Contacts of the helix formed by residues 790 - 816 (chain G) in PDB entry 5JLH
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 790 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G THR* 2.7 23.9 + - - -
115G CYS* 5.5 1.1 - - - -
789G ALA* 1.3 71.6 - - - +
791G VAL* 1.3 65.0 + - - +
792G LEU 3.4 1.3 - - - -
793G ALA* 3.2 13.2 - - - +
794G GLN* 3.0 31.1 + - - +
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Residues in contact with VAL 791 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773G LEU* 4.0 16.8 - - + -
777G LEU* 3.5 46.0 - - + +
787G PHE* 3.3 32.8 - - + -
788G ARG* 3.1 29.2 - - + +
789G ALA 3.3 1.5 - - - +
790G GLY* 1.3 76.6 - - - +
792G LEU* 1.3 68.0 + - + +
794G GLN* 3.0 15.8 + - - +
795G LEU* 2.9 30.7 + - + +
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Residues in contact with LEU 792 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PHE* 5.0 11.6 - - + -
112G GLU 5.5 0.7 - - - +
114G THR* 3.4 16.9 + - + +
734G ASN* 3.7 31.6 - - + -
736G ILE* 4.2 21.3 - - + -
741G PHE* 4.4 13.5 - - + -
745G TYR* 4.6 21.1 + - + +
787G PHE* 4.3 17.9 - - + -
790G GLY 3.4 0.2 - - - -
791G VAL* 1.3 86.5 - - + +
793G ALA* 1.3 60.0 + - - +
795G LEU* 3.9 24.6 - - + +
796G GLU* 2.8 31.9 + - - +
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Residues in contact with ALA 793 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ARG* 6.3 2.9 - - + +
99G MET 5.9 2.2 - - - +
101G PRO* 5.6 5.8 - - + +
114G THR* 2.9 23.9 + - + -
115G CYS* 5.6 4.5 - - + -
790G GLY* 3.2 22.2 - - - +
791G VAL 3.1 0.6 - - - -
792G LEU* 1.3 77.1 - - - +
794G GLN* 1.3 57.4 + - + +
796G GLU* 3.8 5.6 - - - +
797G GLU* 3.0 28.9 + - - +
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Residues in contact with GLN 794 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773G LEU* 4.1 17.2 - - - +
777G LEU* 5.4 7.1 - - - +
790G GLY 3.0 20.0 + - - +
791G VAL* 3.0 15.8 + - - +
793G ALA* 1.3 74.6 - - + +
795G LEU* 1.3 63.7 + - + +
797G GLU* 3.1 13.6 + - - +
798G GLU* 3.0 33.1 + - + +
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Residues in contact with LEU 795 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741G PHE* 4.0 24.5 - - + -
745G TYR* 5.1 4.5 - - + -
748G LEU* 3.2 24.5 - - + +
768G ILE* 4.9 7.4 - - + -
771G LEU* 3.4 38.4 - - + +
773G LEU* 5.6 8.1 - - + -
787G PHE* 5.0 5.4 - - + -
791G VAL* 2.9 19.8 + - + +
792G LEU* 3.4 27.3 + - + +
794G GLN* 1.3 79.7 - - + +
796G GLU* 1.3 58.2 + - - +
798G GLU* 3.1 11.3 + - + +
799G ARG* 2.9 21.3 + - - +
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Residues in contact with GLU 796 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TRP* 5.3 3.4 - - + +
101G PRO* 3.5 35.4 - - + +
103G LYS* 4.0 16.8 - - - +
104G PHE* 4.9 7.5 - - + -
745G TYR* 3.3 31.0 + - - -
792G LEU 2.8 23.2 + - - +
793G ALA* 3.8 4.3 - - - +
795G LEU* 1.3 72.7 - - - +
797G GLU* 1.3 58.0 + - - +
799G ARG* 3.0 32.9 + - - +
800G ALA* 2.9 26.6 + - + +
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Residues in contact with GLU 797 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TRP* 4.8 19.4 - - + -
52G ALA* 5.8 8.8 - - + +
101G PRO* 5.8 0.2 - - - +
793G ALA 3.0 15.9 + - - +
794G GLN* 3.1 13.6 + - - +
796G GLU* 1.3 75.7 - - - +
798G GLU* 1.3 59.7 + - - +
800G ALA* 3.7 5.4 - - + +
801G SER* 2.8 36.1 + - - -
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Residues in contact with GLU 798 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748G LEU* 3.2 14.7 - - + +
771G LEU* 6.2 2.7 - - + -
794G GLN* 3.0 19.7 + - + +
795G LEU* 3.1 17.0 + - + +
797G GLU* 1.3 81.8 - - - +
799G ARG* 1.3 55.8 + - - +
801G SER* 4.1 11.0 - - - -
802G GLU* 2.8 28.6 + - - +
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Residues in contact with ARG 799 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LYS* 3.9 21.1 - - - +
744G ARG* 4.2 29.1 + - - +
745G TYR* 3.7 25.6 - - + +
747G ILE* 4.8 16.4 - - + +
748G LEU* 3.3 15.0 - - + -
795G LEU 2.9 7.7 + - - +
796G GLU* 3.0 42.8 + - - +
798G GLU* 1.3 75.7 - - - +
800G ALA* 1.3 55.2 + - - +
801G SER 3.4 0.2 - - - -
802G GLU* 3.7 1.6 - - - +
803G GLN* 2.7 34.6 + - + +
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Residues in contact with ALA 800 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TRP* 3.6 45.3 - - + +
796G GLU* 2.9 11.5 + - + +
797G GLU 4.0 2.5 - - - +
799G ARG* 1.3 72.9 - - - +
801G SER* 1.3 61.2 + - - +
803G GLN* 3.7 6.4 - - - +
804G THR* 2.9 27.9 + - - -
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Residues in contact with SER 801 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797G GLU* 2.8 25.2 + - - -
798G GLU* 4.1 15.5 - - - -
