Contacts of the strand formed by residues 850 - 857 (chain A) in PDB entry 3LXK
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 ALA 850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840A ARG* 3.5 1.1 - - - -
841A TYR* 2.8 38.7 + - + +
849A GLY* 1.3 72.0 - - - -
851A LEU* 1.3 66.6 + - - +
852A VAL* 3.7 7.4 + - + +
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Residues in contact with LEU 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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825A ILE* 3.5 32.5 - - + -
838A LEU* 4.0 10.3 - - + -
839A CYS 3.5 6.7 - - - +
840A ARG* 3.9 29.4 - - + +
849A GLY 3.6 0.6 + - - -
850A ALA* 1.3 76.8 - - - +
852A VAL* 1.3 63.9 + - - +
903A GLU* 5.5 0.3 - - - -
904A TYR* 3.6 45.1 + - + +
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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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817A PHE* 4.5 12.3 - - + -
822A LEU* 3.9 18.4 - - + -
837A GLU 3.7 0.2 - - - +
838A LEU* 3.7 5.9 - - - +
839A CYS* 2.9 38.6 + - + +
841A TYR* 4.2 10.5 - - + +
850A ALA* 4.3 11.4 - - + +
851A LEU* 1.3 77.9 - - - +
853A ALA* 1.3 58.5 + - - +
854A VAL* 3.6 20.2 - - + -
887A ARG* 5.1 6.3 - - + +
901A VAL* 3.7 23.3 - - + -
902A MET 3.7 6.3 - - - +
903A GLU* 5.7 1.1 - - - -
904A TYR* 3.8 7.0 - - - +
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Residues in contact with ALA 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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828A LEU* 4.0 5.8 - - + -
836A VAL* 3.8 10.3 - - + -
837A GLU 3.5 4.5 - - - -
852A VAL* 1.3 73.0 - - - +
854A VAL* 1.3 60.6 + - - +
900A LEU 3.7 1.0 - - - +
901A VAL* 3.6 1.7 - - - -
902A MET* 2.7 39.7 + - - +
903A GLU 3.6 6.5 - - - +
904A TYR* 3.8 3.4 - - - +
1125A MI1 3.1 46.2 - - + +
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Residues in contact with VAL 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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822A LEU* 4.2 11.7 - - + -
836A VAL* 4.0 2.6 - - - +
837A GLU* 2.8 39.1 + - + +
839A CYS* 3.9 24.5 - - + -
852A VAL* 3.6 26.0 - - + -
853A ALA* 1.3 77.5 - - - +
855A LYS* 1.3 56.7 + - - +
856A GLN* 3.0 27.3 + - - +
899A ARG* 3.4 33.4 - - + -
900A LEU 3.3 4.9 - - - +
901A VAL* 4.4 8.1 - - + -
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Residues in contact with LYS 855 (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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831A GLY 5.2 2.6 + - - -
832A ASN* 5.9 1.8 + - - +
834A GLY* 4.5 11.4 - - - -
835A SER 3.2 11.0 - - - +
836A VAL* 4.0 8.1 - - + +
853A ALA 4.2 0.6 - - - -
854A VAL* 1.3 73.6 - - - +
856A GLN* 1.3 67.0 + - - +
857A LEU* 6.4 0.7 - - - -
868A PHE* 3.5 13.1 - - + -
871A GLU* 2.8 35.3 + - - +
899A ARG* 3.2 6.9 - - - +
900A LEU* 2.8 50.4 + - + +
902A MET* 4.0 18.6 - - + +
967A ASP* 2.7 37.2 + - - +
969A GLY* 3.8 5.7 - - - -
1125A MI1 3.7 15.6 + - - -
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Residues in contact with GLN 856 (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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834A GLY* 3.3 4.1 - - - -
835A SER* 3.0 54.8 + - - +
837A GLU* 3.6 23.8 - - - +
854A VAL* 3.0 41.9 + - - +
855A LYS* 1.3 77.0 - - - +
857A LEU* 1.3 74.1 + - - +
868A PHE* 3.9 9.2 - - - -
898A LEU* 3.6 16.8 - - + +
899A ARG* 3.1 31.1 + - + +
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Residues in contact with LEU 857 (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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832A ASN 5.5 1.3 - - - +
833A PHE* 3.6 17.5 - - + +
834A GLY* 4.9 1.6 - - - -
855A LYS* 6.4 0.7 - - - -
856A GLN* 1.3 88.7 - - - +
858A GLN* 1.3 64.6 + - - +
859A HIS* 3.5 20.7 - - - +
860A SER* 5.2 0.9 - - - -
861A GLY 4.5 4.9 - - - +
864A GLN* 3.6 40.6 - - + +
865A GLN* 3.6 33.2 - - - +
868A PHE* 4.1 26.3 - - + -
898A LEU 4.8 0.8 + - - -
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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