Contacts of the helix formed by residues 946 - 961 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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944A LEU* 3.5 1.3 - - - +
945A HIS* 1.3 75.7 - - - +
947A ARG* 1.3 67.6 + - - +
948A SER* 2.7 31.3 + - - -
949A LEU* 3.3 42.0 + - + +
950A ILE* 3.4 14.7 + - - +
983A LYS* 4.8 8.5 + - - -
1081A TYR* 5.7 2.3 - - - -
1082A ASP* 4.7 10.6 - - - +
1085A THR* 5.0 7.2 + - - +
1086A LYS* 5.7 1.6 + - - -
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Residues in contact with ARG 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A HIS 3.3 9.1 + - - +
946A ASP* 1.3 72.2 + - - +
948A SER* 1.3 66.0 + - - +
950A ILE* 3.1 17.5 + - + +
951A ALA* 3.1 22.0 + - - +
1085A THR 5.8 0.4 - - - +
1086A LYS 5.8 3.8 - - - +
1089A PRO* 3.8 33.1 - - + +
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Residues in contact with SER 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A ASP* 2.7 29.3 + - - -
947A ARG* 1.3 78.7 - - - +
949A LEU* 1.3 71.3 + - - +
951A ALA* 3.3 4.0 + - - +
952A GLU* 3.0 37.0 + - - +
1081A TYR* 4.9 3.9 + - - -
1085A THR* 4.2 23.1 + - - -
1089A PRO* 3.4 32.7 - - - +
1092A LEU* 6.3 0.2 - - - -
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Residues in contact with LEU 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A ILE* 3.7 29.2 - - + -
944A LEU* 3.9 23.1 - - + -
946A ASP* 3.3 40.3 + - + +
947A ARG 3.2 0.4 - - - -
948A SER* 1.3 88.2 + - - +
950A ILE* 1.3 51.1 + - - +
952A GLU* 3.1 19.1 + - - +
953A ALA* 2.7 37.4 + - - +
979A LEU* 3.9 5.5 - - + +
983A LYS* 6.0 3.4 - - - -
986A LYS* 3.9 13.9 - - - +
1081A TYR* 6.3 1.1 - - + -
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Residues in contact with ILE 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938A LEU 5.4 2.5 - - - +
941A MET* 3.8 40.3 - - + +
944A LEU* 3.8 32.1 - - + +
945A HIS 5.5 0.7 - - - -
946A ASP 3.4 13.2 + - - +
947A ARG* 3.1 20.1 + - + +
949A LEU* 1.3 74.9 - - - +
951A ALA* 1.3 55.4 + - - +
953A ALA* 3.7 0.9 - - - +
954A THR* 2.8 43.4 + - - +
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Residues in contact with ALA 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A ARG 3.1 10.6 + - - +
948A SER 3.5 8.7 - - - +
950A ILE* 1.3 77.7 - - - +
952A GLU* 1.3 60.5 + - - +
954A THR* 3.5 7.7 + - - -
955A ASP* 3.3 20.1 + - - +
1018A PHE* 5.6 0.8 - - + -
1089A PRO 4.3 4.0 - - - +
1090A ASN* 3.0 32.8 - - - +
1093A ILE* 4.2 14.9 - - + +
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Residues in contact with GLU 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948A SER* 3.0 35.1 + - - +
949A LEU* 3.5 12.6 - - - +
951A ALA* 1.3 77.6 - - - +
953A ALA* 1.3 60.8 + - - +
955A ASP* 3.1 15.1 + - - +
956A LEU 3.1 10.4 + - - -
977A HIS* 3.5 8.3 - - + -
978A PRO* 4.8 0.7 - - + -
979A LEU* 3.9 23.4 - - + +
986A LYS* 3.1 27.2 + - - -
1081A TYR* 3.9 14.0 + - - -
1089A PRO 4.9 1.0 - - - +
1092A LEU* 4.0 18.5 - - + +
1093A ILE* 3.8 32.9 + - + -
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Residues in contact with ALA 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914A LEU* 3.9 28.7 - - + -
941A MET* 3.9 10.3 - - + -
944A LEU* 4.3 2.0 - - + -
949A LEU 2.7 21.5 + - - +
950A ILE 3.9 3.6 - - - +
952A GLU* 1.3 72.6 - - - +
954A THR* 1.3 57.2 + - - +
956A LEU* 3.9 1.7 - - - +
957A ILE* 3.0 35.8 + - + +
979A LEU* 3.9 23.0 - - + +
