Contacts of the helix formed by residues 1059 - 1081 (chain A) in PDB entry 4DJH
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 THR1059 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015A LEU* 3.7 2.5 - - - -
1052A ARG* 4.6 6.3 - - - +
1058A ILE* 1.3 77.1 - - - +
1060A LYS* 1.3 64.8 + - - +
1061A ASP* 3.4 10.2 + - - +
1062A GLU* 2.8 44.8 + - - +
1063A ALA* 3.0 21.1 + - - +
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Residues in contact with LYS1060 (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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1004A PHE* 4.2 13.3 - - - -
1008A ARG* 3.3 31.3 - - - +
1013A LEU* 4.6 9.0 - - + +
1015A LEU* 3.6 26.3 - - + +
1059A THR* 1.3 72.7 - - - +
1061A ASP* 1.3 62.4 + - - +
1063A ALA* 3.1 5.6 + - - +
1064A GLU* 3.0 42.5 + - - +
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Residues in contact with ASP1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A THR* 3.4 8.2 + - - +
1060A LYS* 1.3 79.9 - - - +
1062A GLU* 1.3 65.0 + - + +
1064A GLU* 3.1 23.2 + - - +
1065A LYS* 3.0 31.0 + - - +
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Residues in contact with GLU1062 (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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1050A ILE* 3.4 31.1 - - + +
1052A ARG* 2.8 41.8 + - - -
1058A ILE* 3.3 12.4 - - + +
1059A THR* 2.8 48.5 + - - +
1061A ASP* 1.3 76.8 - - + +
1063A ALA* 1.3 56.8 + - - +
1065A LYS* 3.2 11.1 + - + +
1066A LEU* 2.9 29.7 + - - +
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Residues in contact with ALA1063 (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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1004A PHE* 5.6 1.1 - - - -
1013A LEU* 3.9 28.5 - - + -
1015A LEU* 4.1 5.8 - - + -
1028A GLY* 4.4 4.2 - - - -
1029A ILE* 5.3 5.2 + - - +
1058A ILE* 4.0 20.8 - - + +
1059A THR 3.0 12.0 + - - +
1060A LYS* 3.4 9.4 - - - +
1062A GLU* 1.3 78.4 - - - +
1064A GLU* 1.3 55.7 + - + +
1066A LEU* 3.4 6.5 + - - +
1067A PHE* 2.9 27.9 + - - +
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Residues in contact with GLU1064 (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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1004A PHE* 3.9 27.4 - - + -
1060A LYS* 3.0 48.9 + - + +
1061A ASP* 3.1 25.7 + - - +
1063A ALA* 1.3 74.5 - - - +
1065A LYS* 1.3 66.6 + - + +
1067A PHE* 3.2 6.8 + - - +
1068A ASN* 2.9 36.1 + - - +
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Residues in contact with LYS1065 (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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1061A ASP* 3.0 29.7 + - - +
1062A GLU* 3.4 10.5 - - - +
1064A GLU* 1.3 76.1 - - + +
1066A LEU* 1.3 63.6 + - - +
1068A ASN* 3.4 9.8 + - - +
1069A GLN* 3.1 36.2 + - - +
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Residues in contact with LEU1066 (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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1027A ILE* 4.5 15.0 - - + +
1028A GLY* 5.9 1.6 - - - -
1031A HIS* 3.6 55.2 - - + +
1046A LEU* 5.0 1.6 - - + -
1049A ALA* 4.2 21.5 - - + +
1050A ILE* 4.4 19.3 - - + -
1058A ILE* 5.1 4.7 - - + -
1062A GLU 2.9 11.9 + - - +
1063A ALA* 3.6 10.3 - - - +
1064A GLU 3.2 0.2 - - - -
1065A LYS* 1.3 74.5 - - - +
1067A PHE* 1.3 64.0 + - - +
1069A GLN* 3.2 24.5 + - + +
1070A ASP* 2.9 25.0 + - - +
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Residues in contact with PHE1067 (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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1003A ILE* 3.7 20.0 - - + -
1004A PHE* 3.5 37.7 - + + -
1007A LEU* 3.5 42.8 - - + -
1029A ILE* 3.7 35.2 - - + +
1063A ALA 2.9 17.4 + - - +
1064A GLU* 3.2 7.2 + - - +
1066A LEU* 1.3 76.0 - - - +
1068A ASN* 1.3 69.4 + - - +
1070A ASP* 2.8 9.6 + - - +
1071A VAL* 2.8 43.9 + - + +
1104A PHE* 4.0 11.2 - + - -
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Residues in contact with ASN1068 (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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1004A PHE* 5.3 2.4 - - - +
1064A GLU* 2.9 27.4 + - - +
1065A LYS* 3.7 8.5 - - - +
1067A PHE* 1.3 91.3 - - - +
1069A GLN* 1.3 61.7 + - + +
1071A VAL* 3.8 5.8 - - - +
1072A ASP* 2.9 34.8 + - - +
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Residues in contact with GLN1069 (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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1049A ALA 4.6 10.4 + - - +
1065A LYS* 3.1 28.0 + - - +
1066A LEU* 3.4 26.7 - - + +
1067A PHE 3.1 0.2 - - - -
1068A ASN* 1.3 76.6 - - + +
1070A ASP* 1.3 60.3 + - - +
1072A ASP* 3.5 6.6 + - - +
1073A ALA* 2.9 29.8 + - - +
1076A ARG* 4.2 5.4 + - - +
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Residues in contact with ASP1070 (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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1029A ILE 4.6 1.0 - - - +
1030A GLY 4.6 1.0 - - - +
1031A HIS* 2.9 49.9 + - - +
1066A LEU* 2.9 11.9 + - - +
1067A PHE* 2.8 10.3 + - - +
1069A GLN* 1.3 75.7 - - - +
1071A VAL* 1.3 64.8 + - - +
