Contacts of the helix formed by residues 1089 - 1110 (chain B) in PDB entry 2KNE
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 GLY1089 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLU* 4.0 18.4 - - - -
144A MET* 4.2 7.2 - - - +
1086B LEU* 3.7 15.5 + - - -
1087B ARG 3.2 3.7 - - - -
1088B ARG* 1.3 74.7 - - - +
1090B GLN* 1.3 71.8 + - - +
1091B ILE 3.3 1.1 + - - -
1092B LEU* 3.6 9.7 + - - +
1093B TRP* 3.4 27.0 + - - +
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Residues in contact with GLN1090 (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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143A GLN 5.0 3.8 - - - +
144A MET* 4.0 28.0 - - - +
146A THR* 5.1 8.1 - - + +
147A ALA* 4.6 24.9 - - + +
1088B ARG* 2.7 37.5 + - + +
1089B GLY* 1.3 80.8 + - - +
1091B ILE* 1.3 66.2 + - + +
1094B PHE* 2.8 31.3 + - + +
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Residues in contact with ILE1091 (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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1088B ARG* 3.0 56.5 - - + +
1089B GLY 3.3 0.2 - - - -
1090B GLN* 1.3 78.0 - - + +
1092B LEU* 1.3 68.4 + - + +
1094B PHE* 4.9 1.8 - - - -
1095B ARG* 3.0 39.2 + - + +
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Residues in contact with LEU1092 (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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112A LEU* 6.0 0.2 - - - +
114A GLU* 4.4 17.7 - - - +
116A LEU* 5.8 7.0 - - + -
120A GLU* 5.5 9.2 - - - +
123A GLU* 5.9 3.1 - - - +
124A MET* 5.0 23.3 - - + +
127A GLU* 4.2 13.7 - - - +
1086B LEU* 4.2 25.4 - - + -
1089B GLY* 3.6 9.7 + - - +
1090B GLN 3.4 0.6 - - - -
1091B ILE* 1.3 86.1 - - + +
1093B TRP* 1.3 70.9 + - + +
1095B ARG* 3.9 9.6 + - - +
1096B GLY 4.3 2.3 + - - -
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Residues in contact with TRP1093 (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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92A PHE* 5.3 5.8 - + - -
100A ILE* 5.4 3.1 - - + -
105A LEU* 5.2 20.4 - - + -
112A LEU* 5.8 0.9 - - - +
124A MET* 3.9 43.8 + - + +
125A ILE* 5.6 0.4 - - + -
127A GLU* 4.1 10.3 - - - -
128A ALA* 4.4 10.5 - - + -
136A VAL* 4.6 18.6 - - + -
141A PHE* 3.6 37.5 - + - -
144A MET* 3.2 62.0 - - + +
145A MET* 3.9 27.8 - - + +
1089B GLY 3.4 9.4 + - - +
1090B GLN 4.1 0.2 - - - +
1091B ILE 3.4 0.6 - - - -
1092B LEU* 1.3 82.5 - - + +
1094B PHE* 1.3 66.1 + - - +
1096B GLY* 3.6 8.0 + - - -
1097B LEU 3.8 4.7 + - - -
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Residues in contact with PHE1094 (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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144A MET 4.9 2.4 + - - +
145A MET* 4.4 14.8 - - - -
147A ALA* 3.1 36.6 - - + -
148A LYS* 5.0 7.4 - - + -
1090B GLN* 2.8 24.7 + - - +
1091B ILE* 4.3 1.3 - - - +
1093B TRP* 1.3 73.2 - - - +
1095B ARG* 1.3 65.9 + - - +
1097B LEU* 2.7 42.8 + - + +
1098B ASN* 2.6 56.2 - - - +
1101B GLN* 5.2 6.7 - - - -
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Residues in contact with ARG1095 (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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114A GLU* 5.4 3.6 - - - +
1091B ILE* 3.0 29.5 + - + +
1092B LEU* 4.0 6.5 - - - +
1093B TRP 3.4 0.2 - - - -
1094B PHE* 1.3 76.0 - - - +
1096B GLY* 1.3 62.4 + - - +
1098B ASN* 3.2 48.2 + - - +
1099B ARG* 3.6 37.7 + - - +
