Contacts of the strand formed by residues 862 - 870 (chain A) in PDB entry 4ASE
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 CYS 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852A ASP* 3.4 24.2 - - - +
853A ALA 3.8 2.9 - - - -
854A PHE* 3.7 27.1 - - - -
860A ALA 4.0 1.0 + - - -
861A THR* 1.3 85.3 - - - +
863A ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 863 (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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852A ASP* 3.3 7.0 + - - -
853A ALA 2.8 42.2 + - - +
856A ILE* 4.2 7.6 - - + -
857A ASP* 3.0 45.0 + - - +
858A LYS* 4.2 13.7 - - - +
861A THR* 4.0 25.4 - - - +
862A CYS* 1.3 77.8 + - - +
864A THR* 1.3 75.6 + - - +
865A VAL* 3.4 12.2 + - + +
902A LEU* 5.0 4.3 - - + -
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Residues in contact with THR 864 (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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850A GLU* 3.9 25.6 - - + +
851A ALA 3.3 11.2 - - - +
852A ASP* 4.3 7.8 + - - +
863A ARG* 1.3 83.6 - - - +
865A VAL* 1.3 65.5 + - - +
917A GLU* 5.3 0.3 - - - -
918A PHE* 3.4 42.3 + - + +
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Residues in contact with VAL 865 (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 LEU* 4.1 2.2 - - + -
850A GLU* 3.7 4.7 - - - +
851A ALA* 2.8 54.1 + - + +
853A ALA* 4.1 21.8 - - + -
856A ILE* 4.5 0.4 - - + -
863A ARG* 3.7 15.9 - - + +
864A THR* 1.3 81.0 - - - +
866A ALA* 1.3 62.4 + - - +
867A VAL* 5.5 0.7 - - + -
902A LEU* 3.7 27.1 - - + -
915A ILE* 3.7 21.8 - - + -
916A VAL 3.5 9.0 - - - +
917A GLU* 5.2 0.2 - - - -
918A PHE* 3.9 11.9 - - - +
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Residues in contact with ALA 866 (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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840A LEU* 4.3 5.4 - - + -
848A VAL* 3.8 9.6 - - + -
849A ILE 3.5 4.3 - - - -
865A VAL* 1.3 75.0 - - - +
867A VAL* 1.3 59.4 + - - +
868A LYS 4.2 0.2 - - - -
914A VAL 3.7 0.3 - - - +
915A ILE* 3.5 2.6 - - - +
916A VAL* 2.9 38.4 + - + +
918A PHE* 4.2 3.2 - - + +
3169A AV9 3.5 48.7 - - + +
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Residues in contact with VAL 867 (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 LEU* 4.8 4.0 - - + -
836A LEU* 4.5 7.4 - - + -
847A GLN 3.7 0.5 - - - +
848A VAL* 3.2 5.2 - - - +
849A ILE* 2.7 73.3 + - + +
851A ALA* 4.3 16.4 - - + -
865A VAL* 5.5 0.2 - - + -
866A ALA* 1.3 76.0 - - - +
868A LYS* 1.3 64.2 + - - +
869A MET* 3.9 3.9 + - + -
913A MET* 3.6 42.6 - - + -
914A VAL 3.4 7.6 - - - +
915A ILE* 4.5 9.9 - - + -
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Residues in contact with LYS 868 (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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846A GLY* 6.2 0.9 - - - -
847A GLN 3.4 10.3 - - - +
848A VAL* 4.3 8.0 - - + +
866A ALA 4.2 0.6 + - - -
867A VAL* 1.3 71.5 - - - +
869A MET* 1.3 69.7 + - - +
870A LEU* 6.5 0.2 - - + -
882A LEU* 4.1 14.1 - - + +
885A GLU* 3.1 37.4 + - - +
912A LEU 3.9 0.7 - - - +
913A MET* 3.6 2.1 - - - -
914A VAL* 2.9 37.5 + - + +
1046A ASP 3.1 19.2 + - - -
1047A PHE* 2.8 29.8 + - - +
1048A GLY* 4.0 4.4 - - - +
1049A LEU* 4.4 9.8 - - - +
1050A ALA* 4.5 8.3 - - + +
3169A AV9 3.5 30.2 - - + +
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Residues in contact with MET 869 (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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836A LEU* 4.7 9.0 - - + -
846A GLY* 3.4 2.6 - - - -
847A GLN* 2.8 51.8 + - + +
849A ILE* 4.2 19.3 - - + -
867A VAL* 4.5 4.5 - - + +
868A LYS* 1.3 79.7 - - - +
870A LEU* 1.3 78.5 - - - +
882A LEU* 3.9 5.2 - - - -
911A PRO* 3.8 28.3 - - + -
912A LEU 3.6 18.2 - - - +
913A MET* 4.1 23.1 - - + -
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Residues in contact with LEU 870 (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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845A PHE 3.4 14.8 - - - +
846A GLY* 4.5 2.5 - - - -
847A GLN* 2.9 17.2 + - - -
869A MET* 1.3 94.4 - - - +
871A LYS* 1.3 62.8 + - - +
874A ALA* 3.8 11.7 - - + -
875A THR 4.5 1.6 - - - +
878A GLU* 3.7 11.4 - - + +
879A HIS* 3.5 45.8 - - + +
882A LEU* 4.0 19.0 - - + +
911A PRO* 5.6 3.6 - - + +
912A LEU* 4.6 2.3 + - + +
1049A LEU* 4.0 24.5 - - + -
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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