800G ALA* 1.3 69.6 - - - +
802G GLU* 1.3 61.1 + - - +
804G THR* 3.2 8.5 + - - -
805G LYS* 2.9 27.5 + - - +
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Residues in contact with GLU 802 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747G ILE* 4.3 26.9 - - + +
748G LEU* 4.6 7.9 - - - +
798G GLU* 2.8 23.9 + - - +
799G ARG* 3.8 6.3 - - - +
801G SER* 1.3 77.9 - - - +
803G GLN* 1.3 57.9 + - - +
805G LYS* 3.2 8.9 + - - +
806G SER* 2.9 28.8 + - - -
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Residues in contact with GLN 803 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747G ILE* 5.1 4.9 - - + +
799G ARG* 2.7 26.8 + - + +
800G ALA* 3.8 7.9 - - - +
802G GLU* 1.3 74.8 - - - +
804G THR* 1.3 58.0 + - - +
806G SER* 3.7 6.6 - - - -
807G ASP* 2.8 30.7 + - - +
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Residues in contact with THR 804 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800G ALA 2.9 17.9 + - - -
801G SER* 3.4 8.7 - - - -
803G GLN* 1.3 74.3 - - - +
805G LYS* 1.3 64.8 + - - +
807G ASP* 3.8 6.1 - - - +
808G TYR* 3.0 25.1 + - - +
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Residues in contact with LYS 805 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801G SER 2.9 13.0 + - - +
802G GLU* 3.2 10.7 + - - +
804G THR* 1.3 75.3 - - - +
806G SER* 1.3 57.8 + - - +
808G TYR* 3.4 6.5 + - - +
809G LEU* 2.9 29.0 + - - +
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Residues in contact with SER 806 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747G ILE* 5.7 6.5 - - - -
802G GLU 2.9 16.2 + - - -
803G GLN* 3.8 7.0 - - - -
805G LYS* 1.3 77.1 - - - +
807G ASP* 1.3 60.0 + - - +
809G LEU* 4.0 5.7 - - - +
810G LYS* 2.9 30.7 + - - +
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Residues in contact with ASP 807 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803G GLN 2.8 19.7 + - - +
804G THR* 3.8 7.4 - - - +
806G SER* 1.3 75.0 - - - +
808G TYR* 1.3 57.8 + - - +
810G LYS* 3.8 4.4 - - - +
811G ARG* 2.9 34.1 + - - +
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Residues in contact with TYR 808 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804G THR 3.0 18.4 + - - +
805G LYS* 3.5 6.7 - - - +
807G ASP* 1.3 74.5 - - - +
809G LEU* 1.3 60.0 + - - +
811G ARG* 3.8 3.2 - - - +
812G ALA* 2.8 35.0 + - - +
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Residues in contact with LEU 809 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805G LYS 2.9 17.1 + - - +
806G SER* 4.0 6.3 - - - +
807G ASP 3.4 0.2 - - - -
808G TYR* 1.3 78.0 - - - +
810G LYS* 1.3 61.9 + - - +
812G ALA* 4.0 4.0 - - - +
813G ASN* 3.1 25.5 + - - +
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Residues in contact with LYS 810 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806G SER 2.9 18.3 + - - +
807G ASP* 3.8 5.2 - - - +
809G LEU* 1.3 78.3 - - - +
811G ARG* 1.3 59.5 + - - +
813G ASN* 3.2 6.0 + - - +
814G GLU* 2.9 29.5 + - - +
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Residues in contact with ARG 811 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807G ASP 2.9 19.0 + - - +
808G TYR* 4.1 3.1 - - - +
810G LYS* 1.3 75.0 - - - +
812G ALA* 1.3 57.1 + - - +
814G GLU* 3.3 6.6 + - - +
815G LEU* 2.9 30.8 + - - +
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Residues in contact with ALA 812 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808G TYR 2.8 19.7 + - - +
809G LEU* 4.0 4.7 - - - +
811G ARG* 1.3 76.8 - - - +
813G ASN* 1.3 57.3 + - - +
815G LEU* 3.2 6.0 + - - +
816G VAL* 2.8 33.9 + - - +
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Residues in contact with ASN 813 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809G LEU 3.1 17.8 + - - +
810G LYS* 3.2 5.1 + - - +
812G ALA* 1.3 80.8 - - - +
814G GLU* 1.3 64.1 + - - +
816G VAL* 3.6 15.2 + - - +
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Residues in contact with GLU 814 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810G LYS 2.9 17.0 + - - +
811G ARG* 3.8 6.1 - - - +
813G ASN* 1.3 78.0 - - - +
815G LEU* 1.3 63.9 + - - +
816G VAL 4.6 1.7 - - - -
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Residues in contact with LEU 815 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811G ARG 2.9 18.2 + - - +
812G ALA* 3.5 7.2 - - - +
814G GLU* 1.3 79.0 - - - +
816G VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 816 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812G ALA 2.8 17.1 + - - +
813G ASN* 3.6 11.4 + - - +
814G GLU 3.4 2.4 - - - -
815G LEU* 1.3 81.8 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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