Contacts of the helix formed by residues 922 - 943 (chain F) in PDB entry 5F28
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 ASP 922 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035E LEU* 4.7 0.5 - - - +
1039E ASP* 3.9 3.3 - - - +
1042E ARG* 2.8 32.2 + - - +
918F ASP 5.1 2.2 - - - +
919F ARG* 2.8 46.9 + - - +
920F SER 3.6 0.4 - - - -
921F ASN* 1.3 74.6 - - - +
923F LYS* 1.3 61.5 + - - +
924F VAL* 3.0 14.2 + - - +
925F TYR* 2.7 38.6 + - + +
926F GLU* 3.2 18.9 + - - +
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Residues in contact with LYS 923 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963E THR* 5.6 3.8 - - - -
967E THR* 3.3 31.6 + - + +
970E GLU* 4.1 14.8 + - - +
1042E ARG* 4.9 2.6 - - - +
921F ASN 3.7 4.6 + - - -
922F ASP* 1.3 71.5 + - - +
924F VAL* 1.3 66.9 + - - +
926F GLU* 3.0 20.1 + - - +
927F ASN* 2.9 38.2 + - - +
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Residues in contact with VAL 924 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964E LEU* 4.0 8.6 - - + +
967E THR* 4.1 19.7 - - + +
968E VAL* 4.5 6.3 - - + -
971E THR* 4.6 13.5 - - + +
1034E LEU* 5.7 0.7 - - + -
1035E LEU* 4.0 19.3 - - + -
1038E ILE* 3.7 44.9 - - + -
1042E ARG* 4.6 8.5 - - - +
922F ASP* 3.0 9.1 + - - +
923F LYS* 1.3 77.0 - - - +
925F TYR* 1.3 56.6 + - - +
927F ASN* 3.9 0.3 - - - -
928F VAL* 2.9 44.8 + - + +
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Residues in contact with TYR 925 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035E LEU* 3.8 24.9 - - + +
919F ARG* 3.4 52.3 - - + +
922F ASP* 2.7 36.0 + - + +
924F VAL* 1.3 74.6 - - - +
926F GLU* 1.3 60.9 + - - +
928F VAL* 4.5 1.1 - - - -
929F THR* 2.9 59.6 + - + +
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Residues in contact with GLU 926 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922F ASP 3.2 10.3 + - - +
923F LYS* 3.0 24.3 + - - +
925F TYR* 1.3 84.6 - - + +
927F ASN* 1.3 67.8 + - - +
929F THR* 3.9 3.8 - - - -
930F GLY* 2.9 24.3 + - - -
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Residues in contact with ASN 927 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960E ALA* 4.7 3.9 - - - +
963E THR* 3.7 24.4 - - + +
964E LEU* 3.6 29.4 - - + +
967E THR* 2.8 33.3 + - - -
923F LYS* 2.9 26.9 + - - +
926F GLU* 1.3 86.6 + - - +
928F VAL* 1.3 61.7 + - - +
930F GLY* 3.3 2.1 + - - -
931F LEU* 2.8 28.8 + - - +
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Residues in contact with VAL 928 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964E LEU* 3.6 27.6 - - + -
1031E ALA* 4.0 30.1 - - + +
1032E LYS* 4.5 5.8 - - + +
1034E LEU* 5.3 2.2 - - + -
1035E LEU* 4.2 26.2 - - + +
924F VAL* 2.9 31.3 + - + +
925F TYR* 3.9 3.6 - - - +
927F ASN* 1.3 76.6 - - - +
929F THR* 1.3 57.6 + - - +
931F LEU* 3.1 7.0 + - - +
932F VAL* 2.8 39.3 + - + +
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Residues in contact with THR 929 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925F TYR* 2.9 51.8 + - + +
926F GLU* 3.9 4.3 - - - -
928F VAL* 1.3 78.2 - - - +
930F GLY* 1.3 59.0 + - - +
932F VAL* 3.4 7.0 + - + +
933F LYS* 3.0 30.5 + - + +
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Residues in contact with GLY 930 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960E ALA* 4.3 7.3 - - - +
926F GLU 2.9 16.2 + - - -
927F ASN* 3.3 4.2 + - - -
928F VAL 3.2 0.2 - - - -
929F THR* 1.3 76.3 - - - +
931F LEU* 1.3 61.7 + - - +
933F LYS* 3.4 9.8 + - - +
934F ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 931 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957E VAL* 3.5 31.0 - - + +
960E ALA* 3.9 12.7 - - + +
961E LEU* 3.7 35.4 - - + +
964E LEU* 3.8 17.0 - - + -
990E LEU* 5.0 0.4 - - + -
1027E LEU* 3.8 25.8 - - + -
1028E ALA* 5.9 0.2 - - - -
1031E ALA* 3.8 20.4 - - + -
927F ASN 2.8 17.2 + - - +
928F VAL* 3.1 5.6 + - - +
930F GLY* 1.3 74.1 - - - +
932F VAL* 1.3 66.6 + - - +
933F LYS 3.3 0.2 + - - -
934F ALA* 3.3 3.6 + - - +
935F VAL* 3.3 19.0 + - + +
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Residues in contact with VAL 932 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028E ALA* 4.1 34.3 - - + +
1031E ALA* 4.7 3.4 - - + -
1032E LYS* 4.3 18.8 - - + -
928F VAL* 2.8 27.4 + - + +
929F THR* 3.8 6.7 - - - +
931F LEU* 1.3 74.6 - - - +
933F LYS* 1.3 62.6 + - - +
935F VAL* 3.2 7.5 + - - +
936F ILE* 3.0 42.1 + - + +
