Contacts of the strand formed by residues 850 - 854 (chain B) in PDB entry 2XBB
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 850 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788B TRP* 3.5 42.0 - + - +
791B HIS 4.1 6.5 + - - +
792B THR* 3.2 32.2 - - + +
793B LYS 2.8 24.6 + - - -
808B PHE* 4.3 18.6 - + - -
809B TRP* 4.5 0.2 - + - -
823B LEU* 5.7 0.2 - - + -
824B LEU* 5.1 0.7 - - + -
827B VAL* 3.5 41.3 - - + -
828B THR* 4.7 12.6 - - - -
838B PHE* 4.5 8.9 + + + -
841B LEU* 4.0 16.1 - - + +
848B GLN 3.8 1.4 + - - -
849B SER* 1.3 68.7 - - - +
851B THR* 1.3 60.2 + - - +
852B VAL* 3.7 22.2 - - + -
869B ASN* 3.5 13.5 - - - -
871B LEU* 4.9 2.5 - - + -
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Residues in contact with THR 851 (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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793B LYS* 3.2 22.6 - - + +
795B LYS* 4.0 32.3 - - + -
848B GLN* 3.7 12.9 + - - +
849B SER 3.0 14.6 + - - -
850B PHE* 1.3 77.2 + - - +
852B VAL* 1.3 65.9 + - - +
868B PHE 4.7 1.6 - - - -
869B ASN 2.9 9.6 + - - +
870B ARG* 3.2 23.4 - - + -
871B LEU* 2.8 31.7 + - - +
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Residues in contact with VAL 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B THR* 4.0 10.3 - - + -
793B LYS 2.9 9.5 + - - -
794B TYR* 3.3 18.2 - - + +
795B LYS 3.1 19.1 + - - -
798B TYR* 3.8 13.0 - - + -
805B ILE* 3.5 23.8 - - + -
808B PHE* 4.5 15.0 - - + -
850B PHE* 3.7 23.3 - - + -
851B THR* 1.3 78.3 - - - +
853B GLU* 1.3 60.6 + - - +
871B LEU* 3.6 16.6 - - + +
873B LEU* 4.0 18.6 - - + -
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Residues in contact with GLU 853 (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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795B LYS* 3.4 41.6 - - + +
796B ASN* 3.8 16.1 + - + +
798B TYR* 3.7 4.3 - - - -
851B THR 4.1 0.6 - - - -
852B VAL* 1.3 74.0 - - - +
854B GLN* 1.3 72.0 + - - +
855B TRP* 3.3 3.1 + - + +
870B ARG* 3.4 32.5 + - - -
871B LEU 3.0 7.6 + - - +
872B ASP* 3.6 15.5 - - - +
873B LEU* 2.9 26.5 + - - +
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Residues in contact with GLN 854 (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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795B LYS 3.3 5.3 + - - -
796B ASN* 2.7 57.4 + - - +
797B GLY* 4.0 9.1 - - - -
798B TYR* 3.3 43.2 - - + +
802B HIS* 4.9 6.7 + - - -
853B GLU* 1.3 75.9 - - - +
855B TRP* 1.3 63.9 + - - +
856B GLY 6.0 0.2 - - - +
873B LEU 3.6 0.2 - - - -
875B PRO* 3.5 28.4 - - + +
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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
------------------------------------------------------------
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