Contacts of the helix formed by residues 833 - 838 (chain C) in PDB entry 2X36
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 ASP 833 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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796C LYS* 5.5 1.6 + - - +
831C ALA 3.4 6.4 + - - +
832C ASN* 1.3 72.6 + - - +
834C TYR* 1.3 66.4 + - - +
835C LEU 3.3 2.5 - - - -
836C VAL* 3.2 14.3 + - + +
837C THR* 3.0 53.4 + - + +
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Residues in contact with TYR 834 (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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784C LEU* 3.5 31.8 - - + +
832C ASN* 3.0 18.7 + - - +
833C ASP* 1.3 81.0 - - - +
835C LEU* 1.3 63.1 + - + +
837C THR* 4.2 1.3 - - - -
838C SER* 2.7 38.9 + - - -
840C ILE* 3.8 21.2 - - + +
867C LEU* 3.4 39.2 - - + +
868C ALA* 3.3 37.0 - - + +
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Residues in contact with LEU 835 (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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798C GLY* 4.7 0.2 - - - -
818C TYR* 3.9 14.2 + - + -
821C ALA* 3.5 36.1 - - + +
822C ARG* 3.4 38.6 + - + +
825C LEU* 3.7 26.4 - - + +
833C ASP 3.3 0.6 - - - -
834C TYR* 1.3 75.2 - - + +
836C VAL* 1.3 64.0 + - + +
837C THR 3.3 0.6 + - - -
838C SER 4.2 5.9 - - - +
840C ILE* 3.8 24.7 - - + +
864C LEU* 4.0 20.6 - - + +
865C LEU* 4.4 5.6 - - + -
868C ALA* 3.9 16.4 - - + -
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Residues in contact with VAL 836 (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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796C LYS 5.3 4.7 - - - +
797C ASP* 3.6 4.0 - - - -
798C GLY* 2.9 20.4 + - - -
822C ARG* 3.9 36.0 + - + +
826C MET* 3.4 33.4 - - + -
832C ASN 5.9 0.7 - - - +
833C ASP* 3.2 15.0 + - + +
835C LEU* 1.3 77.1 - - + +
837C THR* 1.3 70.2 + - + +
808F GLU* 5.3 1.8 - - - +
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Residues in contact with THR 837 (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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788C GLN* 5.1 6.7 + - - +
796C LYS* 3.8 41.6 - - + +
797C ASP 2.5 26.8 - - - +
798C GLY* 2.9 8.2 - - - +
833C ASP* 3.0 41.3 + - + +
834C TYR* 4.2 0.3 - - - -
836C VAL* 1.3 90.4 - - + +
838C SER* 1.4 66.8 + - - +
839C HIS* 4.0 4.5 + - - -
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Residues in contact with SER 838 (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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784C LEU* 3.7 21.2 - - - +
787C PRO 6.6 0.4 - - - -
788C GLN* 6.4 1.6 - - - +
798C GLY* 3.2 2.8 - - - -
799C SER 3.1 19.4 + - - +
818C TYR* 4.5 0.7 + - - -
834C TYR* 2.7 36.8 + - - -
835C LEU 4.2 6.2 - - - +
837C THR* 1.4 83.9 + - - +
839C HIS* 1.3 62.2 + - - +
840C ILE* 3.7 11.9 + - - +
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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