Contacts of the helix formed by residues 929 - 954 (chain B) in PDB entry 5LE0
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 GLN 929 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B LYS* 3.1 22.5 + - + +
928B ALA* 1.3 73.1 - - - +
930B THR* 1.3 59.4 + - - +
931B ILE 3.0 2.2 - - - -
932B GLN* 2.8 34.0 + - + +
933B ARG* 3.4 5.4 + - - +
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Residues in contact with THR 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B LYS 4.2 13.9 - - - +
928B ALA* 4.4 4.4 + - - +
929B GLN* 1.3 76.6 - - - +
931B ILE* 1.3 67.8 + - - +
933B ARG* 3.7 9.5 + - - +
934B ARG* 3.6 17.8 + - - +
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Residues in contact with ILE 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B ALA* 3.5 23.3 + - + +
929B GLN 3.0 0.4 - - - -
930B THR* 1.3 82.8 + - - +
932B GLN* 1.3 64.8 + - - +
934B ARG* 3.3 7.1 + - - +
935B LEU* 2.9 22.4 + - + +
991B LEU* 3.9 37.6 - - + +
994B THR* 3.9 29.2 - - + +
995B VAL* 4.2 20.9 - - + -
998B LEU* 5.1 6.3 - - + -
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Residues in contact with GLN 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B GLN* 2.8 23.3 + - + +
931B ILE* 1.3 75.8 - - - +
933B ARG* 1.3 67.9 + - - +
935B LEU* 2.9 36.0 + - - +
936B ASN* 3.0 46.6 + - - +
995B VAL* 5.4 2.9 - - - +
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Residues in contact with ARG 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B GLN 3.4 6.7 + - - +
930B THR* 4.0 9.9 - - - +
931B ILE 3.4 0.2 - - - -
932B GLN* 1.3 76.5 - - - +
934B ARG* 1.3 64.2 + - - +
936B ASN* 2.9 12.2 + - - +
937B GLU* 2.9 48.4 + - + +
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Residues in contact with ARG 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930B THR 3.6 9.0 + - - +
931B ILE* 3.3 10.7 + - - +
932B GLN 3.3 0.4 - - - -
933B ARG* 1.3 79.8 - - - +
935B LEU* 1.3 62.7 + - - +
937B GLU* 3.2 33.9 + - - +
938B ILE* 3.1 40.0 + - + +
984B LEU* 4.3 13.9 - - - +
987B GLU* 2.7 44.3 + - - +
991B LEU* 4.2 10.8 - - + -
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Residues in contact with LEU 935 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B ILE* 2.9 15.7 + - + +
932B GLN* 2.9 38.0 + - - +
934B ARG* 1.3 78.0 - - - +
936B ASN* 1.3 62.7 + - - +
938B ILE* 3.3 7.5 + - + +
939B GLU* 3.1 28.2 + - + +
988B GLU* 4.0 30.3 - - + +
991B LEU* 4.5 16.6 - - + -
992B MSE 3.7 31.4 - - + -
995B VAL* 4.2 15.5 - - + -
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Residues in contact with ASN 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932B GLN* 3.0 40.6 + - - +
933B ARG* 2.9 8.6 + - - +
935B LEU* 1.3 71.8 - - - +
937B GLU* 1.3 66.4 + - - +
939B GLU* 3.8 7.2 - - - +
940B ALA* 3.1 25.8 + - - +
943B ARG* 5.3 0.2 + - - -
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Residues in contact with GLU 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933B ARG* 2.9 55.9 + - + +
934B ARG* 3.2 44.0 + - - +
936B ASN* 1.3 78.9 - - - +
938B ILE* 1.3 62.0 + - - +
940B ALA* 3.5 4.0 + - - +
941B ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B ARG* 3.1 47.6 + - - +
935B LEU* 3.8 5.2 - - - +
936B ASN 3.2 0.2 - - - -
937B GLU* 1.3 73.0 - - - +
939B GLU* 1.3 56.9 + - - +
941B ALA* 3.2 6.5 + - - +
942B LEU* 2.7 51.1 + - + +
984B LEU* 3.6 42.8 - - + +
987B GLU* 3.7 25.4 - - + +
988B GLU* 4.4 11.2 - - - +
991B LEU* 3.9 13.0 - - + -
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Residues in contact with GLU 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B LEU* 3.1 18.3 + - + +
936B ASN* 3.8 9.0 - - - +
938B ILE* 1.3 75.9 - - - +
940B ALA* 1.3 58.5 + - - +
942B LEU* 3.1 12.9 + - - +
943B ARG* 2.7 52.9 + - - +
988B GLU* 2.9 29.4 - - - +
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Residues in contact with ALA 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936B ASN 3.1 14.2 + - - +
937B GLU* 3.8 4.5 - - - +
939B GLU* 1.3 77.7 - - - +
941B ALA* 1.3 55.5 + - - +
943B ARG* 3.1 26.4 + - - +
944B GLU* 2.7 36.9 + - - +
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Residues in contact with ALA 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B GLU 3.0 19.3 + - - +
938B ILE* 3.5 5.6 - - - +
940B ALA* 1.3 76.0 - - - +
942B LEU* 1.3 52.2 + - - +
944B GLU* 3.4 6.9 - - - +
945B LEU* 2.7 43.4 + - + +
984B LEU* 4.0 17.5 - - + -
