Contacts of the strand formed by residues 846 - 853 (chain A) in PDB entry 4A0L
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 GLY 846 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771A PHE* 3.7 5.1 - - - -
833A THR* 3.6 10.8 - - - -
834A ALA* 4.0 4.7 - - - -
835A MET* 4.6 0.7 - - - -
845A GLN* 1.3 74.8 - - - +
847A ARG* 1.3 69.5 + - - +
865A GLU* 3.6 2.8 - - - -
866A VAL* 2.9 33.2 + - - +
868A GLY 3.2 18.6 + - - -
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Residues in contact with ARG 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A SER* 3.2 25.3 + - - -
767A SER 5.3 0.8 + - - -
768A SER* 4.1 6.6 + - - -
770A LEU* 4.0 17.5 - - + -
771A PHE* 3.6 24.2 - - + -
807A PHE* 3.9 8.5 - - - -
808A LEU* 3.7 13.4 - - - +
811A GLU* 2.7 37.1 + - - +
831A VAL 3.7 1.3 - - - +
832A GLY* 3.5 2.8 - - - -
833A THR* 2.8 40.8 + - - +
846A GLY* 1.3 79.8 - - - +
848A ILE* 1.3 65.3 + - - +
849A VAL* 3.6 29.9 - - + +
851A PHE* 6.2 0.2 - - - -
860A THR* 5.9 0.2 - - - +
863A GLU* 3.5 26.6 + - - +
864A LYS 3.2 10.3 - - - +
866A VAL* 4.0 1.3 - - - +
870A VAL* 3.7 2.7 - - - +
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Residues in contact with ILE 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A ILE* 3.8 20.9 - - + -
831A VAL 3.4 4.3 - - - +
832A GLY* 4.6 0.4 - - - -
847A ARG* 1.3 77.6 - - - +
849A VAL* 1.3 63.1 + - - +
850A VAL* 5.3 0.3 - - - +
862A ALA 3.7 2.8 - - - +
863A GLU* 3.9 0.2 - - - -
864A LYS* 2.9 42.4 + - + +
866A VAL* 4.2 16.4 - - + -
870A VAL* 3.8 28.3 - - + -
873A MET* 4.4 4.5 - - - -
880A LEU* 4.0 6.5 - - + -
882A ALA* 4.5 5.4 - - + -
884A ILE* 4.5 3.1 - - + -
891A TYR* 3.6 33.0 - - + -
899A LEU* 3.7 24.5 - - + +
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Residues in contact with VAL 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A SER* 6.2 0.2 - - - +
807A PHE* 4.9 5.2 - - + -
829A PHE 3.8 1.2 - - - +
830A ILE* 3.3 5.5 - - - +
831A VAL* 2.9 39.2 + - + +
833A THR* 5.2 1.8 - - + -
847A ARG* 3.6 45.3 - - + +
848A ILE* 1.3 78.1 - - - +
850A VAL* 1.3 65.0 + - - +
851A PHE* 3.4 40.2 + - + -
860A THR* 3.9 21.5 - - + +
862A ALA 3.5 4.3 - - - +
863A GLU* 4.9 3.6 - - + -
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Residues in contact with VAL 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A LEU* 5.7 1.1 - - + -
828A TYR* 3.5 40.2 - - + -
829A PHE 3.7 2.9 - - - -
830A ILE* 4.1 22.0 - - + -
848A ILE* 5.2 0.4 - - + +
849A VAL* 1.3 76.7 - - - +
851A PHE* 1.3 56.8 + - - +
860A THR* 3.7 3.1 - - - -
861A VAL* 2.7 41.0 + - + -
862A ALA* 2.9 22.2 + - + +
893A TRP* 4.0 27.6 - - + -
899A LEU* 4.3 14.4 - - + -
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Residues in contact with PHE 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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766A SER* 5.5 0.2 - - - -
791A LEU* 3.9 15.9 - - + -
805A HIS* 3.5 45.1 - + - -
807A PHE* 3.9 7.9 - + - -
828A TYR* 3.3 13.6 - - - -
829A PHE* 2.7 42.4 + - + +
831A VAL* 3.7 24.7 - - + -
849A VAL* 3.4 30.5 - - + -
850A VAL* 1.3 73.7 - - - +
852A GLN* 1.3 61.4 + - - +
858A LEU* 3.7 26.7 - - + -
859A GLN 3.3 10.5 - - - -
860A THR* 3.7 22.4 - - - -
861A VAL* 4.2 0.7 - - - -
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Residues in contact with GLN 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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826A ASN* 3.3 36.9 + - - +
827A THR 4.5 8.8 - - - +
828A TYR* 4.0 11.1 - - + -
851A PHE* 1.3 75.3 - - - +
853A TYR* 1.3 70.5 + - - +
854A SER* 4.2 4.4 + - - +
857A LYS 3.5 1.6 - - - +
858A LEU* 3.4 6.7 - - - -
859A GLN* 2.8 67.1 + - - +
861A VAL* 3.8 19.0 - - + +
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Residues in contact with TYR 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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727A GLN* 4.5 4.7 + - - +
730A SER* 3.8 38.0 + - - -
732A CYS* 4.3 3.4 - - - -
793A ILE* 3.7 39.9 - - + -
802A LEU* 3.4 27.8 - - + +
803A HIS* 4.5 4.3 - - + -
827A THR 4.9 4.6 + - - +
829A PHE* 4.0 18.7 - - + +
851A PHE 4.3 0.2 - - - -
852A GLN* 1.3 79.2 - - - +
854A SER* 1.3 63.5 + - - +
855A ASP* 3.4 16.1 + - - -
856A GLY* 2.9 42.7 + - - -
857A LYS 3.4 14.1 - - - -
858A LEU* 3.8 13.2 - - + +
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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