Contacts of the strand formed by residues 799 - 803 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798B GLY* 1.4 73.3 - - - -
800B LEU* 1.3 62.9 + - - +
801B GLU* 5.9 1.2 - - - +
815B ARG* 5.9 0.4 - - - +
818B TYR* 2.9 18.0 + - - -
838B SER 3.0 8.9 + - - +
839B HIS* 2.5 39.0 + - - +
840B ILE* 3.1 24.2 + - - +
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Residues in contact with LEU 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B SER* 1.3 77.4 - - - +
801B GLU* 1.3 70.1 + - - +
802B VAL* 4.9 7.9 - - + +
814B ALA* 4.5 11.0 - - + +
815B ARG* 4.3 18.0 + - + +
818B TYR* 3.5 52.0 + - + -
840B ILE* 3.5 21.8 - - + +
841B HIS 4.2 0.7 - - - -
842B LEU* 3.6 44.0 - - + +
860B ILE* 5.7 0.2 - - + -
864B LEU* 4.5 9.9 - - + -
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Residues in contact with GLU 801 (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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799B SER* 5.9 1.8 - - - +
800B LEU* 1.3 74.0 - - - +
802B VAL* 1.3 58.6 + - - +
803B THR* 5.3 10.9 - - + +
840B ILE 3.0 13.5 + - - +
841B HIS* 3.5 15.4 - - + +
842B LEU* 2.6 34.8 + - - +
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Residues in contact with VAL 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B LEU* 4.9 9.4 - - + +
801B GLU* 1.3 85.8 - - - +
803B THR* 1.3 64.3 + - - +
805B GLN* 4.2 8.1 + - - +
806B LEU* 3.8 26.0 - - + +
810B MET* 5.9 2.5 - - + -
811B LYS* 4.7 24.7 - - + +
814B ALA* 4.9 6.7 - - + -
815B ARG* 6.5 1.1 - - + -
842B LEU* 3.2 28.3 - - + +
844B VAL* 5.9 2.0 - - + -
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Residues in contact with THR 803 (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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801B GLU* 5.0 9.2 - - + -
802B VAL* 1.3 80.9 - - - +
804B GLY* 1.3 59.2 + - - +
805B GLN* 3.1 7.0 - - - +
806B LEU* 4.6 0.9 - - - +
841B HIS* 2.2 48.2 + - + +
842B LEU 2.8 6.0 + - - -
843B HIS* 3.3 9.4 - - - +
844B VAL 3.1 25.1 + - - -
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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