Contacts of the helix formed by residues 134 - 149 (chain A) in PDB entry 1M1B
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 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU 3.7 2.0 + - - -
133A ALA* 1.3 72.6 - - - +
135A ILE* 1.3 69.4 + - - +
136A GLU* 3.3 13.9 + - - +
137A GLU* 3.1 36.3 + - + +
138A PHE* 3.0 19.6 + - - +
175A ARG* 5.2 0.7 - - - +
293B PRO* 4.0 13.0 - - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ALA 3.1 3.9 + - - -
134A ASP* 1.3 76.3 + - - +
136A GLU* 1.3 69.1 + - - +
137A GLU 3.0 1.2 + - - -
138A PHE* 3.1 2.4 + - - +
139A ALA* 3.0 19.8 + - - +
171A GLU* 4.0 4.7 - - - +
174A LYS* 3.8 32.8 - - + -
175A ARG* 3.1 46.5 - - - +
178A ALA* 3.5 30.5 - - + -
179A TYR* 3.9 12.4 - - + +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP* 3.3 12.7 + - - +
135A ILE* 1.3 82.5 - - - +
137A GLU* 1.3 62.0 + - - +
139A ALA* 3.4 7.8 + - - +
140A LEU* 3.3 28.6 + - + +
293B PRO* 3.2 28.7 - - + +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASN* 6.4 2.0 - - - -
117A LEU* 5.6 4.0 - - - +
133A ALA* 4.3 17.2 - - - +
134A ASP* 3.1 30.4 + - - +
135A ILE 3.0 0.6 - - - -
136A GLU* 1.3 77.5 - - - +
138A PHE* 1.3 67.8 + - - +
140A LEU* 2.9 16.3 + - - +
141A LYS* 3.1 21.6 + - + +
291B TYR 4.9 1.6 - - - +
292B LEU* 5.2 11.3 - - + +
293B PRO* 4.3 25.2 - - + +
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A THR 4.9 0.2 - - - -
113A LEU* 3.5 30.7 - - + -
114A GLU 3.3 27.8 - - - -
115A ASP* 3.6 15.0 - - + -
116A LYS 5.6 0.2 - - - -
133A ALA* 4.2 13.5 - - + -
134A ASP 3.0 11.6 + - - +
135A ILE 3.8 6.3 - - - +
137A GLU* 1.3 78.4 - - - +
139A ALA* 1.3 56.6 + - - +
141A LYS* 3.2 31.0 + - - +
142A ILE* 2.9 59.3 + - + +
158A ALA* 3.9 4.3 - - + -
159A ARG 4.7 0.9 - - - -
179A TYR* 3.3 43.5 - + + +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE 3.0 12.5 + - - +
136A GLU* 3.5 12.6 - - - +
137A GLU 3.0 0.2 - - - -
138A PHE* 1.3 75.7 - - - +
140A LEU* 1.3 61.5 + - + +
142A ILE* 3.0 6.2 + - - +
143A LYS* 2.8 25.7 + - - +
178A ALA* 4.1 14.1 - - + +
179A TYR* 4.1 11.2 - - + -
182A ALA* 3.4 24.9 - - + +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLU* 3.5 18.8 - - + +
137A GLU 2.9 7.2 + - - +
139A ALA* 1.3 78.4 - - + +
141A LYS* 1.3 52.8 + - - +
143A LYS* 3.2 12.9 + - + +
144A ALA* 2.6 38.5 + - - +
290B LYS 3.7 16.2 - - - +
291B TYR* 3.4 40.5 - - + +
292B LEU 3.6 1.6 - - - +
293B PRO* 3.5 32.1 - - + -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A THR* 2.9 32.0 + - - +
91A GLY 2.9 18.0 + - - +
92A ASN* 3.9 13.8 - - - +
93A PHE* 3.9 17.6 - - + +
96A ALA* 3.7 28.5 - - + -
113A LEU* 4.1 11.0 - - + -
116A LYS 5.2 4.6 + - - -
137A GLU* 3.1 21.1 + - + +
138A PHE* 3.3 34.6 - - + +
139A ALA 3.1 0.2 - - - -
140A LEU* 1.3 78.4 - - - +
142A ILE* 1.3 63.2 + - - +
144A ALA* 3.2 1.2 + - - +
145A CYS* 2.9 28.5 + - - -
291B TYR 5.0 0.2 + - - -
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 4.7 10.5 - - + -
