Contacts of the strand formed by residues 850 - 854 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A TRP* 3.4 42.6 - + - +
791A HIS 4.2 4.2 + - - +
792A THR* 3.2 33.6 - - + +
793A LYS 2.8 25.6 + - - -
808A PHE* 4.4 17.3 - + - -
809A TRP* 4.6 0.4 - + - -
823A LEU* 5.6 0.4 - - + -
824A LEU* 5.2 1.1 - - + -
827A VAL* 3.4 39.3 - - + -
828A THR* 4.8 6.3 - - - -
838A PHE* 4.4 6.9 + + + -
841A LEU* 3.6 22.9 - - + +
849A SER* 1.3 75.3 + - - +
851A THR* 1.3 59.7 + - - +
852A VAL* 3.9 22.9 - - + -
869A ASN* 3.7 12.3 - - + -
871A LEU* 5.1 2.7 - - + -
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Residues in contact with THR 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A LYS* 3.2 23.3 - - + +
795A LYS* 4.2 25.8 - - + -
848A GLN* 3.8 12.7 + - - -
849A SER* 3.3 14.5 + - - -
850A PHE* 1.3 77.9 + - - +
852A VAL* 1.3 70.3 + - - +
868A PHE 4.7 1.3 - - - -
869A ASN 3.0 10.0 + - - +
870A ARG* 3.2 28.3 - - + +
871A LEU* 2.8 26.5 + - - +
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Residues in contact with VAL 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A THR* 4.3 7.6 - - + -
793A LYS 3.0 7.5 + - - -
794A TYR* 3.3 21.4 - - + +
795A LYS 3.1 19.3 + - - +
798A TYR* 4.0 5.8 - - + -
805A ILE* 3.7 21.5 - - + -
808A PHE* 4.4 16.6 - - + -
850A PHE* 3.9 22.7 - - + -
851A THR* 1.3 76.8 - - - +
853A GLU* 1.3 62.4 + - - +
871A LEU* 3.5 13.7 - - + +
873A LEU* 3.9 29.4 - - + -
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Residues in contact with GLU 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795A LYS* 3.1 44.8 - - + +
796A ASN* 3.6 18.3 + - + +
798A TYR* 3.8 4.3 - - - -
851A THR 4.1 0.6 + - - -
852A VAL* 1.3 74.4 - - - +
854A GLN* 1.3 71.9 + - - +
855A TRP* 3.4 3.0 + - + +
870A ARG* 3.2 34.1 + - - +
871A LEU 3.0 7.1 + - - -
872A ASP* 3.5 11.0 - - - +
873A LEU 3.0 23.0 + - - -
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Residues in contact with GLN 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795A LYS 3.2 8.1 + - - -
796A ASN* 2.8 52.4 + - - +
797A GLY* 4.2 7.3 - - - -
798A TYR* 3.2 49.2 - - + +
802A HIS* 4.5 6.9 + - - -
853A GLU* 1.3 74.0 - - - +
855A TRP* 1.3 64.0 + - - +
856A GLY 5.7 0.2 - - - +
873A LEU 3.6 0.4 - - - -
875A PRO* 3.3 29.2 - - + +
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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