Contacts of the helix formed by residues 113 - 134 (chain A) in PDB entry 2XIK
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 GLU 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PRO 4.0 2.1 + - - +
112A LEU* 1.3 75.0 - - - +
114A GLU* 1.3 65.6 + - - +
115A THR* 3.2 10.1 - - + +
116A TYR* 3.1 38.2 + - + +
117A ILE* 3.3 8.8 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 3.8 0.6 + - - -
113A GLU* 1.3 72.0 - - - +
115A THR* 1.4 56.4 + - + +
117A ILE* 3.3 8.4 + - + +
118A ALA* 3.0 31.7 + - - +
238A GLN 5.0 0.2 - - - +
239A HIS* 3.5 12.9 + - - +
240A SER* 2.6 52.1 + - - -
243A PHE* 3.7 26.8 - - + -
269A PHE* 3.6 11.5 - - + -
273A TYR* 3.6 23.4 + - + +
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 4.0 14.5 - - + +
114A GLU* 1.4 74.1 - - + +
116A TYR* 1.4 62.7 + - - +
118A ALA* 3.7 2.3 + - - +
119A THR* 2.7 34.2 + - - -
273A TYR* 3.7 35.2 - - + +
275A LYS* 4.3 16.6 - - - +
279A PHE* 3.5 27.1 - - + -
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.4 6.3 - - + -
113A GLU* 3.1 37.8 + - + +
115A THR* 1.4 81.7 + - - +
117A ILE* 1.3 66.3 + - - +
119A THR* 3.2 3.2 + - - -
120A ILE* 3.0 29.6 + - + +
279A PHE* 3.4 48.7 - + - -
280A LEU* 3.9 10.9 - - + +
282A GLU* 3.6 19.5 - - + +
283A LEU* 3.7 50.5 - - + -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.6 42.8 - - + +
113A GLU 3.8 3.4 - - - +
114A GLU* 3.3 13.0 + - + +
116A TYR* 1.3 75.0 - - - +
118A ALA* 1.4 56.8 - - - +
120A ILE* 3.3 8.2 + - - +
121A LEU* 2.9 43.2 + - + +
205A ALA 4.6 0.2 - - - +
208A LEU* 3.7 33.0 - - + +
209A ALA* 3.8 14.6 - - - -
239A HIS* 5.9 1.3 - - + +
243A PHE* 3.7 34.1 - - + -
269A PHE* 4.4 2.5 - - + -
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Residues in contact with ALA 118 (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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114A GLU 3.0 11.2 + - - +
115A THR 4.0 2.0 - - - +
117A ILE* 1.4 75.0 - - - +
119A THR* 1.4 56.9 + - - +
121A LEU 3.6 0.2 + - - -
122A ARG* 3.1 29.2 + - - +
269A PHE* 3.8 30.5 - - + +
270A ILE* 3.8 12.6 - - - +
273A TYR* 3.4 36.8 - - + -
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR 2.7 23.3 + - - -
116A TYR 3.2 4.7 + - - -
118A ALA* 1.4 73.1 - - - +
120A ILE* 1.4 65.4 + - - +
122A ARG* 3.4 33.1 + - - +
123A GLU* 3.2 28.7 + - - +
273A TYR* 5.1 2.3 - - - +
275A LYS* 3.5 25.9 + - + +
276A LYS 4.1 10.5 - - - +
277A THR* 4.4 3.4 - - + -
279A PHE* 4.5 1.0 - - + -
280A LEU* 3.9 27.4 - - + -
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Residues in contact with ILE 120 (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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103A ALA* 4.9 8.1 - - + -
106A LEU* 5.8 2.0 - - + -
112A LEU* 4.0 18.8 - - + -
116A TYR 3.0 21.2 + - - +
117A ILE* 3.7 3.8 - - - +
119A THR* 1.4 72.0 - - - +
121A LEU* 1.3 59.7 + - - +
123A GLU* 3.2 4.2 + - - +
124A ILE* 2.9 47.0 + - + +
146A VAL* 4.4 12.6 - - + -
148A LEU* 5.2 8.1 - - + -
154A VAL* 4.4 7.7 - - + +
208A LEU* 4.0 18.8 - - + -
280A LEU* 3.9 22.0 - - + -
283A LEU* 4.0 26.5 - - + -
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Residues in contact with LEU 121 (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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117A ILE* 2.9 26.9 + - + +
