Contacts of the helix formed by residues 946 - 961 (chain B) in PDB entry 3LJ1
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 946 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944B LEU* 3.5 1.6 - - - +
945B HIS* 1.3 76.0 - - - +
947B ARG* 1.3 65.4 + - - +
948B SER* 2.7 31.8 + - - -
949B LEU* 3.3 41.7 + - + +
950B ILE* 3.4 14.3 + - - +
983B LYS* 4.8 9.0 + - - -
1081B TYR* 5.7 1.4 - - - -
1082B ASP* 4.7 11.0 - - - +
1085B THR* 5.1 6.9 + - - +
1086B LYS* 5.7 1.4 + - - -
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Residues in contact with ARG 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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945B HIS 3.2 8.9 + - - +
946B ASP* 1.3 71.8 + - - +
948B SER* 1.3 66.4 + - - +
950B ILE* 3.1 17.7 + - + +
951B ALA* 3.1 21.5 + - - +
1085B THR 5.9 0.4 - - - +
1086B LYS 5.8 3.4 - - - +
1089B PRO* 3.8 32.9 - - + +
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Residues in contact with SER 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B ASP* 2.7 28.9 + - - -
947B ARG* 1.3 77.6 - - - +
949B LEU* 1.3 72.3 + - - +
951B ALA* 3.2 5.1 + - - +
952B GLU* 3.0 35.9 + - - +
1081B TYR* 4.9 4.2 + - - -
1085B THR* 4.2 22.8 + - - -
1089B PRO* 3.4 32.8 - - - +
1092B LEU* 6.2 0.2 - - - -
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Residues in contact with LEU 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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775B ILE* 3.7 29.8 - - + -
944B LEU* 3.9 22.4 - - + -
946B ASP* 3.3 40.1 + - + +
947B ARG 3.2 0.4 - - - -
948B SER* 1.3 86.4 + - - +
950B ILE* 1.3 51.8 + - - +
952B GLU* 3.2 18.2 + - - +
953B ALA* 2.7 37.6 + - - +
979B LEU* 3.9 6.1 - - + +
983B LYS* 6.0 3.6 - - - -
986B LYS* 3.9 14.4 - - - +
1081B TYR* 6.3 1.3 - - + -
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Residues in contact with ILE 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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938B LEU 5.4 2.5 - - - +
941B MET* 3.8 33.8 - - + +
944B LEU* 3.8 39.3 - - + +
945B HIS 5.4 0.4 - - - +
946B ASP 3.6 13.0 - - - +
947B ARG* 3.1 18.9 + - + +
949B LEU* 1.3 76.2 - - - +
951B ALA* 1.3 58.3 + - - +
953B ALA* 3.7 0.9 - - - +
954B THR* 2.8 40.2 + - - +
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Residues in contact with ALA 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B ARG 3.1 11.4 + - - +
948B SER 3.5 9.2 - - - +
950B ILE* 1.3 77.5 - - - +
952B GLU* 1.3 62.3 + - - +
954B THR* 3.4 6.0 + - - -
955B ASP* 3.3 19.8 + - - +
1018B PHE* 5.6 0.9 - - + -
1089B PRO 4.2 4.3 - - - +
1090B ASN* 3.0 32.8 - - - +
1093B ILE* 4.2 14.2 - - + +
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Residues in contact with GLU 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 SER* 3.0 32.2 + - - +
949B LEU* 3.5 13.0 - - - +
951B ALA* 1.3 75.1 - - - +
953B ALA* 1.3 63.0 + - - +
955B ASP* 3.0 16.3 + - - +
956B LEU 3.1 10.2 + - - -
977B HIS* 3.5 8.0 - - + -
978B PRO 4.7 0.4 - - - -
979B LEU* 3.9 22.9 - - + +
986B LYS* 3.1 26.2 + - - -
1081B TYR* 3.9 16.8 + - - -
1089B PRO 4.9 1.1 - - - +
1092B LEU* 4.0 18.4 - - + +
1093B ILE* 3.9 33.8 + - + -
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Residues in contact with ALA 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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914B LEU* 3.9 27.8 - - + -
941B MET* 3.9 10.8 - - - -
944B LEU* 4.3 2.0 - - + -
949B LEU 2.7 21.1 + - - +
950B ILE 3.9 2.9 - - - +
952B GLU* 1.3 72.4 - - - +
954B THR* 1.3 58.1 + - - +
956B LEU* 3.9 1.6 - - - +
957B ILE* 3.0 35.5 + - + +
979B LEU* 3.9 24.6 - - + +
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Residues in contact with THR 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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938B LEU* 4.0 23.9 + - + +
941B MET* 3.8 16.0 - - - +