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Residues in contact with LYS 933 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 5.0 16.8 + - - +
929F THR* 3.0 20.4 + - + +
930F GLY* 3.7 8.7 - - - +
931F LEU 3.2 0.6 - - - -
932F VAL* 1.3 79.2 - - - +
934F ALA* 1.3 57.6 + - - +
936F ILE* 3.4 7.3 + - + +
937F GLU* 2.8 41.9 + - + +
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Residues in contact with ALA 934 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953E MET 5.3 0.5 - - - +
956E GLU* 4.2 23.1 - - + +
957E VAL* 4.0 20.3 - - + +
960E ALA* 4.8 3.6 - - + -
930F GLY 3.2 11.5 + - - +
931F LEU 3.3 8.0 + - - +
933F LYS* 1.3 78.7 - - - +
935F VAL* 1.3 58.0 + - - +
937F GLU* 3.7 7.2 - - - +
938F MET* 3.0 29.1 + - - +
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Residues in contact with VAL 935 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957E VAL* 4.1 19.1 - - + -
1024E ALA* 3.3 38.8 - - + +
1025E HIS* 4.4 3.1 - - - +
1027E LEU* 4.0 26.5 - - + -
1028E ALA* 4.2 15.7 - - + -
931F LEU 3.3 13.0 + - - +
932F VAL 3.2 7.7 + - - +
934F ALA* 1.3 75.0 - - - +
936F ILE* 1.3 62.5 + - + +
938F MET* 3.2 5.7 + - - +
939F SER* 2.9 37.3 + - - +
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Residues in contact with ILE 936 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028E ALA* 6.1 1.3 - - + -
932F VAL* 3.0 35.4 + - + +
933F LYS* 3.8 7.0 - - + +
935F VAL* 1.3 76.9 - - + +
937F GLU* 1.3 62.8 + - - +
939F SER* 3.2 7.7 + - - -
940F SER* 3.0 25.8 + - - -
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Residues in contact with GLU 937 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937E GLU* 3.9 7.7 - - - +
956E GLU* 5.7 4.7 - - - +
933F LYS* 2.8 32.5 + - + +
934F ALA* 3.7 8.7 - - - +
936F ILE* 1.3 73.8 - - - +
938F MET* 1.3 62.8 + - - +
940F SER* 2.9 23.6 + - - -
941F LYS* 2.6 50.2 + - + +
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Residues in contact with MET 938 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950E TYR* 5.4 0.9 - - + +
953E MET* 4.0 28.0 - - + +
954E VAL* 3.7 32.1 - - + -
957E VAL* 4.3 17.7 - - + -
997E LEU* 4.3 8.1 - - + -
1020E MET* 3.9 22.9 - - + +
1021E LEU* 5.2 2.5 - - + -
1024E ALA* 4.5 17.0 - - + -
934F ALA 3.0 19.2 + - - +
935F VAL 3.2 3.6 + - - +
937F GLU* 1.3 76.9 - - - +
939F SER* 1.3 65.1 + - - +
941F LYS* 3.3 4.3 + - - +
942F ILE* 3.1 48.3 + - + +
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Residues in contact with SER 939 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021E LEU* 3.9 29.6 + - - +
1024E ALA* 4.9 3.3 - - - +
1025E HIS* 5.6 1.2 + - - +
935F VAL* 2.9 25.9 + - - +
936F ILE* 3.2 7.8 + - - -
938F MET* 1.3 77.9 - - - +
940F SER* 1.3 58.7 + - - +
943F GLN* 2.8 38.3 + - - +
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Residues in contact with SER 940 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941E LYS* 3.6 50.1 + - - +
936F ILE* 3.0 16.7 + - - -
937F GLU* 2.9 21.9 + - - -
939F SER* 1.3 77.6 - - - +
941F LYS* 1.3 71.3 + - - +
943F GLN 3.6 14.9 - - - +
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Residues in contact with LYS 941 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937E GLU* 3.7 21.9 + - - -
940E SER* 3.5 40.3 + - - +
941E LYS* 4.7 6.2 - - - +
943E GLN 4.0 0.2 - - - +
944E PRO* 3.6 4.3 - - - +
945E ALA* 2.8 28.1 + - + +
953E MET* 3.6 28.9 - - + -
937F GLU* 2.6 45.5 + - + +
938F MET* 3.3 4.8 + - - +
940F SER* 1.3 85.1 - - - +
942F ILE* 1.3 60.5 + - - +
943F GLN 5.1 0.2 - - - -
944F PRO 5.4 0.2 - - - -
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Residues in contact with ILE 942 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944E PRO* 3.4 15.4 - - - +
945E ALA* 4.3 5.2 - - + +
950E TYR* 3.9 22.0 - - + +
953E MET* 4.1 11.2 - - + -
1017E LYS* 3.7 37.2 + - + +
1020E MET* 3.6 24.5 - - + -
1021E LEU* 3.8 25.4 - - + -
938F MET* 3.1 40.8 + - + +
941F LYS* 1.3 79.1 - - - +
943F GLN* 1.3 57.4 + - - +
944F PRO* 3.2 11.7 - - - +
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Residues in contact with GLN 943 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014E GLN* 6.0 1.8 - - - +
1017E LYS* 5.2 6.1 - - - +
1018E LYS* 5.8 5.9 - - - +
1021E LEU* 3.8 31.7 - - + +
939F SER* 2.8 27.9 + - - +
940F SER* 3.6 11.7 - - - +
942F ILE* 1.3 72.4 - - - +
944F PRO* 1.3 73.4 - - + +
945F ALA* 4.8 0.3 - - - -
946F PRO* 5.5 1.6 - - - +
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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