Contacts of the strand formed by residues 759 - 767 (chain A) in PDB entry 4EJX
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 LYS 759 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A GLU* 3.3 34.7 + - + +
724A TRP 3.4 5.2 - - - +
725A ASP* 3.5 34.1 - - + +
756A ILE* 3.6 17.6 + - - +
757A GLY* 3.7 0.4 - - - -
758A SER* 1.3 80.8 - - - +
760A TYR* 1.3 68.4 + - - +
919A TYR* 3.7 18.2 - - + +
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Residues in contact with TYR 760 (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 GLU* 4.4 2.0 - - - -
724A TRP* 2.4 46.8 + - - +
726A TYR* 3.4 17.5 - + - -
756A ILE* 3.3 34.5 - - + +
757A GLY 3.5 18.0 + - - -
758A SER 3.8 3.1 - - - -
759A LYS* 1.3 75.2 - - - +
761A LYS* 1.3 56.9 + - - +
762A LYS* 3.2 11.9 + - + -
906A GLU* 3.3 39.7 - - + +
915A ASN* 3.4 23.3 - - + +
919A TYR* 4.4 2.2 - - - -
936A SER 3.6 8.7 + - - -
937A ASN* 2.9 20.8 + - - -
939A MET* 3.6 33.7 - - + -
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Residues in contact with LYS 761 (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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721A GLU* 4.3 29.5 + - + -
722A VAL* 4.0 13.7 - - - +
723A GLU* 4.2 2.7 - - + +
760A TYR* 1.3 69.6 - - - +
762A LYS* 1.3 62.0 + - - +
810A THR* 6.1 1.0 - - - +
906A GLU* 5.1 0.3 - - - +
909A SER* 5.1 0.3 + - - -
911A TYR* 3.3 37.5 - - + +
914A ASP* 4.1 27.1 + - + +
915A ASN* 2.8 20.2 + - - +
918A THR* 5.6 6.3 - - + +
919A TYR* 3.7 19.8 - - + +
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Residues in contact with LYS 762 (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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720A VAL 4.1 0.3 - - - +
721A GLU* 3.7 5.5 - - - +
722A VAL* 3.1 29.8 + - - +
724A TRP* 4.0 15.3 - - + -
726A TYR* 3.3 35.7 - - + +
760A TYR* 3.2 14.0 + - + +
761A LYS* 1.3 77.6 - - - +
763A VAL* 1.3 60.8 + - - +
764A VAL* 4.1 8.1 + - + +
788A ILE* 4.1 7.6 - - + +
871A TYR 2.7 26.5 + - - -
872A SER* 2.8 30.2 + - - +
873A GLY* 3.3 9.3 - - - +
904A PHE* 4.5 7.8 - - - -
906A GLU* 3.3 29.8 - - - +
909A SER* 4.6 0.9 + - - +
911A TYR* 4.9 3.8 - - - -
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Residues in contact with VAL 763 (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 ALA* 3.9 23.6 - - + +
720A VAL 3.3 16.4 - - - +
721A GLU* 4.0 3.6 - - + -
762A LYS* 1.3 72.8 - - - +
764A VAL* 1.3 54.4 + - - +
809A ALA* 3.9 6.1 - - + -
813A TYR* 3.3 46.0 - - + +
872A SER* 2.7 25.6 + - - +
873A GLY 2.7 32.4 - - - +
874A LEU* 3.4 7.1 - - + +
911A TYR* 3.6 15.4 - - + +
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Residues in contact with VAL 764 (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 ALA 3.2 0.9 - - - +
719A ALA* 3.3 0.9 - - - -
720A VAL* 2.8 48.0 + - + +
722A VAL* 4.8 14.4 - - + -
724A TRP* 5.8 5.4 - - + -
762A LYS* 5.1 5.8 - - + +
763A VAL* 1.3 77.5 - - - +
765A TYR* 1.3 68.2 + - - +
766A ARG* 3.9 21.5 - - + +
788A ILE* 3.4 40.4 - - + +
873A GLY* 3.2 20.2 - - - +
874A LEU* 3.8 6.5 - - - -
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Residues in contact with TYR 765 (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 ILE* 3.4 26.9 - - + -
718A ALA 3.4 3.4 - - - -
719A ALA 4.7 0.9 - - - -
764A VAL* 1.3 73.6 - - - +
766A ARG* 1.3 93.9 + - - +
788A ILE 5.4 0.2 + - - -
790A GLY* 3.8 11.5 - - - -
791A PRO* 4.4 0.9 - - - -
805A PHE* 3.9 23.1 - + - -
814A SER 3.1 11.2 + - - -
815A ILE* 3.7 20.9 - - + -
860A TYR* 3.9 16.6 - + + -
861A TYR 2.8 28.8 + - - -
873A GLY 4.3 0.4 + - - -
874A LEU* 3.5 29.2 - - + +
875A ILE* 3.5 41.6 + - - -
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Residues in contact with ARG 766 (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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716A TYR 3.5 0.5 - - - +
717A ILE* 3.2 6.3 - - - -
718A ALA* 3.0 30.0 + - - +
720A VAL* 4.0 24.0 - - + -
724A TRP* 4.6 9.1 - - - -
764A VAL* 3.9 14.5 - - + +
765A TYR* 1.3 101.7 + - - +
767A GLN* 1.3 63.4 + - - +
768A TYR* 3.9 12.8 + - + -
776A PRO* 6.3 1.6 - - + -
779A ARG* 2.9 27.6 - - - +
787A GLY 2.7 28.1 + - - -
788A ILE* 3.6 13.3 + - - +
789A LEU 2.8 21.0 + - - -
790A GLY* 3.3 5.9 - - - +
791A PRO* 3.9 9.6 - - - -
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Residues in contact with GLN 767 (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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715A TYR* 4.9 19.1 - - + -
716A TYR 3.3 13.2 - - - +
717A ILE* 5.1 2.7 - - + -
766A ARG* 1.3 76.1 - - - +
768A TYR* 1.3 57.4 + - - +
776A PRO* 3.6 6.8 - - - +
777A VAL* 2.7 67.1 + - + +
780A LYS* 5.7 1.2 - - - +
791A PRO* 3.2 35.1 - - + +
792A GLN 5.1 1.9 + - - +
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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