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Residues in contact with GLY1096 (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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112A LEU* 3.6 44.4 - - - +
114A GLU* 4.9 2.1 + - - -
1092B LEU 4.3 2.6 + - - -
1093B TRP 3.6 6.6 + - - -
1094B PHE 3.1 0.8 - - - -
1095B ARG* 1.3 75.8 - - - +
1097B LEU* 1.3 67.5 + - - +
1098B ASN 3.2 0.3 + - - -
1099B ARG* 3.2 13.8 + - - +
1100B ILE* 3.4 11.7 + - - +
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Residues in contact with LEU1097 (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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84A GLU* 2.7 43.3 - - + +
85A ILE* 5.2 9.0 - - + -
88A ALA* 4.8 11.2 - - + -
145A MET* 3.9 43.5 - - + +
1093B TRP 3.8 2.8 + - - -
1094B PHE* 2.7 42.6 + - + +
1096B GLY* 1.3 71.4 - - - +
1098B ASN* 1.3 63.2 + - - +
1100B ILE* 3.2 27.7 + - + +
1101B GLN* 3.5 9.4 + - - +
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Residues in contact with ASN1098 (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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1094B PHE* 2.6 59.9 + - - +
1095B ARG* 3.3 30.2 - - - +
1096B GLY 3.1 0.4 - - - -
1097B LEU* 1.3 77.1 - - - +
1099B ARG* 1.3 61.4 + - + +
1101B GLN* 3.4 28.3 + - - +
1102B THR* 3.7 8.0 + - - -
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Residues in contact with ARG1099 (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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18A LEU* 4.5 19.0 - - - +
112A LEU* 4.8 29.3 + - + +
1095B ARG* 4.0 40.4 + - - +
1096B GLY* 3.2 9.3 + - - +
1098B ASN* 1.3 75.7 - - + +
1100B ILE* 1.3 66.4 + - - +
1102B THR* 3.0 12.7 + - - -
1103B GLN* 2.9 27.6 + - + +
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Residues in contact with ILE1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 6.4 0.7 - - + -
84A GLU* 5.4 9.0 - - + -
88A ALA* 5.6 7.4 - - + -
92A PHE* 5.1 17.5 - - + -
108A VAL* 6.3 1.6 - - + -
111A ASN* 6.5 0.2 - - + -
112A LEU* 4.8 8.7 - - + -
1096B GLY 3.4 13.7 + - - +
1097B LEU* 3.2 24.7 + - + +
1099B ARG* 1.3 74.6 - - - +
1101B GLN* 1.3 69.7 + - - +
1103B GLN* 3.0 45.5 + - + +
1104B ILE* 3.7 16.0 + - + +
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Residues in contact with GLN1101 (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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79A THR* 4.7 19.1 - - + +
81A SER* 4.8 9.8 + - - -
84A GLU* 2.6 44.2 + - + +
1094B PHE* 5.2 5.9 - - - -
1097B LEU* 3.5 2.6 + - - +
1098B ASN* 3.4 26.3 + - - +
1099B ARG 3.2 0.4 - - - -
1100B ILE* 1.3 79.4 - - - +
1102B THR* 1.3 62.5 + - - +
1104B ILE* 3.8 4.1 + - - +
1105B LYS* 3.3 16.9 + - - +
1108B LYS* 5.4 3.3 + - - -
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Residues in contact with THR1102 (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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1098B ASN 3.7 9.4 + - - -
1099B ARG* 3.0 12.9 + - - -
1101B GLN* 1.3 77.6 - - - +
1103B GLN* 1.3 60.6 + - - +
1105B LYS* 2.4 45.9 + - + +
1106B VAL* 3.3 16.4 + - + +
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Residues in contact with GLN1103 (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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35A VAL* 5.2 11.4 - - + +
38A SER* 5.1 12.7 + - - +
39A LEU* 4.7 20.8 - - + +
111A ASN* 4.8 20.0 + - - +
112A LEU* 5.1 4.9 - - - +
1099B ARG* 2.9 20.0 + - + +
1100B ILE* 3.0 43.1 + - - +
1102B THR* 1.3 77.1 - - - +
1104B ILE* 1.3 62.6 + - + +
1106B VAL* 3.9 8.4 + - - +
1107B VAL* 3.6 17.6 - - - +
