Contacts of the strand formed by residues 813 - 824 (chain A) in PDB entry 4YOC
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 GLU 813 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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799A ALA* 4.5 0.2 - - - -
800A GLY* 3.3 23.0 + - - -
805A LEU* 5.4 0.5 - - - +
809A SER* 4.1 5.8 + - - +
810A ASP* 2.8 24.9 + - + +
811A PRO 3.4 2.0 - - - +
812A LEU* 1.3 77.4 - - - +
814A LEU* 1.3 73.4 + - - +
815A PHE* 3.6 25.3 - - + -
864A PHE* 3.5 26.4 - - + +
865A TYR* 5.1 0.9 - - - -
866A GLN* 3.0 36.0 + - - +
1285A ARG* 3.7 22.7 + - - -
1288A VAL* 3.7 7.6 - - - +
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Residues in contact with LEU 814 (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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776A LEU* 3.7 35.0 - - + -
797A PHE* 3.9 29.8 - - + -
798A CYS 3.4 11.2 - - - +
799A ALA* 4.6 8.5 - - + +
811A PRO 5.8 0.4 - - - +
813A GLU* 1.3 85.0 - - - +
815A PHE* 1.3 74.7 + - - +
834A VAL* 3.8 30.1 - - + -
863A TYR* 3.9 22.2 - - + -
864A PHE 2.8 12.8 + - - +
865A TYR* 3.2 22.9 - - + +
866A GLN 4.3 0.5 + - - -
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Residues in contact with PHE 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A PHE* 3.8 3.1 - - - -
798A CYS* 2.9 44.6 + - + +
800A GLY* 3.6 26.0 - - - -
803A THR* 3.7 18.6 - - + -
805A LEU* 3.8 26.5 - - + -
809A SER* 4.4 0.7 - - - -
813A GLU* 3.6 37.7 - - + -
814A LEU* 1.3 78.9 - - - +
816A LEU* 1.3 67.2 + - - +
817A VAL 3.5 0.3 + - - -
867A LEU* 3.3 34.1 - - + +
869A TYR* 3.8 18.8 - - + -
876A PHE* 3.9 17.9 - + - -
1288A VAL* 4.2 6.1 - - + -
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Residues in contact with LEU 816 (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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778A ARG* 5.3 2.5 - - - +
795A HIS* 5.3 15.0 - - + +
796A TRP 4.9 2.2 - - - +
797A PHE* 3.7 25.4 - - + -
815A PHE* 1.3 73.2 - - - +
817A VAL* 1.3 59.3 + - - +
865A TYR* 3.5 43.7 - - + -
867A LEU 3.2 6.5 + - - +
868A TRP* 3.3 19.4 - - + -
869A TYR* 2.7 31.0 + - - -
879A PRO* 3.9 28.5 - - + -
880A PRO* 4.6 4.7 - - + -
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Residues in contact with VAL 817 (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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718A MET* 4.1 8.3 - - + -
795A HIS* 3.0 24.3 + - - -
796A TRP* 3.4 23.8 + - + +
797A PHE 4.5 1.8 - - - -
798A CYS* 3.5 26.2 - - + -
815A PHE 3.6 1.6 - - - +
816A LEU* 1.3 80.3 - - - +
818A ASP* 1.3 65.5 + - - +
819A GLU* 3.6 22.8 + - + -
868A TRP* 3.8 8.0 + - - +
869A TYR* 3.8 16.2 - - + +
871A GLN* 3.6 25.1 - - - +
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Residues in contact with ASP 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LYS* 5.6 4.7 + - - +
795A HIS* 5.2 0.5 + - - -
817A VAL* 1.3 73.0 - - - +
819A GLU* 1.3 70.9 + - - +
868A TRP* 3.3 20.7 + - - +
869A TYR 5.3 0.2 + - - -
871A GLN* 4.9 2.3 + - - +
894A VAL* 5.5 0.3 - - - +
895A SER* 3.3 17.9 - - - +
898A ARG* 2.4 54.3 + - - -
899A LEU* 3.9 19.4 - - + +
902A MET* 4.4 7.6 - - - +
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Residues in contact with GLU 819 (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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717A LYS* 3.7 16.0 - - + +
718A MET* 3.3 33.7 + - - +
719A HIS* 3.1 36.6 + - - +
795A HIS* 3.6 5.5 - - - -
796A TRP* 3.1 31.6 + - + +
817A VAL* 3.6 15.3 - - + -
818A ASP* 1.3 83.2 - - - +
820A CYS* 1.3 61.6 + - - +
871A GLN* 3.0 23.0 + - - +
895A SER* 3.0 6.1 + - - -
899A LEU* 5.0 1.1 - - - +
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Residues in contact with CYS 820 (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 HIS* 3.5 4.7 - - - +
794A ALA 3.1 14.1 - - - +
795A HIS* 4.1 4.7 - - - -
796A TRP* 3.9 3.0 - - - -
819A GLU* 1.3 75.3 - - - +
821A GLU* 1.3 67.3 + - - +
895A SER* 3.5 20.2 - - - +
896A CYS* 3.5 11.4 - - - -
899A LEU* 5.3 9.6 - - - -
1702A ZN 2.3 35.7 - - - -
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Residues in contact with GLU 821 (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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719A HIS* 4.1 16.6 - - - +
721A GLY 5.5 2.4 - - - +
723A LYS* 5.6 1.9 - - - +
793A HIS* 3.2 9.8 - - - -
794A ALA* 2.9 31.6 + - - +
796A TRP* 3.0 42.9 + - + +
820A CYS* 1.3 76.5 - - - +
822A ASP* 1.3 70.9 + - - +
823A MET* 4.2 12.2 - - + +
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Residues in contact with ASP 822 (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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744A LYS* 5.8 2.8 + - - -
783A TRP* 3.4 31.8 - - + -
791A MET* 3.9 13.1 - - + +
792A PHE 3.6 4.3 - - - -
793A HIS* 2.8 24.8 + - - -
821A GLU* 1.3 83.3 - - - +
823A MET* 1.3 61.9 + - - +
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Residues in contact with MET 823 (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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723A LYS* 4.5 13.5 - - + -
765A VAL* 4.4 6.7 - - - -
791A MET* 3.6 7.9 - - - +
792A PHE* 2.9 62.0 + - + +
794A ALA* 5.0 0.7 - - + -
796A TRP* 3.9 33.0 - - + -
821A GLU* 4.2 17.9 - - - +
822A ASP* 1.3 78.6 - - - +
824A GLN* 1.3 65.2 + - - +
827A TYR* 3.5 42.2 - - + -
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Residues in contact with GLN 824 (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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725A LYS* 4.7 11.8 + - - -
788A ASN* 3.2 33.1 + - - +
789A GLY* 4.8 2.6 - - - -
790A GLN 3.5 9.6 + - - +
791A MET* 3.5 17.5 - - - -
792A PHE* 4.1 1.3 - - - -
823A MET* 1.3 79.4 - - - +
825A LEU* 1.3 59.5 + - - +
826A SER* 2.9 17.2 + - - +
827A TYR* 3.1 39.0 + - + +
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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