1073A ALA* 3.6 7.9 - - - +
1074A ALA* 3.0 23.6 + - - +
1104A PHE* 3.6 27.2 - - + -
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Residues in contact with VAL1071 (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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1003A ILE* 4.6 15.5 - - + -
1007A LEU* 4.8 3.4 - - + -
1067A PHE* 2.8 54.2 + - + +
1068A ASN* 3.8 7.9 - - - +
1070A ASP* 1.3 73.0 - - - +
1072A ASP* 1.3 70.4 + - - +
1074A ALA* 3.0 6.0 + - - +
1075A VAL* 2.8 35.5 + - + +
1100A ILE* 4.6 14.6 - - + -
1104A PHE* 4.1 11.4 - - + -
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Residues in contact with ASP1072 (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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1068A ASN* 2.9 23.3 + - - +
1069A GLN* 3.7 4.2 - - - +
1071A VAL* 1.3 82.1 - - - +
1073A ALA* 1.3 58.8 + - - +
1075A VAL* 3.1 9.9 + - - +
1076A ARG* 2.8 56.1 + - + +
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Residues in contact with ALA1073 (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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1069A GLN 2.9 18.3 + - - +
1070A ASP* 3.6 10.5 - - - +
1071A VAL 3.2 0.2 - - - -
1072A ASP* 1.3 76.9 - - - +
1074A ALA* 1.3 56.5 + - - +
1076A ARG* 3.2 25.6 + - - +
1077A GLY* 3.0 24.1 + - - -
1080A ARG* 5.1 2.6 + - - -
1108A GLU* 4.6 2.7 - - - +
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Residues in contact with ALA1074 (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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1070A ASP 3.0 14.7 + - - +
1071A VAL* 3.0 8.5 + - - +
1073A ALA* 1.3 73.1 - - - +
1075A VAL* 1.3 60.7 + - - +
1077A GLY* 3.1 3.7 + - - +
1078A ILE* 2.9 33.7 + - + +
1100A ILE* 4.4 16.6 - - + -
1103A VAL* 3.9 27.7 - - + +
1104A PHE* 4.6 9.2 - - + -
1108A GLU* 4.9 3.1 - - - -
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Residues in contact with VAL1075 (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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1071A VAL* 2.8 28.9 + - + +
1072A ASP* 3.5 10.8 - - - +
1074A ALA* 1.3 73.0 - - - +
1076A ARG* 1.3 64.0 + - + +
1078A ILE* 3.1 9.4 + - + +
1079A LEU* 3.0 42.1 + - + +
1088A TYR* 4.1 19.1 - - + +
1100A ILE* 3.6 31.2 - - + -
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Residues in contact with ARG1076 (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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1069A GLN* 4.2 6.3 + - - +
1072A ASP* 2.8 39.7 + - + +
1073A ALA* 3.2 38.0 - - - +
1075A VAL* 1.3 74.0 - - + +
1077A GLY* 1.3 57.8 + - - +
1079A LEU* 3.5 7.3 + - - +
1080A ARG* 3.0 50.7 + - - +
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Residues in contact with GLY1077 (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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1073A ALA 3.0 12.0 + - - -
1074A ALA 3.1 2.6 + - - -
1076A ARG* 1.3 74.8 - - - +
1078A ILE* 1.3 62.2 + - - +
1080A ARG* 3.5 15.2 + - - +
1081A ASN* 3.1 21.1 + - - +
1108A GLU* 3.3 40.4 - - - +
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Residues in contact with ILE1078 (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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1074A ALA 2.9 18.3 + - - +
1075A VAL* 3.1 9.4 + - - +
1077A GLY* 1.3 77.1 - - - +
1079A LEU* 1.3 63.9 + - + +
1081A ASN* 3.2 11.4 + - - +
1084A LEU* 3.8 24.6 - - + +
1085A LYS 3.2 15.5 + - - +
1088A TYR* 3.6 37.7 - - + -
1099A LEU* 4.0 17.0 - - + -
1100A ILE* 4.1 27.6 - - + -
1103A VAL* 3.9 30.1 - - + -
1108A GLU* 5.3 0.2 - - + -
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Residues in contact with LEU1079 (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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1075A VAL* 3.0 31.4 + - + +
1076A ARG* 3.9 6.5 - - - +
1078A ILE* 1.3 77.8 - - + +
1080A ARG* 1.3 60.9 + - - +
1081A ASN 3.4 0.2 - - - -
1085A LYS* 3.3 43.7 - - + +
1088A TYR* 3.6 31.9 - - + -
1089A ASP* 3.8 14.6 - - - +
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Residues in contact with ARG1080 (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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1073A ALA 5.1 2.0 + - - -
1076A ARG* 3.0 34.2 + - - +
1077A GLY* 3.8 19.6 - - - +
1078A ILE 3.2 0.2 - - - -
1079A LEU* 1.3 78.3 - - - +
1081A ASN* 1.3 62.1 + - - +
1082A ALA* 3.6 2.4 + - - -
1108A GLU* 5.3 6.2 + - - +
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Residues in contact with ASN1081 (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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1077A GLY 3.1 17.4 + - - +
1078A ILE 3.2 6.1 + - - +
1079A LEU 4.9 0.2 - - - -
1080A ARG* 1.3 76.9 - - - +
1082A ALA* 1.3 65.1 + - - +
1083A LYS* 2.6 36.8 + - - +
1084A LEU* 3.2 23.6 + - + +
1085A LYS* 3.1 25.3 + - - +
1108A GLU* 4.2 15.3 + - - +
1109A THR* 5.0 3.0 + - - +
1112A ALA* 4.0 18.8 - - - +
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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
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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