Contacts of the helix formed by residues 144 - 154 (chain A) in PDB entry 5Z7R
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ASN* 3.3 11.8 + - - -
114A GLU* 4.4 1.1 - - - -
143A PHE* 1.3 76.8 - - - +
145A GLY* 1.3 65.5 + - - +
147A GLN* 2.8 15.4 + - - +
148A ARG* 3.0 21.6 + - - +
226B LEU* 3.6 13.5 - - - -
229B GLU* 2.9 20.8 + - - -
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Residues in contact with GLY 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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114A GLU* 2.8 30.4 + - - +
117A MET* 4.1 9.6 - - - -
132A GLN* 4.2 4.0 - - - -
141A PRO* 3.6 9.6 - - - +
144A GLY* 1.3 77.7 - - - +
146A THR* 1.3 60.5 + - - +
147A GLN 3.1 1.2 + - - -
149A LEU* 3.3 28.6 + - - +
162A ILE* 3.9 6.3 - - - +
229B GLU* 3.2 1.4 + - - -
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Residues in contact with THR 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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140A THR* 4.4 6.3 - - - -
141A PRO* 3.8 32.5 - - + +
144A GLY 3.0 0.2 + - - -
145A GLY* 1.3 73.7 - - - +
147A GLN* 1.3 81.8 + - - +
150A SER* 3.8 8.2 + - - -
162A ILE* 4.1 4.3 - - + -
210B SER* 4.7 5.8 - - - -
213B ALA* 3.7 20.1 - - + +
214B ILE* 3.3 33.7 - - + +
229B GLU* 2.8 29.0 + - + +
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Residues in contact with GLN 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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144A GLY 2.8 7.1 + - - +
146A THR* 1.3 108.2 + - - +
148A ARG* 1.3 62.7 + - - +
149A LEU 3.5 0.9 - - - -
150A SER* 3.3 11.4 + - - -
151A ARG* 3.0 51.0 + - - +
213B ALA* 2.8 28.1 + - - +
214B ILE 4.7 0.2 - - - +
217B GLY* 3.0 21.8 - - - +
218B MET* 3.4 1.9 + - - +
222B ILE* 3.9 12.3 - - + -
225B ALA* 3.4 35.1 + - + +
226B LEU* 4.1 12.1 - - + +
228B PHE* 5.5 0.2 - - - +
229B GLU* 4.7 2.4 - - + +
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Residues in contact with ARG 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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87A ASN* 4.1 3.2 + - - -
90A PHE* 4.2 4.8 - - - +
91A ARG* 3.7 27.3 - - - +
94A GLU* 2.6 43.1 + - - +
114A GLU* 4.8 1.3 + - - -
117A MET* 3.5 41.5 - - + +
118A SER* 3.4 23.5 + - - +
143A PHE 3.8 17.6 + - - -
144A GLY* 3.0 13.9 + - - +
147A GLN* 1.3 78.6 - - + +
149A LEU* 1.3 66.7 + - - +
151A ARG* 3.2 7.7 + - - +
152A LEU* 2.9 27.5 + - + +
222B ILE* 4.6 11.6 - - + +
226B LEU* 3.9 24.1 - - + +
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Residues in contact with LEU 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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113A CYS* 5.0 3.8 - - - -
117A MET* 3.6 26.5 - - + -
132A GLN* 4.4 11.4 - - + -
145A GLY 3.3 16.5 + - - +
148A ARG* 1.3 77.7 - - - +
150A SER* 1.3 54.4 + - - +
152A LEU* 2.8 4.8 + - - +
153A VAL* 2.7 55.8 + - + +
158A ALA* 3.6 34.5 - - + +
161A LEU* 4.0 25.8 - - + -
162A ILE* 4.1 13.2 - - + -
178A LEU* 4.1 11.0 - - + -
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Residues in contact with SER 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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145A GLY 4.8 0.6 + - - -
146A THR 3.8 11.1 + - - -
147A GLN* 3.3 11.6 + - - -
149A LEU* 1.3 76.7 - - - +
151A ARG* 1.3 59.8 + - - +
154A GLY* 2.9 33.6 + - - -
155A MET* 4.0 8.2 + - - -
158A ALA* 3.3 21.6 - - - +
214B ILE* 4.3 17.2 - - - +
218B MET* 3.3 26.4 - - - +
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Residues in contact with ARG 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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147A GLN* 3.0 52.4 + - - +
148A ARG* 3.2 8.0 + - - +
149A LEU 3.1 0.8 - - - -
150A SER* 1.3 85.3 + - - +
152A LEU* 1.3 66.7 + - + +
154A GLY 4.8 0.5 + - - -
219A GLN* 4.9 4.6 + - - +
217B GLY 3.0 11.7 + - - -
218B MET* 4.0 29.9 + - + +
220B CYS 2.7 29.7 + - - -
222B ILE* 3.6 30.3 - - - +
225B ALA* 3.9 5.9 - - - +
154C GLY* 5.6 4.9 - - - -
155C MET* 5.6 6.4 + - + +
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Residues in contact with LEU 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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117A MET* 3.8 38.8 - - + +
122A ARG* 3.5 35.9 - - - +
148A ARG* 2.9 20.1 + - + +
149A LEU* 2.8 6.9 + - - +
151A ARG* 1.3 86.3 - - + +
153A VAL* 1.3 67.4 + - + +
154A GLY 3.6 0.4 - - - -
176A ILE 4.1 4.7 - - - +
177A GLY* 4.5 10.8 - - - +
178A LEU* 4.8 4.3 - - + +
154C GLY* 5.6 5.4 - - - -
155C MET* 4.1 33.0 - - + +
156C GLY 4.6 3.6 - - - +
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Residues in contact with VAL 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 LEU* 2.7 36.0 + - + +
152A LEU* 1.3 77.1 - - + +
154A GLY* 1.3 65.7 + - - +
157A MET* 3.7 18.4 + - + +
158A ALA 3.6 17.0 - - - +
161A LEU* 5.3 0.2 - - + -
176A ILE* 3.7 45.2 - - + +
178A LEU* 3.8 29.8 - - + -
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Residues in contact with GLY 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 SER 2.9 17.6 + - - -
151A ARG 4.6 0.4 - - - -
152A LEU 3.6 1.4 - - - -
153A VAL* 1.3 83.6 - - - +
155A MET* 1.3 65.7 + - - -
156A GLY 3.4 2.4 + - - -
157A MET 3.6 0.2 + - - -
158A ALA* 3.3 21.1 + - - +
151B ARG 5.4 5.8 - - - -
152B LEU 5.4 6.5 - - - -
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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