138A PHE* 2.9 54.8 + - + +
139A ALA* 3.0 10.1 + - - +
141A LYS* 1.3 76.7 - - - +
143A LYS* 1.3 63.5 + - - +
145A CYS* 3.1 7.4 + - - +
146A LYS* 3.0 29.6 + - + +
156A ILE* 4.2 16.1 - - + +
158A ALA* 3.8 13.9 - - + -
179A TYR* 3.9 15.9 - - + +
182A ALA* 3.9 7.9 - - + +
184A ALA* 3.7 32.3 - - + +
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ALA 2.8 19.2 + - - +
140A LEU* 3.6 14.8 - - + +
142A ILE* 1.3 75.3 - - - +
144A ALA* 1.3 56.8 + - - +
146A LYS* 3.2 4.1 + - - +
147A ASP* 2.8 66.8 + - - +
182A ALA* 3.5 24.1 + - + +
291B TYR* 4.3 8.1 - - + -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.8 22.2 - - + +
97A ARG* 4.5 3.4 - - - -
140A LEU 2.6 21.5 + - - +
141A LYS 3.7 4.0 - - - +
143A LYS* 1.3 72.3 - - - +
145A CYS* 1.3 56.5 + - - +
147A ASP* 3.9 0.7 - - - +
148A SER* 2.5 36.3 + - - +
291B TYR* 3.4 41.1 + - + -
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Residues in contact with CYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ALA* 3.6 30.7 - - - -
97A ARG* 4.2 2.2 - - - -
100A VAL* 3.9 28.6 - - + +
113A LEU* 3.9 17.9 - - - -
141A LYS 2.9 22.5 + - - -
142A ILE* 3.1 8.3 + - - +
144A ALA* 1.3 74.5 - - - +
146A LYS* 1.3 64.8 + - - +
148A SER* 3.3 14.4 + - - -
149A GLN* 3.3 19.0 + - - +
156A ILE* 3.9 14.8 - - + -
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Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 4.4 4.0 - - - +
142A ILE* 3.0 25.1 + - + +
143A LYS* 3.6 8.1 - - + +
145A CYS* 1.3 75.5 - - - +
147A ASP* 1.3 64.5 + - - +
148A SER 3.3 0.7 + - - -
149A GLN* 2.8 66.8 + - - +
152A PRO 5.0 1.8 + - - -
154A PHE 3.8 2.2 + - - -
156A ILE* 3.4 15.3 - - + -
182A ALA 4.3 1.8 - - - +
183A GLY* 3.0 40.1 + - - +
184A ALA 4.0 1.1 - - - +
185A ASP* 2.9 31.3 + - - +
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Residues in contact with ASP 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS* 2.8 62.0 + - - +
144A ALA 3.9 1.6 - - - +
146A LYS* 1.3 72.9 - - - +
148A SER* 1.3 61.7 + - - +
149A GLN 3.5 5.4 + - - +
290B LYS* 5.8 0.2 - - - +
291B TYR* 2.9 29.6 + - - +
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 3.2 40.4 + - - +
100A VAL* 5.0 3.8 - - - -
101A ARG* 4.6 14.4 - - - +
144A ALA 2.5 23.7 + - - -
145A CYS 3.6 5.8 - - - -
146A LYS 3.2 0.2 - - - -
147A ASP* 1.3 74.9 - - - +
149A GLN* 1.3 67.4 + - - +
150A THR* 3.6 7.8 + - - +
291B TYR* 5.4 1.6 + - - -
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Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.0 6.0 - - + +
104A GLU* 3.3 14.8 - - - +
145A CYS 3.3 8.5 + - - +
146A LYS* 2.8 58.2 + - - +
147A ASP 3.9 5.9 - - - +
148A SER* 1.3 81.8 - - - +
150A THR* 1.3 62.4 + - - +
151A ASP 3.0 13.7 - - - +
152A PRO* 3.7 7.2 - - + +
154A PHE* 2.9 42.8 + - + +
156A ILE* 3.5 10.9 - - - +
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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