Contacts of the helix formed by residues 140 - 155 (chain A) in PDB entry 5M2C
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 ALA 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLN* 3.9 17.3 - - + +
134A ALA* 4.8 0.3 - - - -
137A ASP* 3.0 34.8 + - + +
139A ASP* 1.3 72.2 - - - +
141A ASN* 1.3 62.9 + - - +
142A ASN* 3.4 2.9 - - - -
143A ALA* 3.3 13.3 + - + +
144A LYS* 3.2 25.9 + - - +
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ASP 3.9 5.9 - - - +
139A ASP* 2.7 34.4 + - - +
140A ALA* 1.3 70.5 - - - +
142A ASN* 1.3 67.2 + - - +
144A LYS* 3.4 13.9 + - - +
145A ALA* 3.1 23.6 + - - +
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Residues in contact with ASN 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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126A PHE* 6.2 0.4 - - - -
133A GLN* 5.9 0.6 + - - -
140A ALA 3.4 0.6 - - - -
141A ASN* 1.3 76.3 - - - +
143A ALA* 1.3 64.8 + - - +
145A ALA* 3.2 7.6 + - - +
146A VAL* 2.9 34.1 + - - +
199B SER* 3.8 17.5 - - - +
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Residues in contact with ALA 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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130A ALA* 3.7 14.6 - - - +
133A GLN* 3.6 39.3 - - + +
134A ALA* 3.9 6.3 - - - +
140A ALA* 3.3 15.0 + - + +
141A ASN 3.3 0.2 - - - -
142A ASN* 1.3 84.8 - - - +
144A LYS* 1.3 62.7 + - - +
146A VAL* 3.2 6.3 + - - +
147A VAL* 2.9 28.2 + - - +
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Residues in contact with LYS 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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134A ALA* 3.3 31.4 + - + +
137A ASP 4.9 0.4 - - - +
138A ASP* 2.8 43.4 + - - +
140A ALA 3.2 14.2 + - - +
141A ASN* 3.7 16.4 - - - +
143A ALA* 1.3 77.1 - - - +
145A ALA* 1.3 58.0 + - - +
147A VAL* 3.4 1.6 + - - +
148A LYS* 2.9 31.4 + - - +
171A LYS* 3.3 19.2 - - - +
173A ASN* 4.1 22.2 - - - +
174A LEU* 3.8 15.0 - - + +
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Residues in contact with ALA 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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141A ASN 3.1 13.7 + - - +
142A ASN* 3.2 10.7 + - - +
144A LYS* 1.3 73.3 - - - +
146A VAL* 1.3 61.5 + - - +
148A LYS* 3.9 4.9 - - - +
149A THR* 2.7 32.9 + - - -
199B SER 4.9 2.2 - - - +
200B GLY* 3.5 21.3 - - - +
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Residues in contact with VAL 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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126A PHE* 3.6 32.3 - - + -
127A TYR* 6.0 0.4 - - + -
130A ALA* 3.9 16.4 - - + -
142A ASN* 2.9 35.0 + - - +
143A ALA* 3.7 4.3 - - - +
145A ALA* 1.3 75.4 - - - +
147A VAL* 1.3 63.3 + - - +
149A THR* 3.2 2.8 + - - -
150A PHE* 2.9 37.3 + - + -
197B LEU 4.4 2.2 - - - +
198B PHE 3.7 18.4 - - - +
199B SER 4.0 13.2 - - - +
200B GLY* 3.8 6.5 - - - -
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Residues in contact with VAL 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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127A TYR* 5.0 4.3 - - + +
130A ALA* 3.5 35.7 - - + +
131A LEU* 3.5 17.7 - - + +
134A ALA* 3.8 6.1 - - + -
143A ALA 2.9 20.4 + - - +
144A LYS* 3.7 3.4 - - - +
146A VAL* 1.3 77.2 - - - +
148A LYS* 1.3 57.6 + - - +
150A PHE* 3.3 5.6 + - - +
151A HIS* 2.9 64.0 + - + +
174A LEU* 4.3 16.4 - - + -
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Residues in contact with LYS 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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144A LYS 2.9 18.8 + - - +
