Contacts of the strand formed by residues 142 - 153 (chain E) in PDB entry 5IXM
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 TRP 142 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137E TYR* 3.9 25.1 - + + -
138E ALA* 3.6 0.2 - - - -
139E ASN* 2.8 72.6 + - - +
140E GLU 3.7 0.4 - - - -
141E ASN* 1.3 85.5 - - + +
143E ASN* 1.3 82.7 + - - +
144E ALA* 3.7 25.6 - - + -
171E MET* 4.0 18.8 - - + -
172E ASN 3.1 17.3 - - - +
173E TYR* 3.9 17.3 - + + -
174E TYR* 4.8 1.6 - - - -
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Residues in contact with ASN 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E TYR 3.3 15.5 - - - +
138E ALA* 3.6 14.5 - - + +
139E ASN 5.5 0.4 + - - -
142E TRP* 1.3 86.3 - - - +
144E ALA* 1.3 62.4 + - - +
145E THR* 5.1 4.6 + - - +
170E ASP 5.1 0.5 - - - +
171E MET* 3.5 1.7 - - - -
172E ASN* 2.9 57.7 + - - +
174E TYR* 3.7 27.1 + - - -
25F TYR 5.6 0.8 + - - -
30F ARG* 4.2 11.7 - - - +
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Residues in contact with ALA 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E GLY* 3.2 0.9 - - - -
137E TYR* 2.9 35.9 + - + +
142E TRP* 3.7 22.3 - - + -
143E ASN* 1.3 75.3 - - - +
145E THR* 1.3 66.3 + - - +
169E LEU* 4.8 6.1 - - + -
170E ASP 3.3 9.6 - - - +
171E MET* 4.1 14.6 - - + -
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Residues in contact with THR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ARG* 5.9 3.1 - - - -
134E THR* 3.7 20.6 - - + -
135E ALA 3.8 6.7 - - - +
136E GLY* 4.0 4.3 - - - -
137E TYR 5.0 0.9 + - - -
143E ASN* 5.1 4.7 + - - +
144E ALA* 1.3 79.7 + - - +
146E LEU* 1.3 61.0 + - - +
147E SER* 3.5 20.6 - - - +
168E GLN 3.6 1.9 - - - +
169E LEU* 3.3 9.9 - - - +
170E ASP* 2.8 49.3 + - + +
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Residues in contact with LEU 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E PHE 4.6 0.2 - - - -
134E THR* 3.5 0.7 - - - -
135E ALA* 2.9 41.4 + - + +
145E THR* 1.3 70.9 - - - +
147E SER* 1.3 64.4 + - - +
167E PRO* 4.3 22.9 - - + -
168E GLN 3.8 12.3 - - - +
169E LEU* 4.1 22.4 - - + +
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Residues in contact with SER 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E PHE 3.1 9.2 - - - -
134E THR* 2.9 19.5 + - - +
145E THR* 3.5 15.4 - - - +
146E LEU* 1.3 79.4 + - - +
148E SER* 1.3 60.0 + - - +
149E LYS* 4.2 22.8 - - - -
167E PRO* 3.4 8.2 - - - +
168E GLN* 2.9 42.7 + - - +
170E ASP* 5.4 2.5 + - - -
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Residues in contact with SER 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLN 3.6 2.4 + - - +
132E ILE* 3.2 6.2 - - - -
133E PHE* 2.9 52.1 + - - +
147E SER* 1.3 73.2 - - - +
149E LYS* 1.3 63.7 + - - +
150E GLN* 4.9 4.9 + - - +
165E ALA 3.6 3.6 - - - -
166E GLN* 3.4 33.0 + - - -
167E PRO* 4.9 4.7 - - - -
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Residues in contact with LYS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLN 3.9 1.8 - - - -
132E ILE* 3.8 24.2 - - + -
134E THR* 5.4 1.1 - - - -
147E SER* 4.4 15.5 - - - -
148E SER* 1.3 77.7 - - - +
150E GLN* 1.3 60.5 + - - +
151E PHE* 4.4 4.9 - - + -
164E ARG* 3.4 8.3 - - - +
165E ALA* 2.9 47.2 + - + +
166E GLN* 4.8 0.4 - - - +
168E GLN* 3.0 37.0 + - - +
170E ASP* 5.0 3.6 + - - -
114F LEU* 4.1 15.2 - - + +
117F GLU* 4.2 24.9 - - + +
118F ALA* 5.7 4.4 - - - +
121F GLU* 4.8 14.1 - - - +
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Residues in contact with GLN 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E TYR* 5.6 4.0 + - - -
131E GLN* 2.8 61.2 + - + +
132E ILE* 4.5 0.4 - - - +
148E SER* 4.9 4.0 + - - +
149E LYS* 1.3 76.2 - - - +
151E PHE* 1.3 74.1 + - - +
164E ARG* 3.2 50.9 + - + +
166E GLN* 3.8 15.4 + - - +
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Residues in contact with PHE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E TYR* 4.1 8.7 - + + -
129E ALA 3.4 12.6 - - - +
130E THR* 3.9 29.2 - - + -
131E GLN* 4.7 4.7 - - - -
132E ILE* 4.6 6.5 - - + -
149E LYS* 4.4 2.7 - - + -
150E GLN* 1.3 91.8 - - - +
152E GLN* 1.3 59.2 + - - +
153E VAL* 3.7 10.7 + - + +
159E ASN* 3.6 12.1 - - - +
162E ALA* 4.9 8.4 - - + +
163E TYR 4.3 11.0 - - - -
164E ARG* 4.5 15.7 + - - +
113F ALA* 3.6 30.3 - - + -
114F LEU* 3.4 45.5 - - + -
117F GLU* 4.0 22.2 - - + -
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Residues in contact with GLN 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E THR 4.0 0.5 - - - +
107E ARG* 3.3 20.2 - - - +
108E VAL* 2.8 59.1 + - - +
109E SER 5.0 0.8 - - - -
110E ASP* 4.8 5.1 + - - +
128E TYR* 3.2 4.6 - - - -
129E ALA* 2.9 37.6 + - + +
131E GLN* 3.8 13.8 - - - +
151E PHE* 1.3 70.3 - - - +
153E VAL* 1.3 63.6 + - - +
154E PHE* 3.4 9.2 - - + -
159E ASN* 4.1 8.5 - - - +
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Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E PRO* 5.6 1.0 - - - +
127E GLY 4.0 7.6 - - - +
128E TYR* 3.7 10.3 - - + -
151E PHE* 4.5 9.4 - - + +
152E GLN* 1.3 75.8 - - - +
154E PHE* 1.3 63.3 + - - +
155E THR* 3.1 16.7 + - - +
158E GLY* 3.7 20.0 - - - +
159E ASN* 3.4 31.7 + - - +
162E ALA* 3.7 29.2 - - + -
110F PRO* 3.4 33.0 - - + +
111F LEU* 4.7 1.3 - - + -
113F ALA* 5.0 1.8 - - + -
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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