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Residues in contact with ILE1104 (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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39A LEU* 3.9 32.8 - - + -
87A GLU* 5.7 4.5 - - - +
1100B ILE* 3.7 20.2 + - + +
1101B GLN* 4.4 3.6 - - - +
1102B THR 2.8 2.2 + - - -
1103B GLN* 1.3 76.3 - - + +
1105B LYS* 1.3 64.3 + - - +
1106B VAL 3.2 2.0 - - - -
1107B VAL* 3.6 22.0 - - + -
1108B LYS* 3.0 49.9 + - + +
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Residues in contact with LYS1105 (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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72A MET* 5.9 8.1 - - + -
75A LYS* 2.8 62.8 + - + +
76A MET* 4.5 6.2 - - - +
77A LYS 4.3 11.9 + - - -
1101B GLN 3.3 12.3 + - - +
1102B THR* 2.4 39.6 + - + +
1104B ILE* 1.3 70.5 - - - +
1106B VAL* 1.3 63.6 + - + +
1108B LYS* 3.5 15.8 + - - +
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Residues in contact with VAL1106 (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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19A PHE* 5.3 17.0 - - + -
32A LEU* 6.4 1.1 - - + -
68A PHE* 5.4 9.2 - - + -
71A MET* 5.9 1.5 - - + +
72A MET* 4.9 22.1 - - + +
1102B THR* 3.3 20.4 + - + +
1103B GLN* 4.1 8.3 - - - +
1104B ILE 3.2 0.4 - - - -
1105B LYS* 1.3 79.1 - - + +
1107B VAL* 1.3 66.3 + - + +
1109B ALA* 3.3 20.8 - - - +
1110B PHE* 3.7 17.3 - - + -
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Residues in contact with VAL1107 (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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35A VAL* 5.6 8.1 - - + -
36A MET* 5.5 21.3 - - + -
39A LEU* 4.9 11.4 - - + -
51A MET* 4.9 5.8 - - + +
1103B GLN 3.6 16.6 - - - +
1104B ILE* 3.4 28.7 - - + +
1106B VAL* 1.3 75.8 - - + +
1108B LYS* 1.3 72.5 + - + +
1109B ALA 3.0 2.5 - - - -
1110B PHE* 2.7 26.3 + - + +
1111B HIS* 3.2 11.2 + - + +
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Residues in contact with LYS1108 (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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75A LYS* 3.5 31.6 - - - +
77A LYS* 5.3 7.6 - - + +
79A THR* 2.8 29.7 + - - +
83A GLU* 3.8 18.8 + - - -
1101B GLN 5.4 3.0 + - - -
1104B ILE* 3.0 51.1 + - + +
1105B LYS* 3.7 2.9 - - - +
1106B VAL 3.3 0.4 - - - -
1107B VAL* 1.3 77.4 - - + +
1109B ALA* 1.3 64.1 + - - +
1111B HIS* 3.1 6.0 + - - +
1112B SER* 2.8 26.3 + - - -
1113B SER 4.4 3.0 + - - +
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Residues in contact with ALA1109 (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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55A VAL* 5.0 1.7 - - - +
71A MET* 4.0 37.1 - - + +
72A MET* 5.5 3.1 - - + -
75A LYS* 3.7 25.4 - - + +
1106B VAL* 3.3 15.4 + - - +
1107B VAL 2.9 0.4 + - - -
1108B LYS* 1.3 80.8 - - - +
1110B PHE* 1.3 62.8 + - - +
1112B SER* 3.3 13.6 + - - +
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Residues in contact with PHE1110 (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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27A ILE* 5.8 1.1 - - + -
32A LEU* 4.1 25.4 - - + -
51A MET* 3.4 48.4 - - + +
52A ILE* 4.1 16.4 - - + -
54A GLU* 4.9 11.4 - - - +
55A VAL* 3.0 47.0 - - + +
63A ILE* 4.5 9.6 - - + -
71A MET* 4.4 13.5 - - + -
1106B VAL* 3.7 25.8 - - + -
1107B VAL* 2.7 19.0 + - + +
1109B ALA* 1.3 76.9 - - + +
1111B HIS* 1.3 61.6 + - - +
1112B SER* 3.3 6.4 + - - -
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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