Contacts of the helix formed by residues 148 - 162 (chain D) in PDB entry 1M54
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 GLY 148 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D THR* 3.5 4.3 + - - -
147D SER* 1.3 92.2 + - - +
149D ASN* 1.3 67.4 + - - +
150D THR 3.3 2.5 - - - -
151D GLY* 3.1 11.2 + - - -
152D ILE* 3.8 10.3 + - - +
173D MET* 5.7 1.1 - - - -
177D LYS* 5.2 10.1 - - - -
304D GLU* 6.1 0.2 - - - -
305D GLY* 6.2 4.0 - - - -
380D ASN* 5.6 0.4 - - - -
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Residues in contact with ASN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D SER* 3.2 33.0 + - - -
119D LYS* 4.1 8.7 - - + +
148D GLY* 1.3 66.3 - - - -
150D THR* 1.3 68.1 + - - +
151D GLY 2.9 2.2 - - - -
152D ILE* 2.8 25.6 + - - +
153D GLY 3.0 10.2 + - - -
305D GLY* 5.6 2.2 - - - -
376D ASP* 3.3 32.7 + - - +
379D ARG* 5.0 3.3 + - - -
380D ASN* 3.3 21.8 + - - +
1410D PLP 2.9 31.5 + - - +
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Residues in contact with THR 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS* 2.7 27.3 - - - +
122D ILE* 3.8 15.3 - - + +
123D SER* 3.3 5.6 + - - +
126D MET* 4.6 6.1 - - + -
144D GLU* 4.5 2.5 - - + -
146D THR* 3.2 14.6 - - + -
148D GLY 3.3 0.8 - - - -
149D ASN* 1.3 78.0 - - - +
151D GLY* 1.3 56.8 + - - +
153D GLY 3.8 0.2 - - - -
154D LEU* 3.0 52.7 + - + +
222D GLN* 2.6 41.8 + - + +
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Residues in contact with GLY 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D THR* 3.2 23.9 + - - -
147D SER 5.3 0.7 - - - -
148D GLY 3.1 9.3 + - - -
149D ASN 2.8 2.4 + - - -
150D THR* 1.3 78.0 - - - +
152D ILE* 1.3 60.5 + - - +
154D LEU* 3.2 5.5 + - - +
155D ALA* 3.0 19.9 + - - +
167D ILE* 4.0 16.4 - - - +
181D LEU* 3.4 13.9 - - - +
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLY* 4.5 12.8 - - - +
117D SER* 5.0 3.4 - - - +
147D SER 5.4 0.7 - - - +
148D GLY 4.0 13.5 - - - +
149D ASN* 2.8 29.7 + - - +
151D GLY* 1.3 70.8 - - - +
153D GLY* 1.3 58.4 + - - +
155D ALA 3.5 0.2 + - - -
156D LEU* 2.9 28.8 + - - +
177D LYS* 5.2 6.7 - - + +
180D VAL* 3.3 39.3 - - + -
181D LEU* 3.5 17.0 - - + -
184D LEU* 3.5 7.7 - - + +
379D ARG* 4.3 15.9 - - - +
380D ASN* 3.8 21.3 - - - +
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Residues in contact with GLY 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS 4.4 0.2 - - - -
120D ASP* 3.7 22.1 + - - -
123D SER* 3.0 28.7 - - - -
149D ASN 3.0 11.0 + - - -
152D ILE* 1.3 75.3 - - - +
154D LEU* 1.3 64.4 + - - +
156D LEU* 3.6 4.7 + - - +
157D ALA* 3.4 21.5 + - - +
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER* 3.1 23.3 + - - +
126D MET* 5.0 2.0 - - + -
127D ILE* 4.1 8.9 - - + +
142D ILE* 4.2 10.5 - - + +
144D GLU* 3.2 42.4 - - + -
146D THR* 3.8 5.8 - - + -
150D THR* 3.0 32.5 + - + +
151D GLY* 3.2 5.8 + - - +
153D GLY* 1.3 79.2 - - - +
155D ALA* 1.3 56.7 + - - +
157D ALA* 3.8 2.4 + - - +
158D ALA* 3.0 27.2 + - - +
165D CYS* 4.0 12.4 - - - -
166D ILE 6.1 0.2 - - - +
167D ILE* 5.4 2.7 - - + -
220D LEU* 3.4 31.6 - - + -