145A ALA* 3.9 5.6 - - - +
147A VAL* 1.3 76.9 - - - +
149A THR* 1.3 58.2 + - - +
151A HIS* 3.4 1.2 + - - +
152A GLU* 2.9 42.7 + - + +
173A ASN* 3.2 22.6 + - - +
174A LEU* 3.8 17.2 - - + +
175A CYS 3.3 24.5 + - - -
177A SER* 4.5 8.5 - - - +
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Residues in contact with THR 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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145A ALA 2.7 22.5 + - - -
146A VAL 3.6 3.1 - - - -
148A LYS* 1.3 75.5 - - - +
150A PHE* 1.3 59.0 + - - +
152A GLU* 3.9 4.1 - - + +
153A THR* 2.6 46.5 + - - +
196B ASP* 4.0 1.6 - - + +
197B LEU* 4.0 26.0 - - - -
200B GLY* 3.4 20.2 + - - -
201B LYS 3.5 18.7 + - - +
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Residues in contact with PHE 150 (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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123A VAL* 3.9 20.4 - - + -
126A PHE* 4.0 14.1 - + - -
127A TYR* 3.9 37.9 - + + -
146A VAL* 2.9 37.0 + - + +
147A VAL 3.6 7.4 - - - +
149A THR* 1.3 76.7 - - - +
151A HIS* 1.3 57.4 + - - +
153A THR 3.8 0.2 - - - -
154A LEU* 2.9 56.1 + - + +
194A ILE* 4.3 4.7 - - + -
197B LEU* 3.5 49.1 - - + -
198B PHE* 4.0 21.3 - + - -
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Residues in contact with HIS 151 (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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127A TYR* 2.6 37.0 + + - -
131A LEU* 4.3 6.3 - - + -
147A VAL* 2.9 37.2 + - + +
148A LYS 3.7 2.0 - - - +
150A PHE* 1.3 75.6 - - - +
152A GLU* 1.3 57.8 + - - +
155A ASP* 2.8 31.5 + - - -
156A CYS* 3.0 23.4 + - - +
157A CYS* 3.5 27.8 - - - -
167A THR* 4.7 0.7 - - + -
174A LEU* 2.7 31.5 + - + +
176A PRO* 3.5 10.2 - - + +
190A CYS* 3.4 11.9 - - - -
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Residues in contact with GLU 152 (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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148A LYS* 2.9 26.9 + - + +
149A THR* 4.1 4.3 - - - +
151A HIS* 1.3 77.7 - - - +
153A THR* 1.3 64.1 + - - +
155A ASP* 3.8 6.8 + - - +
176A PRO* 3.3 12.0 - - + +
177A SER* 3.1 36.5 + - - +
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Residues in contact with THR 153 (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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149A THR* 2.6 33.2 + - - +
150A PHE 3.8 2.5 - - - -
152A GLU* 1.3 80.6 - - - +
154A LEU* 1.3 62.9 + - + +
155A ASP* 5.3 0.3 - - - +
153B THR* 3.6 42.8 - - + +
154B LEU* 4.2 15.5 - - + -
197B LEU* 4.1 14.7 - - + +
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Residues in contact with LEU 154 (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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150A PHE* 2.9 37.4 + - + +
153A THR* 1.3 80.7 - - + +
155A ASP* 1.3 69.7 + - - +
156A CYS* 3.7 18.2 - - - -
190A CYS* 4.5 3.4 - - + +
193A LYS* 3.1 47.7 + - + +
194A ILE* 3.7 29.8 - - + -
197A LEU* 4.7 15.5 - - + -
153B THR* 4.2 22.2 - - + -
197B LEU* 5.6 3.8 - - + -
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Residues in contact with ASP 155 (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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151A HIS 2.8 14.3 + - - -
152A GLU 3.8 6.1 + - - +
153A THR 3.5 2.9 - - - +
154A LEU* 1.3 81.1 - - - +
156A CYS* 1.3 56.4 + - - +
176A PRO* 3.7 14.9 - - - +
187A LYS* 3.2 42.0 + - - +
193A LYS* 3.6 15.1 + - - +
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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