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Residues in contact with THR 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938A LEU* 4.0 23.4 + - + +
941A MET* 3.8 15.2 - - - +
950A ILE* 2.8 30.5 + - - +
951A ALA* 3.7 8.3 - - - -
952A GLU 3.2 0.2 - - - -
953A ALA* 1.3 74.2 - - - +
955A ASP* 1.3 57.4 + - - +
958A SER* 2.6 40.2 + - - +
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Residues in contact with ASP 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951A ALA 3.3 9.3 + - - +
952A GLU 3.1 10.0 + - - +
954A THR* 1.3 80.0 - - - +
956A LEU* 1.3 62.7 + - - +
958A SER* 3.3 14.8 + - - -
959A GLN* 3.2 34.0 + - - +
977A HIS* 2.7 25.5 + - - -
1093A ILE* 3.9 20.9 - - + +
1096A TYR* 5.2 3.5 - - - -
1097A MET* 4.1 21.7 - - - +
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Residues in contact with LEU 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A PHE* 4.3 7.9 - - + -
952A GLU 3.1 4.8 + - - +
953A ALA* 3.9 7.6 - - - +
955A ASP* 1.3 79.3 + - - +
957A ILE* 1.3 65.7 + - + +
959A GLN* 3.3 9.4 + - + +
960A MET* 3.0 43.9 + - + +
969A PRO* 4.7 7.2 - - + -
974A VAL* 4.2 20.2 - - + -
977A HIS* 3.6 50.5 - - + +
979A LEU* 4.0 16.6 - - + -
980A PHE* 3.9 22.9 - - + -
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Residues in contact with ILE 957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778A LEU* 5.9 0.2 - - + -
907A GLY 3.5 17.3 - - - +
910A PHE* 4.0 24.0 - - + -
911A TYR* 3.8 26.9 - - + +
914A LEU* 4.2 11.4 - - + -
938A LEU* 3.7 26.9 - - + -
941A MET* 3.7 20.9 - - + -
953A ALA* 3.0 21.7 + - - +
956A LEU* 1.3 79.0 - - + +
958A SER* 1.3 58.6 + - - +
960A MET* 2.8 10.0 + - - +
961A ILE* 2.8 35.0 + - + +
979A LEU* 6.3 0.7 - - + -
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Residues in contact with SER 958 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936A PHE* 3.9 24.7 - - - -
938A LEU* 4.1 6.1 - - - -
954A THR* 2.6 27.9 + - - +
955A ASP* 3.3 10.0 + - - -
957A ILE* 1.3 76.8 - - - +
959A GLN* 1.3 59.1 + - - +
961A ILE* 3.9 12.1 - - - +
962A ASP* 3.4 23.6 + - - +
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Residues in contact with GLN 959 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955A ASP* 3.2 37.9 + - - +
956A LEU* 3.3 11.1 + - - +
957A ILE 3.1 0.4 - - - -
958A SER* 1.3 77.4 + - - +
960A MET* 1.3 64.7 + - - +
962A ASP* 3.2 22.7 + - - +
967A LYS 4.7 7.7 - - - +
968A ARG* 3.6 11.6 + - - +
969A PRO* 3.8 29.4 - - + +
973A LYS* 4.3 14.0 + - - +
977A HIS* 4.6 7.7 + - - -
1096A TYR* 6.3 0.4 - - - -
1100A LYS* 6.3 1.0 - - - +
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Residues in contact with MET 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A ILE* 3.7 24.2 - - + +
904A PHE* 3.3 19.6 + - - -
906A MET* 3.9 15.7 - - + -
907A GLY* 3.6 32.1 - - - +
910A PHE* 3.7 33.7 - - + -
956A LEU* 3.0 45.2 + - + +
957A ILE* 2.8 13.8 + - - +
959A GLN* 1.3 72.8 - - - +
961A ILE* 1.3 59.3 + - - +
962A ASP 3.3 0.2 - - - -
968A ARG* 3.4 15.6 - - - +
969A PRO* 4.0 9.0 - - + -
974A VAL* 4.2 11.9 - - + -
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Residues in contact with ILE 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904A PHE* 3.4 29.6 - - + +
907A GLY* 3.5 35.9 - - - +
908A CYS* 3.8 10.1 - - - +
920A PRO* 3.8 20.4 - - + -
921A PHE* 4.0 10.0 - - + -
936A PHE* 3.4 44.9 - - + -
938A LEU* 4.1 8.3 - - + -
957A ILE* 2.8 25.9 + - + +
958A SER* 3.9 9.2 - - - +
960A MET* 1.3 72.1 - - - +
962A ASP* 1.3 65.8 + - - +
963A 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