Contacts of the strand formed by residues 142 - 153 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C TYR* 3.6 29.1 - + + -
138C ALA* 3.6 0.3 - - - -
139C ASN* 2.9 70.2 + - - +
140C GLU 3.7 0.6 - - - -
141C ASN* 1.3 85.2 - - + +
143C ASN* 1.3 83.0 + - - +
144C ALA* 3.6 28.9 - - + -
171C MET* 4.3 16.4 - - + -
172C ASN 3.1 15.9 - - - +
173C TYR* 4.0 17.7 - + + -
174C TYR* 4.8 1.1 - - - -
30D ARG* 5.7 0.2 - - - -
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Residues in contact with ASN 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C TYR 3.2 15.5 - - - +
138C ALA* 3.6 14.1 - - + +
139C ASN 5.5 0.2 + - - -
142C TRP* 1.3 87.7 - - - +
144C ALA* 1.3 62.1 + - - +
145C THR* 5.0 5.5 + - - +
170C ASP 4.9 1.4 - - - +
171C MET* 3.4 2.3 - - - -
172C ASN* 2.9 63.5 + - - +
174C TYR* 3.9 14.8 + - - -
25D TYR 5.6 1.0 + - - -
30D ARG* 4.2 10.9 - - - +
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLY* 3.2 0.9 - - - -
137C TYR* 2.9 36.1 + - + +
142C TRP* 3.6 21.6 - - + -
143C ASN* 1.3 75.5 - - - +
145C THR* 1.3 66.1 + - - +
169C LEU* 4.8 6.1 - - + -
170C ASP 3.3 9.2 - - - +
171C MET* 4.0 16.4 - - + -
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Residues in contact with THR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG* 5.9 2.3 - - - -
134C THR* 3.7 22.7 - - + -
135C ALA 3.7 6.7 - - - +
136C GLY* 4.0 4.8 - - - -
137C TYR 5.0 0.9 + - - -
143C ASN* 5.0 5.5 + - - +
144C ALA* 1.3 79.8 + - - +
146C LEU* 1.3 61.3 + - - +
147C SER* 3.6 19.0 + - - +
168C GLN 3.5 2.3 - - - +
169C LEU* 3.4 8.9 - - - +
170C ASP* 2.8 50.0 + - + +
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Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE 4.6 0.2 - - - -
134C THR* 3.5 0.7 - - - -
135C ALA* 2.9 41.0 + - + +
145C THR* 1.3 71.7 - - - +
147C SER* 1.3 66.5 + - - +
167C PRO* 4.1 25.4 - - + -
168C GLN 3.5 11.7 - - - +
169C LEU* 4.1 21.5 - - + +
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE 3.2 9.0 - - - -
134C THR* 3.3 16.5 + - - +
145C THR* 3.6 14.4 + - - +
146C LEU* 1.3 80.1 + - - +
148C SER* 1.3 60.7 + - - +
149C LYS* 4.2 22.9 - - - -
165C ALA 4.0 0.5 - - - +
167C PRO* 3.3 9.6 - - - +
168C GLN* 2.9 43.1 + - - +
170C ASP* 5.1 3.5 + - - -
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C GLN 3.5 2.5 + - - +
132C ILE* 3.2 5.9 - - - -
133C PHE* 2.9 51.3 + - - +
147C SER* 1.3 72.8 - - - +
149C LYS* 1.3 63.7 + - - +
150C GLN* 5.2 2.1 + - - +
165C ALA 3.6 4.3 - - - -
166C GLN* 2.9 36.4 + - - -
167C PRO* 5.5 1.8 - - - -
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Residues in contact with LYS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C GLN 3.8 2.2 - - - -
132C ILE* 3.8 24.5 - - + -
134C THR* 5.5 1.1 - - - -
147C SER* 4.3 18.8 - - - -
148C SER* 1.3 77.3 + - - +
150C GLN* 1.3 60.7 + - - +
151C PHE* 4.3 6.7 - - + -
164C ARG* 3.4 6.8 - - - +
165C ALA* 2.8 45.6 + - + +
166C GLN* 5.0 0.4 - - - +
168C GLN* 3.2 31.4 + - - +
170C ASP* 5.1 1.8 + - - -
114D LEU* 4.0 16.8 - - + -
117D GLU* 4.2 18.4 - - + +
118D ALA* 5.6 2.0 - - - +
121D GLU* 2.7 38.6 + - - -
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Residues in contact with GLN 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C GLN* 2.9 58.6 + - + +
148C SER* 5.2 1.7 + - - +
149C LYS* 1.3 75.9 - - - +
151C PHE* 1.3 76.6 + - - +
164C ARG* 3.4 52.6 - - + +
166C GLN* 3.8 19.5 + - - +
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Residues in contact with PHE 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C TYR* 4.2 9.4 - + + -
129C ALA 3.4 4.9 - - - +
130C THR* 3.9 36.3 - - + -
131C GLN* 4.8 3.1 - - - -
132C ILE* 4.5 3.4 - - + -
149C LYS* 4.3 9.6 - - + -
150C GLN* 1.3 96.7 + - - +
152C GLN* 1.3 60.3 + - - +
153C VAL* 3.7 9.8 + - + +
159C ASN* 3.4 12.6 - - - +
162C ALA* 4.8 8.6 - - + +
163C TYR 4.1 11.9 - - - -
164C ARG* 4.6 9.7 + - - +
113D ALA* 3.7 30.1 - - + -
114D LEU* 3.5 44.2 - - + -
117D GLU* 4.1 20.2 - - + -
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Residues in contact with GLN 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C THR 4.1 1.0 - - - +
107C ARG* 3.3 21.2 - - - +
108C VAL* 2.8 60.6 + - - +
109C SER 5.0 0.4 - - - -
110C ASP* 4.8 5.9 + - - +
111C PRO* 6.0 0.4 - - - +
128C TYR* 3.2 4.5 - - - -
129C ALA* 2.9 37.2 + - + +
131C GLN* 3.9 13.8 - - - +
151C PHE* 1.3 70.3 - - - +
153C VAL* 1.3 64.1 + - - +
154C PHE* 3.4 9.3 - - + -
159C ASN* 3.8 9.9 - - - +
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C PRO* 5.5 1.4 - - - +
127C GLY 3.9 7.2 - - - +
128C TYR* 3.7 10.8 - - + -
151C PHE* 4.5 7.9 - - + +
152C GLN* 1.3 75.0 - - - +
154C PHE* 1.3 63.6 + - - +
155C THR* 3.1 19.0 + - + +
158C GLY* 3.7 16.8 - - - +
159C ASN* 3.2 32.8 + - - +
162C ALA* 3.7 29.4 - - + -
110D PRO* 3.5 32.8 - - + +
111D LEU* 4.7 1.6 - - + -
113D ALA* 5.1 1.3 - - + -
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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
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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