Contacts of the helix formed by residues 845 - 865 (chain A) in PDB entry 3RJO
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 845 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814A LEU* 3.6 20.9 - - - -
839A ILE* 3.2 22.9 - - - +
842A ASN* 3.1 12.3 + - - +
844A VAL* 1.3 78.7 - - - +
846A TYR* 1.3 64.4 + - - +
847A PRO* 3.3 2.5 - - - -
848A LEU* 3.1 19.1 + - - +
849A ALA 3.2 9.7 + - - -
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Residues in contact with TYR 846 (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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688A GLU 3.7 14.6 + - - -
689A LYS* 3.6 53.2 + - + -
839A ILE 3.7 1.8 - - - -
840A GLY* 3.0 29.9 - - - +
842A ASN 3.1 9.1 + - - +
843A PRO* 3.0 34.1 - - + -
845A GLY* 1.3 78.0 - - - +
847A PRO* 1.4 85.6 - - + +
849A ALA* 3.3 9.0 + - - +
850A TRP* 3.4 13.9 + - - +
878A THR 5.4 0.9 - - - +
882A PHE* 4.2 11.3 - + + -
887A ARG* 4.0 21.5 + - - -
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Residues in contact with PRO 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A LYS* 6.5 0.4 - - - -
844A VAL 3.5 13.2 - - - +
845A GLY 3.4 5.6 - - - -
846A TYR* 1.4 120.4 - - + +
848A LEU* 1.3 62.6 + - + +
850A TRP* 4.4 4.8 - - + +
851A GLN* 3.1 32.3 + - - +
854A ARG* 5.1 0.9 + - - -
882A PHE* 6.4 0.2 - - + -
887A ARG* 5.4 7.0 - - - +
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Residues in contact with LEU 848 (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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811A LYS* 3.5 45.3 - - + +
814A LEU* 3.7 23.3 - - + -
815A GLN* 3.8 22.3 - - + +
818A LEU* 3.8 13.4 - - + +
839A ILE* 4.7 1.6 - - + -
844A VAL 4.7 9.6 - - - +
845A GLY* 3.1 9.1 + - - +
847A PRO* 1.3 82.8 - - + +
849A ALA* 1.3 59.1 + - - +
851A GLN* 3.7 13.4 - - - +
852A PHE* 2.9 30.8 + - - +
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Residues in contact with ALA 849 (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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818A LEU* 4.5 2.7 - - - -
836A LEU* 3.5 27.6 - - + +
839A ILE* 4.1 4.3 - - + -
840A GLY* 3.4 37.7 - - - +
845A GLY 3.2 7.0 + - - +
846A TYR 3.3 3.1 + - - +
848A LEU* 1.3 79.6 - - - +
850A TRP* 1.3 56.5 + - - +
852A PHE 3.5 0.3 + - - -
853A LEU* 3.1 27.4 + - - +
878A THR* 3.8 11.5 - - + +
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Residues in contact with TRP 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A TYR 3.4 12.2 + - - +
847A PRO* 4.4 4.3 - - + +
849A ALA* 1.3 75.6 - - - +
851A GLN* 1.3 65.5 + - - +
853A LEU* 3.5 8.0 + - + -
854A ARG* 2.9 74.6 + - + +
878A THR* 3.8 24.4 - - - +
879A THR* 3.6 24.7 - - + -
882A PHE* 3.8 22.2 - + + -
887A ARG* 4.0 5.4 - - - -
890A GLU* 2.8 32.4 + - - +
891A VAL* 3.7 31.4 - - + +
894A PHE* 4.0 7.2 - + + -
895A PHE* 3.6 34.3 - + - -
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Residues in contact with GLN 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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815A GLN* 5.0 5.2 - - - +
847A PRO 3.1 21.1 + - - +
848A LEU* 3.7 16.9 - - - +
850A TRP* 1.3 74.2 - - - +
852A PHE* 1.3 56.3 + - - +
854A ARG* 3.0 22.0 + - - +
855A LYS* 2.8 67.5 + - + +
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Residues in contact with PHE 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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815A GLN* 3.9 16.4 - - - +
818A LEU* 3.9 25.4 - - + -
819A ASP* 3.4 24.5 - - - -
822A PHE* 3.6 49.1 - + + -
832A PHE* 3.6 22.2 - + - -
836A LEU* 4.4 3.1 - - + -
848A LEU 2.9 16.8 + - - +
849A ALA 3.7 4.0 - - - +
851A GLN* 1.3 80.3 - - - +
853A LEU* 1.3 65.3 + - - +
855A LYS* 4.6 2.7 - - - +
856A ASN* 2.9 54.6 + - + +
860A LEU* 4.7 1.1 - - + -
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Residues in contact with LEU 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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836A LEU* 4.1 18.4 - - + +
849A ALA 3.1 14.6 + - - +
850A TRP* 3.8 19.7 - - + +
851A GLN 3.2 0.2 - - - -
852A PHE* 1.3 79.9 - - - +
854A ARG* 1.3 63.1 + - - +
857A TRP* 3.1 51.2 + - + +
860A LEU* 3.1 31.2 - - + -
871A ILE* 5.6 0.2 - - + -
874A MET* 4.0 17.0 - - + +
875A VAL* 4.1 13.7 - - + +
878A THR* 3.6 20.0 - - + +
894A PHE* 5.0 0.9 - - + -
895A PHE* 4.5 2.2 - - + -
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Residues in contact with ARG 854 (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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847A PRO 5.1 0.8 + - - -
850A TRP* 2.9 70.1 + - + +
851A GLN* 3.0 29.7 + - - +
853A LEU* 1.3 79.4 - - - +
855A LYS* 1.3 63.6 + - + +
856A ASN 3.5 0.3 + - - -
857A TRP* 3.7 6.6 + - - +
887A ARG* 5.5 0.8 - - - +
890A GLU* 4.4 18.9 + - - +
894A PHE* 3.5 51.0 - - + +
