Contacts of the helix formed by residues 106 - 123 (chain B) in PDB entry 3EJW
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 THR 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLY* 1.3 73.7 - - - +
107B PRO* 1.3 76.0 - - - +
108B GLU* 3.6 13.4 + - - +
109B GLN* 3.0 42.2 + - - +
110B LEU* 2.9 22.6 + - - +
284B VAL* 3.7 22.0 - - + +
285B GLN* 3.9 2.9 - - - +
298B LEU* 4.3 22.0 - - + -
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Residues in contact with PRO 107 (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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106B THR* 1.3 86.7 - - - +
108B GLU* 1.3 68.3 + - - +
111B GLY 2.7 29.5 + - - -
143B ALA* 3.9 32.3 - - + +
144B TRP* 4.0 13.0 - - + -
147B ALA* 3.2 14.4 - - + +
285B GLN* 3.2 50.3 - - - +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR* 3.8 16.3 + - - +
107B PRO* 1.3 89.3 - - - +
109B GLN* 1.3 58.9 + - + +
112B GLY* 2.9 26.7 + - - +
147B ALA* 4.4 10.7 - - + +
284B VAL 4.4 5.5 - - - +
285B GLN 5.6 1.8 - - - +
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLY* 3.7 8.0 - - - -
106B THR* 3.0 48.9 + - - +
108B GLU* 1.3 79.4 - - + +
110B LEU* 1.3 59.1 + - - +
112B GLY* 3.8 0.3 - - - -
113B LEU* 2.9 28.8 + - - +
298B LEU* 5.2 4.8 - - - +
302B ARG* 3.8 34.3 + - - +
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Residues in contact with LEU 110 (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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104B GLN* 3.6 23.1 - - + -
105B GLY* 3.6 22.2 - - - +
106B THR 2.9 11.5 + - - +
109B GLN* 1.3 73.7 - - - +
111B GLY* 1.3 65.7 + - - +
113B LEU* 3.3 6.4 + - + +
114B LEU* 3.1 28.6 + - - +
144B TRP* 3.4 44.0 - - + +
220B PHE* 3.6 25.8 - - + -
241B TRP* 4.1 12.1 - - + -
302B ARG* 3.9 27.6 - - + -
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO 2.7 23.5 + - - -
110B LEU* 1.3 74.6 - - - +
112B GLY* 1.3 60.3 + - - -
114B LEU* 3.4 4.0 + - - +
115B VAL* 3.3 25.1 + - - +
144B TRP* 3.5 25.3 - - - +
147B ALA* 4.2 1.6 - - - -
148B ALA* 3.5 15.9 - - - +
151B LYS* 4.9 0.2 - - - -
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Residues in contact with GLY 112 (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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108B GLU* 2.9 20.7 + - - +
109B GLN 3.8 0.7 - - - -
110B LEU 3.2 0.2 - - - -
111B GLY* 1.3 75.7 - - - +
113B LEU* 1.3 57.9 + - - +
115B VAL* 3.1 3.8 + - - +
116B ASP* 2.8 38.6 + - - +
147B ALA* 5.4 0.4 - - - +
151B LYS* 3.6 23.3 - - - +
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Residues in contact with LEU 113 (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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109B GLN 2.9 17.5 + - - +
110B LEU* 3.6 11.4 - - + +
112B GLY* 1.3 73.6 - - - +
114B LEU* 1.3 66.0 + - - +
116B ASP* 4.4 9.6 - - + +
117B MET* 2.9 43.6 + - + +
220B PHE* 4.3 17.5 - - + -
239B GLY* 4.8 7.2 - - - -
240B LEU 5.4 1.3 - - - +
302B ARG* 4.4 24.2 - - + -
303B THR 5.0 2.5 - - - +
304B VAL* 3.8 27.8 - - + -
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Residues in contact with LEU 114 (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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110B LEU 3.1 20.3 + - - +
111B GLY* 3.5 10.1 - - - +
112B GLY 3.3 0.2 - - - -
113B LEU* 1.3 75.6 - - - +
115B VAL* 1.3 63.2 + - - +
117B MET* 3.7 8.6 - - + +
118B ALA* 3.1 23.6 + - - +
131B PHE* 5.2 1.3 - - + -
144B TRP* 4.4 13.9 - - + +
148B ALA* 4.6 9.9 - - + -
192B ILE* 3.8 24.1 - - + +
194B PRO* 3.7 29.6 - - + -
218B VAL* 3.7 5.3 - - - +
219B GLY* 3.9 23.6 - - - +
