Contacts of the strand formed by residues 926 - 930 (chain A) in PDB entry 2B7A
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 LYS 926 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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846A GLU* 2.9 40.2 + - - -
849A LEU* 4.0 11.8 - - + +
864A GLU* 6.2 0.2 - - - +
881A VAL* 3.8 26.2 - - + -
882A LYS 3.4 3.4 - - - -
883A LYS* 3.8 29.8 - - + +
895A PHE* 4.5 0.2 - - - -
916A VAL* 3.3 9.2 - - - +
917A CYS* 2.9 61.3 + - + -
924A ASN* 4.1 16.6 - - + +
925A LEU* 1.3 82.3 - - - +
927A LEU* 1.3 59.8 + - - +
928A ILE* 4.5 0.7 - - + -
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Residues in contact with LEU 927 (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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880A ALA 3.6 0.9 - - - +
881A VAL* 3.4 3.8 - - - -
882A LYS* 2.8 41.1 + - + +
895A PHE* 3.7 19.1 - - + -
898A GLU* 4.1 21.3 - - + +
899A ILE* 4.0 24.9 - - + -
902A LEU* 4.0 24.2 - - + -
913A TYR* 3.6 35.9 - - + -
915A GLY 3.9 1.6 - - - +
916A VAL* 4.8 1.8 - - + -
926A LYS* 1.3 70.8 - - - +
928A ILE* 1.3 69.2 + - - +
929A MET* 3.8 20.9 + - + +
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Residues in contact with ILE 928 (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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844A PHE* 3.8 42.4 - - + -
849A LEU* 4.2 8.7 - - + -
879A VAL* 3.8 30.5 - - + -
880A ALA 3.5 2.2 - - - +
881A VAL* 3.8 31.0 - - + -
914A LYS* 2.9 28.0 + - + -
915A GLY 2.8 29.6 + - - +
916A VAL 4.2 4.3 - - - -
917A CYS* 4.1 18.8 - - + -
926A LYS 4.4 0.9 - - - +
927A LEU* 1.3 78.1 - - - +
929A MET* 1.3 62.5 + - - +
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Residues in contact with MET 929 (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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863A VAL* 4.7 5.4 - - + -
879A VAL* 3.6 9.5 - - - +
880A ALA 2.8 29.9 + - - +
882A LYS* 3.8 36.8 - - + +
902A LEU* 3.8 32.8 - - + -
911A VAL* 4.0 13.2 - - + -
912A LYS 3.4 10.5 - - - +
913A TYR* 4.9 0.2 - - - -
914A LYS* 3.8 6.4 - - - +
927A LEU* 4.0 15.5 - - + +
928A ILE* 1.3 77.7 - - - +
930A GLU* 1.3 66.7 + - - +
993A GLY 4.2 5.4 - - - +
994A ASP* 5.6 2.7 - - - +
2001A IZA 3.7 32.3 - - + -
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Residues in contact with GLU 930 (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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880A ALA* 3.8 0.6 - - - +
911A VAL* 3.7 7.1 - - + -
912A LYS* 2.9 57.2 + - + +
914A LYS* 3.8 23.3 - - - +
929A MET* 1.3 74.7 - - - +
931A TYR* 1.3 61.7 + - - +
932A LEU* 3.5 20.5 + - + +
985A GLU* 4.6 4.2 - - - +
991A LYS* 2.7 37.3 + - - +
2001A IZA 3.0 23.4 + - - -
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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
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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