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Residues in contact with LYS 855 (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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851A GLN* 2.8 55.9 + - + +
852A PHE* 4.0 4.5 - - - +
854A ARG* 1.3 73.5 - - + +
856A ASN* 1.3 72.1 + - - +
857A TRP 3.4 0.7 + - - -
858A ASN 5.3 0.5 + - - -
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Residues in contact with ASN 856 (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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822A PHE* 3.8 25.5 - - + -
852A PHE* 2.9 65.1 + - + +
853A LEU 4.0 1.1 - - - -
855A LYS* 1.3 86.7 - - - +
857A TRP* 1.3 66.4 + - - +
858A ASN 2.9 5.0 + - - -
859A LYS* 3.0 18.5 + - - +
860A LEU* 3.0 12.0 + - + -
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Residues in contact with TRP 857 (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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853A LEU* 3.1 42.4 + - + +
854A ARG 3.9 4.5 - - - +
855A LYS 3.4 2.6 + - - -
856A ASN* 1.3 76.9 - - - +
858A ASN* 1.3 77.3 + - - +
860A LEU* 3.7 4.7 - - + +
861A VAL* 3.0 44.9 + - + +
866A LEU* 4.1 7.6 - - + -
871A ILE* 3.8 28.7 - - + -
875A VAL* 4.0 12.3 - - + -
894A PHE* 3.9 24.0 - + + -
895A PHE* 3.9 23.1 - + - -
898A LEU* 3.6 32.3 - - + +
901A ASN* 3.5 32.3 + - - -
905A LEU* 4.2 6.3 - - + -
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Residues in contact with ASN 858 (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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855A LYS 5.3 0.8 + - - -
856A ASN 2.9 2.8 + - - -
857A TRP* 1.3 84.0 - - - +
859A LYS* 1.3 59.9 + - + +
861A VAL* 3.5 5.8 + - - +
862A GLN* 2.9 38.5 + - + +
898A LEU* 5.5 1.6 - - - +
901A ASN* 3.4 19.1 - - - +
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Residues in contact with LYS 859 (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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822A PHE* 3.6 25.3 - - + -
856A ASN* 3.0 12.4 + - + +
858A ASN* 1.3 77.8 - - + +
860A LEU* 1.3 62.4 - - - +
862A GLN* 3.3 19.4 + - - +
863A LYS* 3.1 49.8 + - - +
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Residues in contact with LEU 860 (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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822A PHE* 3.1 30.5 - - + -
832A PHE* 3.3 38.4 - - + -
852A PHE* 4.7 0.4 - - + -
853A LEU* 3.1 46.9 - - + +
856A ASN* 3.0 15.6 + - + +
857A TRP* 3.2 8.7 + - + +
859A LYS* 1.3 76.0 - - - +
861A VAL* 1.3 56.4 + - - +
863A LYS* 3.4 0.7 + - - -
864A PHE* 2.9 51.1 + - + +
871A ILE* 3.8 13.6 - - + +
874A MET* 4.5 3.1 - - + -
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Residues in contact with VAL 861 (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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857A TRP* 3.0 51.6 + - + +
858A ASN 3.7 5.2 - - - +
860A LEU* 1.3 76.9 - - - +
862A GLN* 1.3 59.7 + - + +
865A GLU* 2.9 40.1 + - - +
866A LEU* 3.8 33.4 - - + +
871A ILE* 4.3 12.3 - - + -
901A ASN* 4.1 16.6 - - - +
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Residues in contact with GLN 862 (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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858A ASN* 2.9 29.0 + - - +
859A LYS* 3.3 23.2 + - - +
861A VAL* 1.3 77.3 - - + +
863A LYS* 1.3 62.9 + - + +
865A GLU* 4.5 9.0 + - - +
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Residues in contact with LYS 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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822A PHE* 2.9 56.9 + - + -
823A LYS* 4.5 6.9 + - - +
829A THR* 4.1 21.7 + - + +
859A LYS* 3.1 32.3 + - - +
860A LEU* 3.7 4.0 - - - +
862A GLN* 1.3 82.0 - - + +
864A PHE* 1.3 76.1 + - + +
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Residues in contact with PHE 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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822A PHE* 5.8 0.2 - + - -
829A THR* 3.4 44.2 - - + -
830A GLN* 5.1 3.8 - - - -
832A PHE* 4.0 17.3 - + - -
833A PRO* 3.6 25.1 - - + -
860A LEU* 2.9 31.8 + - + +
863A LYS* 1.3 89.0 - - + +
865A GLU* 1.3 68.3 + - - +
868A SER* 3.2 27.6 - - - +
870A SER* 3.6 21.7 - - - -
871A ILE* 4.0 8.3 - - + -
874A MET* 3.8 11.7 - - + -
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Residues in contact with GLU 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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860A LEU 4.1 0.2 + - - -
861A VAL* 2.9 26.4 + - - +
862A GLN* 4.5 8.4 - - - +
863A LYS 3.8 0.2 - - - -
864A PHE* 1.3 80.3 - - - +
866A LEU* 1.3 92.3 + - - +
867A GLY 3.4 3.1 - - - +
868A SER* 2.9 24.7 + - - +
871A ILE* 3.5 5.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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