Contacts of the helix formed by residues 111 - 129 (chain B) in PDB entry 5J8E
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 ASP 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 3.2 41.2 + - + +
106B ILE* 4.0 4.7 - - - +
109B HIS* 3.1 7.9 - - + +
110B SER* 1.3 72.9 - - - +
112B ALA* 1.3 56.9 - - - +
113B ALA* 3.0 24.4 + - - +
114B GLU* 3.0 21.1 + - + +
115B LEU* 3.1 26.7 + - - +
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Residues in contact with ALA 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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10B ALA* 3.9 25.8 - - + +
13B CYS* 3.2 16.1 - - + +
14B GLU* 5.8 0.7 - - - +
32B VAL* 4.2 23.6 - - + -
110B SER 3.1 7.5 + - - +
111B ASP* 1.3 70.1 + - - +
113B ALA* 1.3 60.4 + - - +
115B LEU* 4.2 6.1 - - - -
116B GLY 2.9 24.8 + - - -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER 6.1 0.7 - - - +
8B GLU 5.1 2.0 - - - +
9B ARG* 3.0 55.3 + - + +
10B ALA* 4.6 2.7 - - + +
111B ASP* 3.0 9.9 + - - +
112B ALA* 1.3 78.3 - - - +
114B GLU* 1.3 69.7 + - - +
116B GLY 3.3 0.2 + - - -
117B ARG* 3.2 13.7 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU 4.2 1.2 - - - +
101B PRO* 3.5 12.5 - - - +
102B ASP* 2.8 45.2 + - - +
105B LEU* 3.9 15.7 - - + +
106B ILE* 3.6 21.5 - - + +
111B ASP* 3.0 24.3 + - + +
113B ALA* 1.3 76.5 - - - +
115B LEU* 1.3 67.6 + - - +
117B ARG* 3.1 24.2 + - - +
118B MET 3.1 16.6 + - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B CYS* 3.5 20.0 - - - -
32B VAL* 4.0 24.9 - - + +
35B LEU* 3.8 34.1 - - + +
36B THR* 5.5 0.4 - - + -
41B MET* 3.8 35.9 - - + -
106B ILE* 3.7 25.5 - - + +
110B SER 6.1 0.2 - - - -
111B ASP 3.1 17.2 + - - +
112B ALA* 3.7 4.7 - - - +
114B GLU* 1.3 76.0 - - - +
116B GLY* 1.3 57.3 + - - +
118B MET* 3.0 3.2 + - + +
119B LEU* 2.8 31.6 + - + +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.6 20.2 - - - -
13B CYS* 3.6 20.4 - - - -
16B LEU* 3.5 4.8 - - - +
112B ALA 2.9 13.6 + - - -
113B ALA 3.3 0.2 + - - -
114B GLU 3.2 0.2 - - - -
115B LEU* 1.3 78.0 - - - +
117B ARG* 1.3 55.3 + - - +
119B LEU* 3.4 4.4 + - - -
120B GLN* 3.0 32.1 + - - +
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.1 32.1 - - - +
99B THR* 3.1 38.9 + - - +
100B LEU 4.2 12.3 - - - -
101B PRO* 4.1 12.1 - - + +
113B ALA* 3.2 11.8 + - - +
114B GLU* 3.1 36.5 + - - +
116B GLY* 1.3 75.5 - - - +
118B MET* 1.3 62.2 + - - +
120B GLN* 3.3 14.6 + - - +
121B LEU* 3.2 25.3 + - - +
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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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41B MET* 3.6 25.1 - - + -
76B LEU* 3.6 28.3 - - + +
79B ILE* 3.5 32.1 - - + -
80B LEU* 3.8 15.3 - - + +
83B ILE* 4.6 8.3 - - + -
101B PRO* 3.9 15.4 - - + +
103B VAL* 4.0 11.2 - - + -
106B ILE* 3.9 20.9 - - + -
114B GLU 3.1 10.2 + - - +
115B LEU* 3.0 10.0 + - - +
117B ARG* 1.3 74.5 - - - +
119B LEU* 1.3 65.8 + - - +
121B LEU* 3.2 9.1 + - + +
122B ILE* 3.1 21.1 + - + +
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Residues in contact with LEU 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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13B CYS* 4.1 17.5 - - - +
16B LEU* 3.7 41.9 - - + +
17B LEU* 4.1 4.5 - - + +
19B TRP* 4.2 4.0 - - + -
20B ILE* 3.9 20.0 - - + -
35B LEU* 3.7 33.0 - - + -
41B MET* 3.8 23.8 - - + -
115B LEU* 2.8 21.0 + - + +
116B GLY* 3.7 5.2 - - - +
117B ARG 3.3 0.2 - - - -
118B MET* 1.3 77.3 - - - +
120B GLN* 1.3 55.8 + - - +
122B ILE* 3.1 7.8 + - + +
123B LEU* 2.9 28.6 + - - +
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Residues in contact with GLN 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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152A THR* 3.9 22.7 + - + +
155A GLN* 6.3 0.6 - - - +
156A GLU* 3.8 21.0 + - - +
9B ARG* 2.4 35.2 + - - -
12B LEU* 3.6 12.1 - - + +
16B LEU* 3.6 16.3 - - + +
116B GLY 3.0 13.8 + - - +
117B ARG* 3.3 13.9 + - - +
118B MET 3.2 0.2 - - - -
119B LEU* 1.3 76.1 - - - +
121B LEU* 1.3 58.0 + - + +
123B LEU* 3.2 4.1 + - - +
124B GLY* 2.8 25.6 + - - -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLU* 5.1 1.8 - - - +
80B LEU* 3.8 18.8 - - + -
83B ILE* 4.1 18.6 - - + -
84B LEU* 5.3 0.7 - - + -
95B ILE* 3.7 25.8 - - + +
96B ASN 3.8 21.8 - - - +
