PHE 911 (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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806C LYS* 4.6 13.9 - - + -
808C LEU* 4.3 10.3 - - + -
820C THR* 3.8 24.0 - - + -
889C ILE* 3.3 31.9 - - + -
894C VAL* 4.1 20.0 - - + -
905C TYR* 3.6 33.4 - + + -
907C LYS 4.0 0.8 + - - -
908C TRP* 3.1 19.2 + + - +
910C ASP* 1.3 76.9 - - - +
912C HIS* 1.3 62.5 + - - +
913C PHE* 3.5 41.0 + + + -
915C LYS* 3.0 30.1 + - - -
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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