Contacts of the helix formed by residues 147 - 159 (chain A) in PDB entry 1A4I
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 CYS 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A VAL 3.7 16.2 - - - -
125A ASP* 3.6 24.9 + - - +
145A ILE 4.1 3.4 - - - -
146A PRO* 1.3 73.2 - - - +
148A THR* 1.3 58.2 + - - +
150A LYS* 3.6 3.4 - - - +
151A GLY* 3.0 23.9 + - - -
279A THR* 3.5 31.8 - - + +
282A MET* 3.7 13.8 - - + +
283A LEU* 3.5 31.2 - - + +
286A SER* 4.9 1.3 - - - -
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Residues in contact with THR 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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146A PRO* 4.8 0.2 - - - +
147A CYS* 1.3 73.2 - - - +
149A PRO* 1.3 74.5 - - - +
151A GLY* 3.0 4.5 + - - -
152A CYS* 2.9 20.8 + - - -
176A ILE* 4.4 4.3 + - - +
177A VAL* 3.9 32.5 - - + -
236A CYS* 4.0 8.3 - - + -
275A VAL* 3.8 23.7 - - + +
279A THR* 3.1 22.2 + - - +
302A NDP 3.3 23.9 - - + -
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Residues in contact with PRO 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 ILE* 4.8 0.7 - - + -
146A PRO* 3.3 14.1 - - + +
148A THR* 1.3 97.3 - - + +
150A LYS* 1.4 61.8 + - - +
152A CYS* 3.2 2.1 + - - +
153A LEU 2.8 19.9 + - - -
176A ILE 3.4 12.1 - - - +
177A VAL* 3.7 9.9 - - + +
180A PRO* 3.6 32.1 - - + -
181A MET* 3.8 29.6 - - - +
184A LEU* 3.4 24.3 - - + +
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Residues in contact with LYS 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 ILE* 3.3 56.5 - - + +
146A PRO 3.1 11.9 + - - +
147A CYS* 3.6 7.4 - - - +
148A THR 3.3 0.2 - - - -
149A PRO* 1.4 76.9 - - - +
151A GLY* 1.3 62.0 + - - +
153A LEU* 3.3 4.7 + - - +
154A GLU* 3.1 22.3 + - - +
184A LEU* 3.9 7.5 - - + +
282A MET* 3.7 24.5 - - + +
285A GLN* 3.7 26.7 - - - +
286A SER* 4.0 19.9 + - - +
289A GLU* 5.4 5.2 + - - -
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Residues in contact with GLY 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 CYS 3.0 12.1 + - - -
148A THR 3.0 4.0 + - - -
150A LYS* 1.3 72.5 - - - +
152A CYS* 1.3 59.6 + - - +
154A GLU* 3.3 3.1 + - - +
155A LEU* 3.0 33.6 + - - +
275A VAL* 5.6 1.1 - - - -
278A MET* 3.8 24.7 - - - +
279A THR* 4.8 1.1 - - - -
282A MET* 3.5 16.5 - - - +
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Residues in contact with CYS 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 THR* 2.9 19.0 + - - -
149A PRO* 3.2 2.0 + - - +
151A GLY* 1.3 73.7 - - - +
153A LEU* 1.3 64.0 + - - +
155A LEU* 3.1 7.1 + - - +
156A ILE* 3.0 28.6 + - + +
177A VAL* 5.4 0.4 - - - -
181A MET* 3.4 29.6 - - + -
213A VAL* 4.3 2.0 - - + -
234A ILE* 3.6 24.3 - - + +
236A CYS* 3.5 32.5 - - - -
275A VAL* 4.0 9.4 - - - -
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Residues in contact with LEU 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 PRO 2.8 16.7 + - - +
150A LYS* 3.7 5.4 - - - +
152A CYS* 1.3 75.5 - - - +
154A GLU* 1.3 56.5 + - - +
156A ILE* 3.2 7.9 + - + +
157A LYS* 2.9 49.7 + - + +
163A ILE* 3.5 31.4 - - + -
181A MET* 4.2 2.6 - - + +
184A LEU* 4.0 27.6 - - + -
