Contacts of the helix formed by residues 111 - 132 (chain B) in PDB entry 4DTZ
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 ALA 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PRO 3.6 10.5 - - - +
106B SER* 3.4 35.2 - - - +
108B SER* 3.0 16.5 + - - +
110B GLN* 1.3 75.0 - - - +
112B MET* 1.3 62.2 + - - +
114B GLY* 3.0 14.5 + - - +
115B TYR* 3.4 19.1 + - + +
236B HIS* 6.1 0.9 - - - +
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Residues in contact with MET 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.6 23.3 - - + +
108B SER 3.3 22.2 + - - +
109B GLN* 3.1 21.9 + - - +
110B GLN 3.0 1.2 - - - -
111B ALA* 1.3 75.3 - - - +
113B LYS* 1.3 65.9 + - - +
115B TYR* 3.2 35.3 + - + +
116B HIS* 3.1 24.8 + - - +
119B MET* 4.3 7.4 - - - -
305B TYR* 3.8 15.6 - - + -
404B GLN* 4.0 12.6 - - + +
405B PHE* 3.5 39.0 - - + +
408B HIS* 4.2 13.6 + - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 2.7 55.7 + - - +
111B ALA 3.0 0.8 - - - -
112B MET* 1.3 79.5 - - - +
114B GLY* 1.3 58.6 + - - +
115B TYR 3.6 0.3 + - - -
116B HIS* 3.6 13.0 + - - +
117B ALA 4.8 1.0 + - - -
305B TYR* 3.7 50.3 - - + +
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN 4.4 0.2 + - - -
111B ALA 3.0 9.5 + - - -
113B LYS* 1.3 81.1 - - - +
115B TYR* 1.3 63.0 + - - +
116B HIS 3.4 0.4 + - - -
117B ALA* 4.8 4.2 + - - +
118B MET* 5.4 2.1 + - - +
231B ASP* 4.0 26.6 - - - +
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B SER* 2.7 30.1 + - - -
107B PHE* 5.5 0.7 - + - -
111B ALA* 3.4 20.8 - - + +
112B MET* 3.2 28.5 + - + +
114B GLY* 1.3 78.5 - - - +
116B HIS* 1.3 64.5 + - - +
117B ALA 3.3 1.3 - - - -
118B MET* 3.1 10.0 + - - +
119B MET* 3.0 32.1 + - + +
156B CYS* 3.8 36.5 - - + -
231B ASP 3.2 26.0 - - - -
232B ASP* 4.4 1.3 - - - -
233B LEU* 3.4 16.0 - - + +
236B HIS* 3.4 27.0 - - - -
405B PHE* 4.1 12.3 - + - -
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Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B MET 3.1 16.4 + - - +
113B LYS 3.6 10.8 - - - +
114B GLY 3.4 1.4 - - - -
115B TYR* 1.3 78.6 - - - +
117B ALA* 1.3 61.7 + - + +
119B MET* 3.2 8.3 + - - +
120B VAL* 2.9 44.8 + - + +
303B PRO 2.8 25.8 + - - -
304B SER* 3.4 23.3 - - - -
305B TYR* 3.6 18.7 - - + -
308B VAL* 3.8 10.8 - - + -
408B HIS* 2.9 28.6 + - - +
412B LEU* 4.3 5.7 - - + +
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Residues in contact with ALA 117 (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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113B LYS 4.8 1.6 + - - -
114B GLY 4.8 3.7 + - - +
115B TYR 3.3 0.6 - - - -
116B HIS* 1.3 83.8 - - + +
118B MET* 1.3 76.2 + - + +
120B VAL* 3.3 9.4 + - - +
121B ASP* 3.0 21.8 + - - +
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Residues in contact with MET 118 (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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114B GLY 5.4 2.2 + - - +
115B TYR* 3.1 11.2 + - - +
117B ALA* 1.3 92.7 - - + +
119B MET* 1.3 62.6 + - - +
121B ASP* 3.2 26.7 + - + +
122B ILE* 3.4 8.1 + - - +
152B THR* 5.1 0.9 - - - -
155B LEU* 3.5 48.1 - - + +
156B CYS* 4.2 15.0 - - - -
159B ASN* 5.4 4.5 - - - +
161B ARG* 4.2 11.2 - - - +
231B ASP* 5.9 8.1 - - + +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B MET* 4.3 6.7 - - - -
115B TYR* 3.0 23.1 + - + +
116B HIS* 3.5 8.7 - - - +
118B MET* 1.3 74.2 - - - +
120B VAL* 1.3 62.4 + - - +