950B ILE* 2.8 30.8 + - - +
951B ALA* 3.6 7.5 - - - -
952B GLU 3.2 0.2 - - - -
953B ALA* 1.3 74.1 - - - +
955B ASP* 1.3 58.7 + - - +
958B SER* 2.7 39.8 + - - +
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Residues in contact with ASP 955 (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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951B ALA 3.3 8.5 + - - +
952B GLU 3.0 10.4 + - - +
954B THR* 1.3 81.9 - - - +
956B LEU* 1.3 62.8 + - - +
958B SER* 3.3 12.1 + - - -
959B GLN* 3.2 32.7 + - - +
977B HIS* 2.7 25.5 + - - -
1093B ILE* 3.9 22.3 - - + +
1096B TYR* 5.2 3.5 - - - -
1097B MET* 4.0 21.9 - - - +
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Residues in contact with LEU 956 (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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910B PHE* 4.3 5.2 - - + -
952B GLU 3.1 6.6 + - - +
953B ALA* 3.9 6.3 - - - +
954B THR 3.3 0.2 - - - -
955B ASP* 1.3 80.7 + - - +
957B ILE* 1.3 64.3 + - + +
959B GLN* 3.3 7.5 + - + +
960B MET* 3.0 46.1 + - + +
969B PRO* 4.7 6.3 - - + -
974B VAL* 4.2 20.0 - - + -
977B HIS* 3.6 44.2 - - + +
979B LEU* 4.0 15.7 - - + -
980B PHE* 3.8 30.3 - - + -
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Residues in contact with ILE 957 (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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907B GLY 3.6 17.3 - - - +
910B PHE* 4.0 25.1 - - + -
911B TYR* 3.8 27.6 - - + +
914B LEU* 4.3 10.8 - - + -
938B LEU* 3.6 26.7 - - + -
941B MET* 3.8 19.7 - - + -
953B ALA* 3.0 23.0 + - + +
956B LEU* 1.3 75.7 - - + +
958B SER* 1.3 54.5 + - - +
960B MET* 2.8 10.7 + - - +
961B ILE* 2.8 40.5 + - + +
979B LEU* 6.3 1.1 - - + -
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Residues in contact with SER 958 (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 PHE* 3.9 24.6 - - - -
938B LEU* 3.9 6.2 - - - +
954B THR* 2.7 29.1 + - - +
955B ASP* 3.3 10.4 + - - -
957B ILE* 1.3 76.1 - - - +
959B GLN* 1.3 59.6 + - - +
961B ILE* 3.9 11.3 - - - +
962B ASP* 3.4 23.2 + - - +
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Residues in contact with GLN 959 (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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955B ASP* 3.2 38.3 + - - +
956B LEU* 3.3 11.6 + - - +
957B ILE 3.1 0.2 - - - -
958B SER* 1.3 78.6 + - - +
960B MET* 1.3 66.3 + - - +
962B ASP* 3.2 22.6 + - - +
967B LYS 4.7 7.7 - - - +
968B ARG* 3.6 12.3 - - - +
969B PRO* 3.7 28.3 - - + +
973B LYS* 4.3 14.1 + - - +
977B HIS* 4.6 7.9 + - - -
1096B TYR* 6.3 0.4 - - - -
1100B LYS* 6.3 1.2 - - - +
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Residues in contact with MET 960 (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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903B ILE* 3.6 22.7 - - + +
904B PHE* 3.4 19.6 + - - -
906B MET* 3.9 11.2 - - + -
907B GLY* 3.6 33.4 - - - +
910B PHE* 3.6 36.6 - - + -
956B LEU* 3.0 41.3 + - + +
957B ILE* 2.8 15.2 + - - +
959B GLN* 1.3 76.2 - - - +
961B ILE* 1.3 58.0 + - - +
962B ASP 3.4 0.2 - - - -
968B ARG* 3.4 15.1 - - - +
969B PRO* 4.0 7.6 - - + -
974B VAL* 4.2 13.0 - - + -
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Residues in contact with ILE 961 (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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904B PHE* 3.3 29.8 - - + +
907B GLY* 3.5 36.6 - - - +
908B CYS* 3.8 9.9 - - - +
920B PRO* 3.8 20.2 - - + -
921B PHE* 4.0 9.3 - - + -
936B PHE* 3.4 44.6 - - + -
938B LEU* 4.1 9.0 - - + -
957B ILE* 2.8 23.9 + - + +
958B SER* 3.9 9.2 - - - +
960B MET* 1.3 71.0 - - - +
962B ASP* 1.3 65.6 + - - +
963B HIS* 3.6 1.4 + - - -
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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
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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