Contacts of the strand formed by residues 799 - 803 (chain E) 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 SER 799 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785E ARG* 3.3 15.2 + - - -
797E ASP* 5.7 0.2 - - - -
798E GLY* 1.3 74.4 - - - -
800E LEU* 1.3 62.9 + - - +
818E TYR* 3.5 12.5 + - - -
838E SER 3.3 7.1 + - - +
839E HIS* 2.3 33.3 + - - -
840E ILE* 2.8 26.0 + - - +
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Residues in contact with LEU 800 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785E ARG* 4.9 0.4 - - - -
799E SER* 1.3 78.6 - - - +
801E GLU* 1.3 59.4 + - - +
802E VAL* 4.0 22.5 + - + +
814E ALA 4.6 9.0 - - - +
815E ARG* 5.3 2.9 - - + +
818E TYR* 3.6 49.2 + - + -
840E ILE* 3.3 29.4 - - + +
842E LEU* 3.9 29.2 - - + +
860E ILE* 5.9 0.2 - - + -
864E LEU* 4.4 10.8 - - + -
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Residues in contact with GLU 801 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785E ARG* 2.9 50.2 + - - +
799E SER 4.1 0.4 - - - -
800E LEU* 1.3 73.9 - - - +
802E VAL* 1.3 61.3 + - - +
803E THR* 5.2 4.0 - - + +
840E ILE 2.7 12.1 + - - +
841E HIS* 3.2 22.2 + - + -
842E LEU 2.8 24.5 + - - -
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Residues in contact with VAL 802 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800E LEU* 4.2 21.8 - - + +
801E GLU* 1.3 77.6 - - - +
803E THR* 1.3 79.9 + - - +
805E GLN* 4.4 12.9 + - - +
811E LYS* 5.6 11.0 - - + +
814E ALA* 4.0 24.7 - - + -
815E ARG* 6.3 2.0 - - + -
842E LEU* 3.2 25.6 - - + +
844E VAL* 5.2 4.0 - - + -
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Residues in contact with THR 803 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801E GLU* 5.2 5.2 - - + +
802E VAL* 1.3 86.6 - - - +
804E GLY* 1.3 64.6 + - - +
805E GLN* 3.6 6.7 - - - +
841E HIS* 2.6 34.6 + - + +
842E LEU 2.8 11.2 + - - +
843E HIS* 3.0 18.4 - - - -
844E VAL* 3.0 24.9 + - - +
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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