Contacts of the helix formed by residues 871 - 888 (chain D) in PDB entry 5C0V
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 ARG 871 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869B GLY 5.1 0.9 - - - -
871B ARG* 3.4 31.3 - - + +
875B GLU* 4.5 3.2 + - - -
908B GLY 5.0 0.2 + - - -
909B GLN* 3.2 15.3 + - - +
866D ALA* 4.2 13.2 + - + +
869D GLY* 3.8 15.3 - - - +
870D TYR* 1.3 75.2 - - - +
872D TYR* 1.3 59.7 + - - +
873D GLY 3.4 2.2 - - - -
874D LEU* 3.1 33.2 + - - +
875D GLU* 2.7 50.1 + - - +
878D PHE* 4.7 1.6 - - - -
904D ASP* 2.7 37.7 + - - -
909D GLN* 3.6 25.3 + - - +
911D TYR* 4.2 14.5 - - - +
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Residues in contact with TYR 872 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B GLY 5.6 2.4 + - - +
909B GLN* 4.5 4.2 + - - -
910B LEU* 3.5 51.2 - - + +
914B GLU* 4.6 11.8 + - - -
941B PHE* 5.0 6.4 - + - -
836D ASN* 3.3 48.6 + - + +
839D PHE* 4.3 2.9 - - + -
840D ARG* 3.5 28.1 - - - +
870D TYR 3.6 2.2 - - - -
871D ARG* 1.3 76.1 - - - +
873D GLY* 1.3 54.6 + - - +
875D GLU* 3.1 18.0 + - - +
876D CYS* 2.7 51.3 + - - -
879D ARG* 3.6 18.0 + - - -
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Residues in contact with GLY 873 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839D PHE* 3.4 44.5 - - - -
858D PHE* 3.7 2.6 - - - -
862D ALA* 3.4 14.1 - - - +
865D ASP* 5.4 1.3 + - - -
870D TYR 4.7 2.8 + - - -
871D ARG 3.4 0.4 - - - -
872D TYR* 1.3 78.4 - - - +
874D LEU* 1.3 57.4 + - - +
876D CYS* 3.2 5.2 + - - +
877D LEU* 2.9 23.2 + - - +
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Residues in contact with LEU 874 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862D ALA* 3.5 11.1 + - + +
863D LEU* 4.2 20.9 - - + -
866D ALA* 3.7 31.0 - - + -
871D ARG* 3.1 28.7 + - - +
873D GLY* 1.3 73.4 - - - +
875D GLU* 1.3 60.2 + - - +
877D LEU* 3.1 26.3 + - + -
878D PHE* 2.9 50.3 + - + -
900D GLU* 5.4 1.8 - - + -
904D ASP* 3.8 14.8 - - + +
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Residues in contact with GLU 875 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B ARG* 5.0 2.8 + - - -
875B GLU* 3.8 17.0 - - - +
909B GLN* 5.0 2.2 - - - +
910B LEU 5.2 0.5 + - - -
911B TYR* 4.1 31.6 + - - +
871D ARG* 2.7 44.1 + - + +
872D TYR* 3.4 24.8 + - - +
874D LEU* 1.3 72.2 - - - +
876D CYS* 1.3 63.7 + - - +
878D PHE* 3.2 3.5 + - - +
879D ARG* 3.0 46.6 + - - +
911D TYR* 3.8 26.8 - - + -
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Residues in contact with CYS 876 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839D PHE* 3.8 16.6 - - - +
840D ARG* 3.9 17.7 - - - -
843D SER* 2.8 26.9 + - - -
858D PHE* 3.7 4.9 - - + -
872D TYR* 2.7 48.1 + - - +
873D GLY* 3.3 10.1 - - - +
875D GLU* 1.3 74.3 - - - +
877D LEU* 1.3 56.9 + - - +
879D ARG* 3.3 23.9 + - - +
880D TYR* 3.0 16.1 + - - +
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Residues in contact with LEU 877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855D TYR* 4.2 12.3 - - + -
858D PHE* 3.5 32.1 - - + -
859D LYS* 4.0 31.2 - - + +
862D ALA* 4.4 4.0 - - + -
863D LEU* 5.1 1.8 - - + -
873D GLY 2.9 13.8 + - - +
874D LEU* 3.1 29.6 + - + +
876D CYS* 1.3 75.3 - - - +
878D PHE* 1.3 57.3 + - - +
880D TYR* 3.2 6.1 + - + +
881D TYR* 3.0 63.9 + - + +
900D GLU* 4.6 6.3 - - + -
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Residues in contact with PHE 878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871D ARG* 4.7 0.9 - - - -
874D LEU* 2.9 45.8 + - + +
875D GLU 3.7 4.3 - - - +
877D LEU* 1.3 76.2 - - - +
879D ARG* 1.3 59.7 + - - +
881D TYR* 3.5 8.9 + + - +
882D SER* 3.0 30.0 + - - -
897D PHE* 3.8 19.5 - + - -
900D GLU* 3.4 33.0 - - + -
901D THR* 3.5 26.2 - - - -
904D ASP* 3.6 16.2 - - + -
911D TYR* 3.9 21.5 - + + -
912D GLY* 3.6 29.4 - - - -
915D LYS* 4.1 9.7 - - + +
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Residues in contact with ARG 879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B TYR* 5.8 2.0 - - - -