185A LEU* 4.7 13.5 - - + -
188A ASN* 3.9 27.1 - - + +
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Residues in contact with GLU 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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12A ILE* 4.8 5.5 - - + +
16A ILE* 4.2 19.7 - - + +
19A ARG* 5.1 4.5 + - - -
150A LYS 3.1 12.3 + - - +
151A GLY* 3.7 3.8 - - - +
152A CYS 3.2 0.2 - - - -
153A LEU* 1.3 76.9 - - - +
155A LEU* 1.3 60.8 + - - +
157A LYS* 3.2 20.4 + - - +
158A GLU* 3.0 28.5 + - + +
278A MET* 3.6 26.2 - - + -
282A MET* 4.9 10.0 - - + +
285A GLN* 6.1 0.2 - - - -
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Residues in contact with LEU 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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7A LEU* 3.7 29.8 - - + +
9A GLY* 4.3 7.2 - - - -
12A ILE* 3.7 27.6 - - + -
151A GLY 3.0 21.1 + - - +
152A CYS* 3.1 7.6 + - - +
154A GLU* 1.3 74.4 - - - +
156A ILE* 1.3 62.7 + - - +
158A GLU* 3.1 18.3 + - - +
159A THR 3.7 2.9 + - - -
234A ILE* 4.1 12.6 - - + -
269A THR* 4.0 10.5 - - + -
274A GLY 4.1 1.8 - - - +
275A VAL* 3.8 32.8 - - + -
278A MET* 3.9 29.4 - - + -
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Residues in contact with ILE 156 (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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152A CYS 3.0 24.3 + - - +
153A LEU* 3.6 10.3 - - + +
155A LEU* 1.3 74.6 - - - +
157A LYS* 1.3 60.3 + - - +
159A THR* 2.7 34.8 + - - +
160A GLY 4.1 0.2 + - - -
161A VAL 4.6 3.6 - - - +
163A ILE* 3.8 28.9 - - + -
181A MET* 4.5 2.5 - - + -
185A LEU* 4.0 16.8 - - + -
211A ILE* 3.8 34.3 - - + -
213A VAL* 4.3 8.3 - - + -
232A ILE* 4.3 14.8 - - + -
234A ILE* 3.8 22.7 - - + -
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Residues in contact with LYS 157 (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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153A LEU* 2.9 42.4 + - + +
154A GLU* 3.6 22.6 + - - +
155A LEU 3.2 0.2 - - - -
156A ILE* 1.3 76.8 - - - +
158A GLU* 1.4 55.6 + - - +
160A GLY* 2.9 22.2 + - - +
161A VAL 5.5 2.9 - - - -
163A ILE* 4.5 14.1 - - + -
188A ASN* 4.4 14.9 + - - -
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Residues in contact with GLU 158 (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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7A LEU* 4.2 9.2 - - + +
12A ILE* 3.8 49.3 - - + +
15A GLN* 5.1 4.8 - - - +
154A GLU* 3.0 22.5 + - + +
155A LEU 3.1 13.4 + - - +
157A LYS* 1.4 72.7 - - - +
159A THR* 1.3 63.2 + - - +
160A GLY 3.2 0.4 + - - -
267A PHE* 5.2 1.4 - - - -
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Residues in contact with THR 159 (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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7A LEU* 3.9 4.5 - - + -
155A LEU 3.9 8.7 - - - +
156A ILE 2.7 20.7 + - - +
158A GLU* 1.3 79.1 - - - +
160A GLY* 1.3 58.5 + - - +
161A VAL* 3.0 26.8 + - - +
232A ILE* 3.6 20.5 - - + +
267A PHE* 3.5 62.3 - - + -
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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