122B ILE* 3.4 3.6 + - - +
123B ALA* 3.0 22.2 + - - +
148B LEU* 5.8 0.2 - - - +
152B THR* 3.6 22.4 + - + -
156B CYS* 4.2 2.9 - - - -
405B PHE* 3.4 52.7 - - + +
408B HIS* 3.7 22.4 - - + -
409B GLU* 3.6 33.3 - - - +
412B LEU* 3.7 13.6 - - + +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B HIS* 2.9 49.8 + - + +
117B ALA* 3.6 10.8 - - - +
118B MET 3.2 0.2 - - - -
119B MET* 1.3 74.4 - - - +
121B ASP* 1.3 55.6 + - - +
123B ALA* 4.2 3.4 - - - -
124B VAL* 2.8 49.0 + - + +
302B VAL* 4.1 21.3 - - + -
303B PRO* 3.8 11.2 - - + +
412B LEU* 4.0 16.2 - - + -
416B MET* 5.4 1.1 - - + -
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Residues in contact with ASP 121 (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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132A ARG* 4.4 9.7 + - - -
117B ALA 3.0 13.2 + - - +
118B MET* 3.2 22.0 + - + +
120B VAL* 1.3 77.1 - - - +
122B ILE* 1.3 63.9 + - - +
124B VAL* 3.4 6.5 + - - +
125B GLN* 3.1 32.1 + - - +
155B LEU* 4.2 5.8 - - + -
161B ARG* 2.9 43.0 + - - -
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Residues in contact with ILE 122 (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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118B MET 3.7 11.7 - - - +
119B MET 3.4 3.2 + - - +
120B VAL 3.3 0.2 - - - -
121B ASP* 1.3 89.4 - - - +
123B ALA* 1.3 66.9 + - - +
125B GLN* 3.1 18.0 + - - +
126B LEU* 3.0 19.8 + - - +
148B LEU* 3.6 26.0 - - + +
151B ASP* 3.8 24.2 - - + +
152B THR* 3.3 36.8 - - - +
155B LEU* 3.9 14.4 - - + -
161B ARG* 4.3 5.4 - - + +
165B PHE* 4.1 10.4 - - + -
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Residues in contact with ALA 123 (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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119B MET 3.0 18.4 + - - +
120B VAL* 3.7 5.6 - - - +
122B ILE* 1.3 75.8 - - - +
124B VAL* 1.3 62.4 + - - +
126B LEU* 3.2 4.7 + - + +
127B VAL* 3.0 27.5 + - + +
148B LEU* 3.9 13.1 - - - +
412B LEU* 4.4 3.4 - - + -
413B VAL* 4.1 21.8 - - + -
416B MET* 3.6 26.0 - - + -
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Residues in contact with VAL 124 (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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132A ARG* 5.9 3.4 - - - +
120B VAL* 2.8 30.9 + - + +
121B ASP* 3.8 6.1 - - - +
123B ALA* 1.3 73.3 - - - +
125B GLN* 1.4 55.7 + - + +
127B VAL* 3.2 6.5 + - - +
128B GLN* 2.8 51.4 + - - +
302B VAL* 3.8 28.7 - - + -
416B MET* 4.1 10.5 - - + -
455B LEU* 4.0 16.4 - - + -
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Residues in contact with GLN 125 (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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132A ARG* 3.6 38.6 + - - +
166A TYR* 4.7 3.5 + - + -
121B ASP* 3.1 32.7 + - - +
122B ILE* 3.1 24.6 + - - +
124B VAL* 1.4 74.5 - - - +
126B LEU* 1.4 57.3 + - - +
128B GLN* 3.9 9.8 - - - +
129B LYS* 2.9 29.3 + - - +
151B ASP* 5.3 3.3 + - - +
161B ARG* 3.7 5.7 - - - +
163B ASN* 5.2 3.0 + - - +
165B PHE* 3.8 28.0 + - + +
166B TYR* 3.8 20.6 - - - -
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Residues in contact with LEU 126 (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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122B ILE 3.0 6.4 + - - +
123B ALA* 3.2 8.7 + - - +
125B GLN* 1.4 76.1 - - - +
127B VAL* 1.3 66.9 + - + +
129B LYS* 3.1 6.8 + - + +