914B GLU* 4.6 13.7 + - - -
1001B SO4 4.2 8.8 + - - -
843D SER* 4.2 1.8 + - - +
844D PHE* 6.3 1.9 - - - -
847D ARG* 3.9 11.1 + - - +
872D TYR* 3.6 18.2 + - - -
875D GLU* 3.0 28.4 + - - +
876D CYS* 3.3 39.6 - - - +
878D PHE* 1.3 74.9 - - - +
880D TYR* 1.3 66.6 + - - +
882D SER* 4.5 2.0 - - - -
883D TYR* 2.9 59.5 + - + +
911D TYR* 2.6 39.7 + - - +
915D LYS* 3.9 7.6 - - - +
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Residues in contact with TYR 880 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843D SER* 3.5 28.1 + - - +
846D LEU* 3.4 34.8 - - + -
847D ARG* 3.8 13.7 - - + +
850D PHE* 3.4 28.6 - - - -
855D TYR* 3.9 26.7 - + - -
858D PHE* 4.1 11.9 - + + -
876D CYS 3.0 14.2 + - - +
877D LEU* 3.2 13.9 + - + +
879D ARG* 1.3 76.3 - - - +
881D TYR* 1.3 78.6 + + - +
884D GLY* 2.8 33.4 + - - -
885D LEU* 3.9 0.6 + - + -
890D ARG* 3.8 10.4 + - - -
893D ILE* 3.9 11.6 - - + +
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Residues in contact with TYR 881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855D TYR* 2.7 42.0 + + - -
859D LYS* 3.7 13.3 - - - +
877D LEU* 3.0 39.0 + - + +
878D PHE* 3.6 14.8 - + - +
879D ARG 3.3 0.2 - - - -
880D TYR* 1.3 81.1 - + - +
882D SER* 1.3 58.4 + - - +
885D LEU* 2.8 40.4 + - - +
893D ILE* 3.7 30.5 - - + -
896D ASP* 3.6 5.7 - - - +
897D PHE* 3.4 50.7 - + + -
900D GLU* 3.7 16.0 - - + +
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Residues in contact with SER 882 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D PHE 3.0 15.8 + - - -
879D ARG* 4.1 2.2 - - - -
881D TYR* 1.3 80.9 - - - +
883D TYR* 1.3 70.9 + - - +
886D GLU* 3.5 21.1 + - - +
897D PHE* 4.0 11.9 - - - -
915D LYS* 3.1 41.1 + - - +
918D ALA* 4.5 4.2 - - - +
919D PHE* 3.6 18.4 + - - +
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Residues in contact with TYR 883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B SO4 4.4 6.4 + - - -
847D ARG* 3.4 29.2 - - - +
879D ARG* 2.9 53.9 + - + +
882D SER* 1.3 81.8 - - - +
884D GLY* 1.3 63.9 + - - +
886D GLU* 3.6 19.5 - - - +
887D LYS* 3.6 23.9 + - - +
915D LYS* 4.0 17.8 - - + -
918D ALA* 6.3 2.0 - - + -
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Residues in contact with GLY 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847D ARG* 3.9 28.7 - - - +
879D ARG 3.9 0.2 + - - -
880D TYR* 2.8 23.5 + - - -
883D TYR* 1.3 77.6 - - - +
885D LEU* 1.3 58.3 + - - +
887D LYS* 3.2 5.4 + - - +
888D LYS* 2.9 31.1 + - - +
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Residues in contact with LEU 885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880D TYR* 3.9 0.4 + - + -
881D TYR* 2.8 26.7 + - - +
884D GLY* 1.3 70.1 - - - -
886D GLU* 1.3 64.9 + - - +
888D LYS 3.7 5.4 - - - +
889D PHE* 3.3 28.8 + - + +
890D ARG* 3.5 40.2 - - + +
893D ILE* 4.0 24.9 - - + +
894D PHE* 3.6 31.9 - - + +
897D PHE* 3.7 20.6 - - + -
919D PHE* 3.5 18.5 - - + -
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Residues in contact with GLU 886 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882D SER 3.5 20.5 + - - +
883D TYR* 3.6 21.1 - - - +
884D GLY 3.2 0.4 - - - -
885D LEU* 1.3 80.1 - - - +
887D LYS* 1.3 78.3 + - + +
919D PHE* 3.7 13.0 - - + -
922D TYR* 3.9 47.5 - - + +
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Residues in contact with LYS 887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847D ARG* 6.2 3.4 - - + +
848D ASP* 6.0 2.5 - - - +
883D TYR 3.6 12.5 + - - +
884D GLY* 3.2 7.2 + - - +
885D LEU 3.2 0.4 - - - -
886D GLU* 1.3 102.4 - - + +
888D LYS* 1.3 62.5 + - + +
889D PHE 4.0 1.6 + - - -
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Residues in contact with LYS 888 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847D ARG 4.5 13.9 - - - +
884D GLY 2.9 17.1 + - - +
885D LEU* 3.5 9.6 - - - +
887D LYS* 1.3 81.0 - - + +
889D PHE* 1.3 71.6 + - - +
890D ARG* 3.5 40.3 + - - +
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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