220B PHE* 3.5 32.5 - - + -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLY 3.3 14.1 + - - +
112B GLY 3.1 6.3 + - - +
114B LEU* 1.3 74.6 - - - +
116B ASP* 1.3 61.2 + - - +
118B ALA* 3.2 6.5 + - - +
119B ALA* 2.8 29.1 + - - +
148B ALA* 3.5 33.7 - - + +
151B LYS* 3.7 23.3 - - + -
152B ILE* 3.8 16.6 - - + -
156B HIS* 3.5 34.1 - - + +
159B TRP* 4.3 2.9 - - + -
192B ILE* 4.8 3.1 - - + -
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY* 2.8 25.5 + - - +
113B LEU* 3.8 12.2 + - + +
115B VAL* 1.3 73.5 - - - +
117B MET* 1.3 62.2 + - + +
119B ALA* 3.4 7.4 + - - +
120B GLU* 3.2 23.7 + - - +
151B LYS* 3.5 20.8 + - - -
156B HIS* 5.7 1.0 + - - -
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Residues in contact with MET 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 LEU* 2.9 38.9 + - + +
114B LEU* 3.7 18.2 - - + +
116B ASP* 1.3 78.9 - - + +
118B ALA* 1.3 62.1 + - - +
120B GLU* 3.4 16.0 + - - +
121B GLY 3.7 2.9 + - - -
216B THR* 4.7 0.5 - - - +
218B VAL* 3.7 19.4 - - + +
219B GLY 3.8 15.7 - - - +
220B PHE* 4.1 12.8 - - + -
237B ARG* 3.8 20.8 + - - +
238B PHE* 3.4 32.8 - - - +
239B GLY* 3.5 16.6 - - - +
304B VAL* 4.2 15.9 - - + -
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Residues in contact with ALA 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 LEU 3.1 17.0 + - - +
115B VAL 3.5 4.3 - - - +
117B MET* 1.3 75.3 - - - +
119B ALA* 1.3 59.4 + - - +
121B GLY* 3.0 4.5 + - - -
122B VAL* 2.9 35.3 + - + +
159B TRP* 4.2 10.1 - - + -
190B ALA* 5.0 6.3 - - + -
192B ILE* 3.9 21.8 - - + -
216B THR* 3.7 4.1 - - - +
218B VAL* 3.8 20.3 - - + +
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Residues in contact with ALA 119 (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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115B VAL 2.8 17.5 + - - +
116B ASP* 3.7 9.0 - - - +
118B ALA* 1.3 75.6 - - - +
120B GLU* 1.3 63.6 + - - +
121B GLY 3.2 1.0 + - - -
122B VAL* 4.4 0.7 - - - +
123B LYS* 3.3 22.0 + - - +
156B HIS* 4.0 28.3 - - + +
159B TRP* 3.9 13.4 - - + -
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Residues in contact with GLU 120 (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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116B ASP 3.2 13.2 + - - +
117B MET 3.5 11.9 - - - +
118B ALA 3.2 0.4 - - - -
119B ALA* 1.3 76.4 - - - +
121B GLY* 1.3 57.7 + - - +
123B LYS* 3.3 23.9 + - - +
237B ARG* 3.4 36.9 + - - +
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Residues in contact with GLY 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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117B MET 3.7 2.8 + - - -
118B ALA 3.0 6.4 + - - -
120B GLU* 1.3 80.3 - - - +
122B VAL* 1.3 64.9 + - - +
123B LYS* 3.0 19.7 + - - -
216B THR* 3.1 25.7 + - - -
236B GLN* 6.3 2.2 - - - -
237B ARG* 4.5 6.4 - - - +
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Residues in contact with VAL 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 ALA* 2.9 24.1 + - + +
119B ALA 3.5 1.5 + - - +
121B GLY* 1.3 79.4 - - - +
123B LYS* 1.3 70.6 + - - +
124B LYS* 3.3 29.7 + - + +
127B ALA* 3.6 30.7 - - + -
129B VAL* 5.5 0.4 - - + -
159B TRP* 4.1 22.7 - - + -
189B ASP* 4.6 5.8 - - + +
190B ALA* 3.9 27.8 - - + -
216B THR* 4.1 5.6 - - - -
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Residues in contact with LYS 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 ALA 3.3 11.7 + - - +
120B GLU* 3.3 24.5 + - - +
121B GLY* 3.0 23.7 + - - -
122B VAL* 1.3 77.0 - - - +
124B LYS* 1.3 62.9 + - - +
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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