130B TRP* 3.1 55.3 + - + +
144B ASP* 3.9 12.1 - - + +
145B MET* 3.7 22.0 - - + -
148B LEU* 3.9 18.4 - - + -
165B PHE* 3.8 27.0 - - + -
413B VAL* 3.7 25.1 - - + -
417B MET* 4.1 14.8 - - + -
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Residues in contact with VAL 127 (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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123B ALA* 3.0 20.0 + - + +
124B VAL* 3.8 4.3 - - - +
126B LEU* 1.3 80.2 - - + +
128B GLN* 1.3 59.4 + - - +
130B TRP* 3.0 3.3 + - + -
131B GLU* 2.8 37.3 + - + +
416B MET* 4.3 33.0 - - + +
417B MET* 5.0 2.9 - - + +
420B HIS* 4.0 19.3 - - + -
421B PHE* 3.6 29.3 - - + -
455B LEU* 3.7 22.0 - - + -
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Residues in contact with GLN 128 (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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128A GLN* 4.5 20.3 + - - +
132A ARG* 5.0 7.1 + - - -
166A TYR* 4.0 3.4 - - - +
124B VAL* 2.8 35.6 + - - +
125B GLN* 3.9 9.3 - - - +
127B VAL* 1.3 75.4 - - - +
129B LYS* 1.3 63.7 + - - +
131B GLU* 3.2 8.9 + - - +
132B ARG* 3.1 62.9 + - - +
455B LEU* 3.9 18.4 - - + +
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Residues in contact with LYS 129 (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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163A ASN* 5.4 0.7 + - - -
166A TYR* 3.5 44.7 + - + -
125B GLN 2.9 16.1 + - - +
126B LEU* 3.1 11.2 + - - +
128B GLN* 1.3 77.0 - - - +
130B TRP* 1.3 69.2 + - + +
132B ARG* 3.1 13.9 + - - +
133B LEU* 3.5 24.7 + - + +
144B ASP* 2.8 39.5 + - - +
147B ARG* 3.7 19.0 - - - +
165B PHE* 3.8 18.2 + - + -
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Residues in contact with TRP 130 (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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126B LEU* 3.1 24.5 + - + +
127B VAL* 3.0 4.0 + - + +
129B LYS* 1.3 86.7 - - + +
131B GLU* 1.4 63.8 + - - +
132B ARG 3.2 0.9 + - - -
133B LEU* 3.3 24.5 + - + +
139B ILE* 3.4 51.0 - - + +
141B VAL* 5.5 0.9 - - + -
144B ASP* 2.9 25.9 + - + -
145B MET* 3.7 31.6 - - + -
277B LEU* 4.9 5.4 - - + -
417B MET* 3.7 32.1 - - + -
421B PHE* 3.6 38.1 - + + -
423B PHE* 3.8 23.1 - + - -
448B ALA* 5.3 3.1 - - + +
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Residues in contact with GLU 131 (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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161A ARG* 5.2 1.9 + - - -
127B VAL* 2.8 28.2 + - + +
128B GLN* 3.2 9.4 + - + +
130B TRP* 1.4 76.2 - - - +
132B ARG* 1.4 62.2 + - + +
133B LEU 3.7 5.9 + - - +
420B HIS* 4.1 19.9 + - - +
421B PHE* 3.8 15.5 - - + -
450B SER* 2.5 38.1 + - - -
452B LYS* 4.9 12.7 + - - +
453B ILE 4.2 9.9 + - - +
455B LEU* 5.4 4.4 - - + +
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Residues in contact with ARG 132 (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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121A ASP* 4.4 10.7 + - - -
124A VAL* 5.8 3.0 - - - +
125A GLN* 3.4 45.4 - - - +
128A GLN* 5.0 7.1 + - - -
161A ARG* 3.3 41.8 - - - +
163A ASN* 2.9 32.3 + - - +
166A TYR* 2.9 35.6 + - + +
128B GLN* 3.1 48.7 + - - +
129B LYS* 3.6 7.0 - - - +
130B TRP 3.0 1.4 - - - -
131B GLU* 1.4 79.5 - - + +
133B LEU* 1.3 64.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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