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D GLY 3.0 15.1 + - - +
154D LEU* 1.3 75.6 - - - +
156D LEU* 1.3 64.5 + - - +
157D ALA 3.1 1.8 - - - -
158D ALA* 4.0 2.9 - - - +
159D ALA* 3.2 25.3 + - - +
165D CYS* 3.9 7.8 - - - -
181D LEU* 3.9 5.6 - - + -
184D LEU* 3.6 23.4 - - + +
186D ALA* 3.2 34.5 - - + -
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C GLY* 3.4 33.4 - - - +
345C LEU* 5.1 9.0 - - + -
80D ILE* 4.1 5.2 - - + -
81D LEU* 3.4 26.9 - - + -
84D ILE* 5.1 1.8 - - + -
114D ALA* 4.0 18.6 - - + +
115D GLY* 4.3 20.2 - - - +
120D ASP* 5.7 1.1 - - - +
152D ILE 2.9 18.4 + - - +
153D GLY* 3.6 6.7 + - - +
154D LEU 3.6 0.2 - - - -
155D ALA* 1.3 77.1 - - - +
157D ALA* 1.3 57.7 + - + +
159D ALA* 4.1 3.6 + - - +
160D VAL* 3.4 18.5 + - - +
184D LEU* 3.2 23.6 - - + +
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Residues in contact with ALA 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU* 4.0 30.1 - - + -
123D SER* 5.0 4.9 - - - +
124D LEU* 5.7 5.4 - - + -
127D ILE* 4.0 19.7 - - + -
153D GLY 3.4 15.1 + - - +
155D ALA 3.1 0.2 - - - -
156D LEU* 1.3 79.0 - - - +
158D ALA* 1.3 64.9 + - - +
159D ALA 3.2 2.2 - - - -
160D VAL* 2.9 9.7 + - - -
161D ARG* 3.0 23.5 + - + +
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 4.8 1.5 - - - +
142D ILE* 5.0 3.8 - - + -
154D LEU 3.0 20.5 + - - +
155D ALA 3.4 4.0 + - - +
157D ALA* 1.3 76.9 - - - +
159D ALA* 1.3 59.4 + - - +
160D VAL 3.0 3.9 + - - -
162D GLY* 3.3 5.1 + - - +
163D TYR* 2.8 58.8 + - + +
164D ARG 4.6 0.9 - - - +
165D CYS* 3.9 23.8 - - + -
184D LEU 5.8 0.4 - - - +
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 2.4 30.4 + - - +
339C ILE 5.4 0.7 - - - +
340C ALA* 4.7 16.4 - - - +
341C GLN* 4.3 2.9 - - - +
342C GLU 4.0 8.7 + - - -
343C GLY* 5.4 2.5 - - - +
155D ALA 3.2 8.5 + - - +
156D LEU* 4.4 4.5 - - - +
157D ALA 3.2 0.8 - - - -
158D ALA* 1.3 77.5 - - - +
160D VAL* 1.4 53.9 + - + +
163D TYR 4.9 1.6 - - - -
184D LEU* 3.3 31.4 - - + +
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 3.7 14.4 - - - +
342C GLU* 4.2 5.8 - - - +
343C GLY* 3.6 27.6 - - - +
79D ASP* 3.6 37.5 - - + +
80D ILE* 4.7 6.5 - - + -
81D LEU* 3.7 20.0 - - + -
156D LEU 3.4 18.2 - - - +
157D ALA 2.9 7.6 + - - +
159D ALA* 1.4 79.4 - - - +
161D ARG* 1.3 65.6 + - + +
162D GLY 3.5 0.7 - - - -
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Residues in contact with ARG 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 4.9 2.0 - - - -
79D ASP* 5.9 0.6 + - - -
81D LEU* 3.9 23.3 - - + +
124D LEU* 3.1 17.3 - - - +
127D ILE* 4.5 10.9 - - + +
128D GLU* 2.5 49.8 + - - +
131D GLU* 2.9 40.7 + - - +
157D ALA* 3.0 17.2 + - + +
160D VAL* 1.3 78.4 - - + +
162D GLY* 1.3 59.0 + - - +
163D TYR* 4.5 14.1 - - + -
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Residues in contact with GLY 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 4.7 8.5 - - - -
139D GLY* 3.1 21.7 - - - -
158D ALA 3.3 6.5 + - - -
160D VAL 3.5 1.4 - - - -
161D ARG* 1.3 79.7 - - - +
163D TYR* 1.3 68.7 + - - +
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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