118A ALA 4.0 0.2 - - - +
120A ILE* 1.3 75.9 - - - +
122A ARG* 1.4 56.1 + - - +
124A ILE* 3.4 8.9 + - + +
125A LEU* 3.0 35.1 + - - +
201A LEU* 3.8 26.4 - - + +
204A THR* 5.0 0.7 - - + -
205A ALA* 3.9 23.3 - - + +
208A LEU* 3.9 20.2 - - + -
243A PHE* 4.4 0.4 - - + -
246A PHE* 3.7 24.5 - - + -
269A PHE* 3.8 25.4 - - + -
270A ILE* 3.8 13.5 - - + -
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Residues in contact with ARG 122 (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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118A ALA 3.1 19.0 + - - +
119A THR* 3.5 27.5 + - - +
120A ILE 3.3 0.2 - - - -
121A LEU* 1.4 75.1 - - - +
123A GLU* 1.4 80.4 + - - +
125A LEU* 3.4 1.9 + - - -
126A LYS* 3.1 32.4 + - - +
265A LEU* 3.4 15.3 - - + +
270A ILE* 3.7 23.0 - - + +
273A TYR 4.4 8.7 + - - -
274A THR* 4.4 4.2 - - - +
275A LYS 2.8 37.8 + - - +
276A LYS* 4.4 1.0 - - - +
277A THR* 3.9 12.9 - - - +
1293A EDO 3.6 33.7 - - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.3 31.4 + - - +
119A THR* 3.2 13.4 + - + +
120A ILE 3.2 5.4 + - - +
122A ARG* 1.4 94.5 + - - +
124A ILE* 1.4 63.5 + - - +
126A LYS* 2.8 41.1 + - - +
127A GLY* 3.2 9.9 + - - -
154A VAL* 3.5 36.8 + - + +
156A LEU* 5.9 0.2 - - - +
277A THR* 3.4 31.4 - - + +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 2.9 40.4 + - + +
121A LEU* 3.7 19.5 - - + +
123A GLU* 1.4 74.0 - - - +
125A LEU* 1.3 58.3 + - - +
127A GLY* 3.1 4.2 + - - -
128A LEU* 2.8 36.4 + - + +
141A ILE* 4.8 8.5 - - + -
146A VAL* 3.7 35.9 - - + -
154A VAL* 4.3 2.5 - - + -
156A LEU* 3.9 22.0 - - + +
201A LEU* 3.8 19.3 - - + -
204A THR* 4.6 12.1 - - + -
208A LEU* 4.8 0.4 - - + -
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Residues in contact with LEU 125 (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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121A LEU 3.0 22.6 + - - +
122A ARG* 3.5 5.4 - - - +
123A GLU 3.3 0.2 - - - -
124A ILE* 1.3 74.8 - - - +
126A LYS* 1.4 57.6 + - - +
128A LEU* 3.7 6.5 - - + +
129A ASP* 2.8 30.8 + - - +
198A ILE* 5.1 0.4 - - + -
201A LEU* 3.6 27.1 - - + -
246A PHE* 4.1 8.5 - - + -
261A ALA* 3.7 24.9 - - + +
264A LEU* 3.6 44.6 - - + +
265A LEU* 3.7 18.1 - - + +
270A ILE* 4.1 16.4 - - + -
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Residues in contact with LYS 126 (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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77A TYR* 3.4 45.1 + - + +
122A ARG* 3.1 25.0 + - - +
123A GLU* 2.8 39.6 + - - +
125A LEU* 1.4 75.4 - - - +
127A GLY* 1.3 60.3 + - - +
129A ASP* 3.6 8.0 + - - +
130A TYR* 3.2 22.0 + - - +
265A LEU* 4.2 11.9 - - + -
1293A EDO 3.7 26.7 - - - -
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Residues in contact with GLY 127 (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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77A TYR* 3.6 22.6 - - - +
78A ILE* 3.9 4.4 - - - +
123A GLU 3.2 7.9 + - - -
124A ILE 3.1 7.6 + - - -
126A LYS* 1.3 74.7 - - - +
128A LEU* 1.3 57.6 + - - +
130A TYR* 3.3 4.8 + - - +
131A LEU* 3.0 31.0 + - - +
156A LEU* 3.7 17.3 - - - -