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Residues in contact with LEU 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938B ILE* 2.7 38.0 + - + +
939B GLU* 3.5 17.9 - - - +
941B ALA* 1.3 70.3 - - - +
943B ARG* 1.3 56.7 + - - +
945B LEU* 2.9 6.4 + - + +
946B GLU* 2.5 48.2 + - + +
981B LYS* 3.8 30.7 - - + +
984B LEU* 3.5 31.0 - - + -
985B VAL* 4.4 8.5 - - + -
988B GLU* 3.8 18.2 - - - +
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Residues in contact with ARG 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936B ASN 5.3 0.2 + - - -
939B GLU* 2.7 40.1 + - - +
940B ALA* 3.2 31.3 + - - +
942B LEU* 1.3 71.7 - - - +
944B GLU* 1.3 60.9 + - - +
946B GLU* 3.4 20.1 - - - +
947B ALA* 3.1 21.1 + - - +
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Residues in contact with GLU 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940B ALA 2.7 21.8 + - - +
941B ALA* 3.4 7.6 - - - +
943B ARG* 1.3 67.9 - - - +
945B LEU* 1.3 77.6 + - - +
947B ALA* 2.5 32.7 + - + +
948B GLU* 2.5 59.6 + - - +
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Residues in contact with LEU 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941B ALA* 2.7 25.6 + - + +
942B LEU* 2.9 6.9 + - + +
944B GLU* 1.3 75.6 + - - +
946B GLU* 1.3 55.9 + - - +
948B GLU* 3.7 15.5 - - - +
949B GLY* 2.6 33.3 + - - -
977B LEU* 3.5 38.4 - - + +
980B LYS* 4.0 29.6 - - + +
981B LYS* 4.3 13.5 - - + +
984B LEU* 4.0 23.6 - - + -
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Residues in contact with GLU 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942B LEU* 2.5 30.1 + - + +
943B ARG* 3.4 21.0 + - - +
945B LEU* 1.3 73.1 - - - +
947B ALA* 1.3 62.6 + - - +
949B GLY* 3.5 1.2 + - - -
950B VAL* 3.2 24.6 + - - +
981B LYS* 5.8 8.1 - - + -
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Residues in contact with ALA 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943B ARG 3.1 9.0 + - - +
944B GLU* 2.5 15.7 + - + +
946B GLU* 1.3 72.9 - - - +
948B GLU* 1.3 65.7 + - - +
950B VAL* 2.8 21.0 + - - +
951B LYS* 3.2 12.7 + - - +
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Residues in contact with GLU 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944B GLU* 2.5 56.2 + - - +
945B LEU* 3.7 18.8 - - + +
947B ALA* 1.3 73.5 - - - +
949B GLY* 1.3 62.0 + - - +
951B LYS* 3.5 7.1 + - + +
952B LEU* 3.0 21.8 + - - +
977B LEU* 4.3 11.2 - - + +
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Residues in contact with GLY 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945B LEU 2.6 22.0 + - - -
946B GLU 3.9 1.6 - - - -
948B GLU* 1.3 75.0 - - - +
950B VAL* 1.3 59.8 + - - +
952B LEU* 3.1 3.7 + - - +
953B GLU* 3.0 30.7 + - - +
974B LEU* 4.9 4.9 - - - +
977B LEU* 3.5 21.9 - - - +
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Residues in contact with VAL 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946B GLU 3.2 18.5 + - - +
947B ALA* 2.8 17.1 + - - +
949B GLY* 1.3 66.8 - - - +
951B LYS* 1.3 62.8 + - - +
952B LEU 3.0 1.1 - - - -
953B GLU* 2.8 30.8 + - + +
954B LEU* 3.2 9.7 + - - +
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Residues in contact with LYS 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947B ALA 3.2 7.2 + - - +
948B GLU* 3.9 9.4 - - + +
950B VAL* 1.3 81.3 - - - +
952B LEU* 1.3 59.8 + - - +
954B LEU* 3.5 22.7 + - - +
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Residues in contact with LEU 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948B GLU 3.0 14.6 + - - +
949B GLY 3.3 10.1 - - - +
950B VAL 3.0 1.0 - - - -
951B LYS* 1.3 76.9 - - - +
953B GLU* 1.3 63.8 + - - +
954B LEU 3.4 4.3 + - - -
970B TRP* 4.4 25.7 - - + +
973B GLN* 3.9 18.2 - - + -
974B LEU* 3.3 47.1 - - + +
977B LEU* 3.4 19.5 - - + -
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Residues in contact with GLU 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949B GLY 3.0 18.5 + - - +
950B VAL* 2.8 15.2 + - + +
952B LEU* 1.3 75.6 - - - +
954B LEU* 1.3 63.4 + - - +
974B LEU* 4.6 22.6 - - + +
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Residues in contact with LEU 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950B VAL 3.2 8.4 + - - +
951B LYS* 3.7 18.1 - - - +
952B LEU 3.2 6.3 - - - -
953B GLU* 1.3 82.8 - - - +
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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
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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