97B ASP* 4.0 12.6 - - + -
99B THR 5.7 2.0 - - - +
100B LEU* 4.0 8.7 - - + -
101B PRO* 3.5 31.6 - - + -
117B ARG 3.2 8.7 + - - +
118B MET* 3.2 9.7 + - - +
120B GLN* 1.3 78.4 - - + +
122B ILE* 1.3 62.4 + - - +
124B GLY* 3.1 4.2 + - - -
125B CYS* 3.0 26.4 + - - -
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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
----------------------------------------------------------
19B TRP* 4.0 8.5 - - + -
20B ILE* 4.9 2.5 - - + -
41B MET* 3.6 51.8 - - + +
44B VAL* 3.9 16.4 - - + -
45B LEU* 4.2 11.2 - - + -
48B ILE* 3.7 23.1 - - + +
79B ILE* 5.1 0.7 - - + -
83B ILE* 3.7 21.8 - - + -
118B MET 3.1 12.4 + - - +
119B LEU* 3.1 13.0 + - + +
121B LEU* 1.3 75.7 - - - +
123B LEU* 1.3 62.1 + - - +
125B CYS* 3.1 11.5 + - - +
126B ALA 3.0 17.5 + - - -
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Residues in contact with LEU 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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149A VAL* 4.1 17.5 - - + +
152A THR* 4.3 8.3 - - + +
153A ALA* 3.5 35.0 - - + +
156A GLU* 4.5 1.3 - - + -
16B LEU* 4.0 20.6 - - + -
19B TRP* 3.4 47.4 - - + +
119B LEU 2.9 13.9 + - - +
120B GLN* 3.6 10.3 - - - +
122B ILE* 1.3 75.5 - - - +
124B GLY* 1.3 63.4 + - - +
126B ALA* 3.2 1.9 + - - +
127B VAL* 3.0 32.0 + - + +
139B ILE* 4.3 3.8 - - + -
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Residues in contact with GLY 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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156A GLU* 3.4 34.2 - - - +
95B ILE* 3.5 9.6 - - - -
120B GLN 2.8 11.3 + - - -
121B LEU 3.1 5.1 + - - -
123B LEU* 1.3 76.5 - - - +
125B CYS* 1.3 59.9 + - - +
127B VAL* 3.5 0.4 + - - -
128B ASN* 2.8 31.0 + - - +
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Residues in contact with CYS 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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45B LEU* 4.6 12.1 - - + -
48B ILE* 4.2 10.5 - - + -
83B ILE* 3.9 25.4 - - - -
86B TYR* 4.0 28.7 - - + -
91B LEU* 4.1 13.0 - - - +
95B ILE* 3.9 7.6 - - - +
121B LEU 3.0 18.4 + - - -
122B ILE* 3.1 10.7 + - - +
124B GLY* 1.3 75.5 - - - +
126B ALA* 1.3 64.6 + - - +
128B ASN 3.3 0.3 + - - -
129B CYS* 3.0 28.9 + - - +
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Residues in contact with ALA 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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19B TRP* 3.8 22.0 - - + -
48B ILE* 3.7 29.5 - - + +
122B ILE 3.0 5.6 + - - +
123B LEU 3.2 7.6 + - - +
125B CYS* 1.3 78.6 - - - +
127B VAL* 1.3 62.5 + - + +
128B ASN 3.2 0.2 - - - -
129B CYS* 3.3 17.7 - - - -
132B LYS* 3.4 11.1 - - - -
135B TYR* 3.5 23.5 - - + +
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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
----------------------------------------------------------
153A ALA* 4.2 2.9 - - + +
156A GLU* 3.9 17.7 - - + -
157A LEU* 3.3 30.5 - - + +
123B LEU* 3.0 38.4 + - + +
124B GLY 3.8 6.5 - - - +
126B ALA* 1.3 78.7 - - + +
128B ASN* 1.3 64.8 + - - +
132B LYS* 3.3 23.0 - - - +
135B TYR* 5.0 0.4 - - + -
136B ILE* 3.6 35.8 - - + +
139B ILE* 3.9 13.2 - - + -
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Residues in contact with ASN 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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156A GLU 3.3 21.4 + - - +
157A LEU* 4.3 2.5 - - - +
91B LEU* 3.9 20.3 - - + +
92B GLY 5.5 2.1 + - - -
93B GLN* 2.9 56.3 + - + +
95B ILE* 4.0 7.9 - - - +
124B GLY* 2.8 27.4 + - - +
125B CYS 3.8 0.4 - - - -
126B ALA 3.2 0.4 - - - -
127B VAL* 1.3 87.8 - - - +
129B CYS* 1.3 64.4 + - - +
132B LYS* 4.1 13.5 + - - +
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Residues in contact with CYS 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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48B ILE* 3.9 24.2 - - + +
86B TYR* 3.8 19.5 - - + +
91B LEU* 3.9 10.8 - - + -
125B CYS 3.0 14.0 + - - +
126B ALA 3.3 21.8 - - - -
128B ASN* 1.3 82.3 - - - +
130B GLU* 1.3 66.8 + - - +
131B GLN* 3.1 16.8 - - - -
132B LYS* 3.0 23.7 + - - +
135B TYR* 3.9 12.3 - - - -
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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