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Residues in contact with LEU 128 (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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124A ILE* 2.8 34.6 + - + +
125A LEU* 3.8 7.6 - - + +
127A GLY* 1.3 73.1 - - - +
129A ASP* 1.3 59.0 + - - +
131A LEU* 3.3 7.2 + - + +
132A HIS* 2.8 47.1 + - + +
141A ILE* 3.7 26.9 - - + -
156A LEU* 4.0 8.5 - - + -
197A ASP* 3.8 33.2 - - + +
198A ILE* 5.0 3.6 - - + -
201A LEU* 4.3 27.8 - - + -
261A ALA* 4.0 12.6 - - + -
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Residues in contact with ASP 129 (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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125A LEU 2.8 20.4 + - - +
126A LYS* 3.7 8.8 - - - +
128A LEU* 1.3 70.9 - - - +
130A TYR* 1.4 62.6 + - - +
132A HIS* 4.1 3.3 - - - +
133A SER* 3.1 26.9 + - - -
261A ALA* 3.6 14.3 - - + +
262A LYS* 3.5 39.2 + - - +
265A LEU* 4.6 10.4 - - + +
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Residues in contact with TYR 130 (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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72A GLN 3.7 6.1 + - - -
73A CYS* 3.4 29.3 - - + -
74A ASP* 2.9 39.5 + - - +
75A SER* 3.7 30.5 - - - +
77A TYR* 5.4 1.3 - - + -
78A ILE* 3.8 10.8 - - + -
126A LYS 3.2 14.3 + - - +
127A GLY* 3.7 7.0 - - - +
128A LEU 3.3 0.4 - - - -
129A ASP* 1.4 76.9 + - - +
131A LEU* 1.4 68.7 + - + +
133A SER* 2.6 25.4 + - - -
134A GLU* 3.2 39.2 + - + +
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Residues in contact with LEU 131 (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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73A CYS* 3.8 28.9 - - - -
78A ILE* 3.8 13.5 - - + -
127A GLY 3.0 13.0 + - - +
128A LEU* 3.8 9.0 - - + +
130A TYR* 1.4 77.8 - - + +
132A HIS* 1.3 61.2 + - + +
134A GLU* 3.0 21.1 + - - +
136A LYS* 3.0 41.2 + - + +
137A ILE 5.3 0.4 - - - -
138A HIS* 4.1 21.8 - - + +
156A LEU* 3.9 24.2 - - + -
159A PHE* 3.8 26.7 - - + -
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Residues in contact with HIS 132 (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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128A LEU* 2.8 41.6 + - + +
129A ASP* 4.2 4.0 - - - +
131A LEU* 1.3 74.6 - - + +
133A SER* 1.3 55.8 + - - +
135A ARG* 3.1 16.3 + - - +
136A LYS 3.3 18.2 - - - -
194A PHE* 3.3 61.5 + + + +
197A ASP* 2.9 34.0 + - + +
198A ILE* 4.3 12.8 - - + +
260A THR* 6.0 0.4 - - - -
261A ALA* 4.5 10.0 + - + +
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASP* 3.1 19.5 + - - -
130A TYR* 2.6 26.5 + - - -
132A HIS* 1.3 74.0 - - - +
134A GLU* 1.4 64.4 + - - +
135A ARG* 3.3 8.1 + - - +
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Residues in contact with GLU 134 (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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72A GLN 4.9 7.2 - - - +
73A CYS* 6.1 0.2 - - - -
130A TYR* 3.5 47.3 - - + +
131A LEU* 3.0 11.3 + - - +
133A SER* 1.4 80.2 + - - +
135A ARG* 1.3 68.8 + - - +
136A LYS* 3.2 24.6 + - + +
164A GLN* 3.4 11.6 + - - +
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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