Contacts of the strand formed by residues 789 - 799 (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 GLY 789 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784A GLU* 3.8 10.5 - - - -
785A ASP* 2.3 52.4 + - - -
786A SER* 4.6 1.1 + - - -
788A ASN* 1.3 71.3 - - - +
790A GLN* 1.3 61.5 + - - -
791A MET* 3.5 6.8 + - - +
824A GLN* 4.8 2.9 - - - -
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Residues in contact with GLN 790 (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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731A ILE* 3.3 53.8 + - - +
732A SER* 4.8 0.2 - - - +
733A TRP* 3.7 29.1 - - + +
783A TRP 3.9 3.8 - - - -
784A GLU* 3.3 20.0 + - - +
789A GLY* 1.3 70.2 - - - -
791A MET* 1.3 60.6 + - - +
824A GLN* 3.5 9.8 - - - +
825A LEU* 3.1 32.9 + - + -
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Residues in contact with MET 791 (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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733A TRP* 4.2 4.0 - - - -
782A LEU* 3.7 1.0 - - - -
783A TRP* 2.7 78.3 + - + +
788A ASN* 3.6 30.3 - - + +
789A GLY 3.6 17.0 - - - +
790A GLN* 1.3 77.2 - - - +
792A PHE* 1.3 62.0 + - - +
822A ASP* 3.9 21.1 - - + +
823A MET* 3.6 10.3 - - - +
824A GLN* 3.5 36.1 - - - -
825A LEU* 4.2 4.7 - - - +
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Residues in contact with PHE 792 (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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763A VAL* 4.1 12.3 - - + -
765A VAL* 5.1 4.0 - - + -
779A VAL* 3.9 29.2 - - + -
781A ALA 3.1 14.1 - - - +
782A LEU* 3.6 16.2 - - + -
783A TRP* 3.5 8.0 - - - -
791A MET* 1.3 74.9 - - - +
793A HIS* 1.3 65.8 + - - +
794A ALA* 3.7 30.1 + - + -
822A ASP* 3.6 1.4 - - - -
823A MET* 2.9 83.6 + - + +
824A GLN 4.1 3.6 - - - -
825A LEU* 3.7 17.0 - - + -
828A ILE* 4.0 22.9 - - + -
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Residues in contact with HIS 793 (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 3.3 1.7 - - - +
779A VAL* 3.7 2.4 - - - -
780A THR* 3.0 55.0 + - + +
781A ALA* 3.0 15.0 + - + -
783A TRP* 3.5 9.1 - - + -
792A PHE* 1.3 73.8 - - - +
794A ALA* 1.3 59.4 + - - +
820A CYS* 3.5 7.4 - - + +
821A GLU* 3.2 34.5 + - - -
822A ASP* 2.8 25.2 + - - +
891A LYS 5.2 1.3 - - - -
893A CYS* 3.7 9.9 - - + -
896A CYS* 3.1 9.7 - - - -
1702A ZN 2.1 35.7 - - - -
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Residues in contact with ALA 794 (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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777A ALA* 3.7 16.2 - - + -
778A ARG 3.6 3.8 - - - -
792A PHE* 3.7 27.9 + - + -
793A HIS* 1.3 71.6 - - - +
795A HIS* 1.3 61.1 + - - +
796A TRP* 3.7 21.7 + - + -
820A CYS* 3.1 6.8 - - - +
821A GLU 2.9 41.3 + - - +
823A MET* 5.0 2.7 - - + -
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Residues in contact with HIS 795 (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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777A ALA* 3.4 0.8 - - - -
778A ARG* 2.9 44.9 + - + +
780A THR* 3.6 23.2 - - + +
793A HIS 3.7 0.8 + - - -
794A ALA* 1.3 70.3 - - - +
796A TRP* 1.3 73.0 + - - +
797A PHE* 4.7 2.8 - - - -
816A LEU* 5.3 15.9 - - + +
817A VAL 3.0 24.4 + - - -
818A ASP* 5.7 0.4 - - - -
819A GLU 3.6 13.0 - - - -
820A CYS* 4.1 1.8 - - - -
868A TRP* 6.5 0.2 - + - -
893A CYS* 4.1 14.5 - - - -
894A VAL* 4.3 16.3 + - + +
895A SER* 3.6 24.5 - - - -
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Residues in contact with TRP 796 (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* 3.1 40.3 + + + +
723A LYS* 3.9 22.7 - - + -
765A VAL* 4.3 12.6 - - + -
775A TYR* 3.6 25.8 - + + -
776A LEU 3.1 29.6 - - - -
777A ALA* 3.5 16.8 - - + -
794A ALA* 4.0 14.5 + - + -
795A HIS* 1.3 83.2 + - - +
797A PHE* 1.3 62.6 + - - +
816A LEU* 4.9 0.7 - - - -
817A VAL* 3.4 18.6 + - + +
819A GLU* 3.1 37.7 + - + +
820A CYS* 3.9 4.5 - - - -
821A GLU* 3.0 40.6 + - + +
823A MET* 3.9 18.2 - - + -
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Residues in contact with PHE 797 (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* 3.2 23.3 + - - -
762A CYS* 3.8 16.2 - - + -
776A LEU* 2.9 40.0 + - + +
777A ALA* 3.7 22.4 - - - -
778A ARG* 3.1 35.0 - - + -
795A HIS 5.0 1.1 - - - -
796A TRP* 1.3 78.0 - - - +
798A CYS* 1.3 60.8 + - - +
799A ALA 4.2 0.9 + - - -
814A LEU* 3.9 33.0 - - + -
815A PHE 3.9 5.2 - - - -
816A LEU* 3.7 27.6 - - + -
817A VAL* 4.5 1.8 - - - -
834A VAL* 4.1 18.6 - - + -
865A TYR* 4.6 5.2 - + + -
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Residues in contact with CYS 798 (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* 3.6 22.9 - - + -
719A HIS* 5.2 0.2 - - - -
797A PHE* 1.3 75.0 - - - +
799A ALA* 1.3 78.8 + - - +
802A ASP* 4.1 15.7 - - - -
803A THR* 3.8 17.0 - - + -
814A LEU* 3.4 6.6 - - - -
815A PHE* 2.9 45.2 + - + +
817A VAL* 3.5 19.5 - - + -
869A TYR* 4.5 4.7 - - - -
871A GLN* 4.7 1.8 - - - -
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Residues in contact with ALA 799 (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* 5.8 0.6 - - - -
719A HIS* 5.9 0.4 + - - -
773A PRO* 6.0 4.7 - - + -
797A PHE 4.2 1.0 + - - -
798A CYS* 1.3 86.5 - - - +
800A GLY* 1.3 60.7 + - - +
801A THR* 3.9 11.0 - - + -
802A ASP* 2.8 41.1 + - - +
803A THR* 3.5 2.3 + - - +
813A GLU 4.5 3.1 - - - -
814A LEU* 4.6 8.0 - - + +
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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