Contacts of the helix formed by residues 147 - 159 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL 5.6 0.4 + - - -
125B ASP* 4.5 16.0 + - - +
145B ILE 3.4 3.5 + - - -
146B PRO* 1.3 74.4 - - - +
148B THR* 1.3 73.3 + - - +
150B LYS* 4.2 0.7 - - - -
151B GLY* 3.0 18.5 + - - -
176B ILE* 6.3 2.0 - - - -
279B THR* 3.4 38.1 - - - +
282B MET* 3.5 20.0 - - + +
283B LEU* 4.3 11.2 - - + +
302B NDP 6.0 0.4 - - - -
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B PRO* 4.8 0.4 - - - +
147B CYS* 1.3 83.2 - - - +
149B PRO* 1.3 71.9 - - - +
151B GLY* 3.1 3.3 + - - -
152B CYS* 2.9 23.6 + - - -
176B ILE* 4.4 4.6 + - - +
177B VAL* 3.8 31.0 - - + -
236B CYS* 4.0 7.2 - - + -
275B VAL* 3.8 24.1 - - + +
279B THR* 3.9 13.8 - - + +
302B NDP 3.2 30.2 - - + -
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Residues in contact with PRO 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 4.7 1.1 - - + -
146B PRO* 3.3 16.8 - - + +
148B THR* 1.3 96.2 - - - +
150B LYS* 1.3 60.0 + - - -
152B CYS* 3.1 3.8 + - + +
153B LEU 2.9 19.6 + - - -
176B ILE 3.3 15.5 - - - +
177B VAL* 4.0 8.5 - - + +
180B PRO* 3.8 28.0 - - + -
181B MET* 3.8 37.4 - - - +
184B LEU* 3.4 17.1 - - + +
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.7 46.6 - - + +
146B PRO 3.1 18.7 + - - +
147B CYS* 3.6 5.6 - - - +
149B PRO* 1.3 74.7 - - - +
151B GLY* 1.3 60.5 + - - +
153B LEU* 3.3 4.9 + - + +
154B GLU* 3.1 22.0 + - - +
184B LEU* 4.2 3.1 - - - -
282B MET* 3.7 21.9 - - + +
285B GLN* 3.3 28.2 + - - +
286B SER* 3.6 22.3 + - - +
289B GLU* 2.9 30.5 + - - -
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B CYS 3.0 11.4 + - - -
148B THR* 3.1 3.1 + - - -
150B LYS* 1.3 74.1 - - - +
152B CYS* 1.3 64.6 + - - +
154B GLU* 3.3 2.4 + - - +
155B LEU* 3.0 32.4 + - - +
275B VAL* 5.4 2.2 - - - -
278B MET* 3.8 17.7 - - - +
282B MET* 3.5 21.5 - - - +
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Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR 2.9 19.1 + - - -
149B PRO* 3.4 2.7 - - - +
151B GLY* 1.3 76.6 - - - +
153B LEU* 1.3 62.9 + - - +
155B LEU* 3.2 6.8 + - - +
156B ILE* 3.0 27.7 + - - +
177B VAL* 5.2 0.2 - - - -
181B MET* 3.4 24.9 - - + -
213B VAL* 4.2 6.1 - - + -
234B ILE* 3.6 24.1 - - + +
236B CYS* 3.3 34.3 - - - -
275B VAL* 4.0 8.3 - - - -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ILE* 5.4 4.9 - - + -
149B PRO 2.9 13.5 + - - +
150B LYS* 3.7 8.1 - - + +
151B GLY 3.3 0.2 - - - -
152B CYS* 1.3 77.2 - - - +
154B GLU* 1.3 57.2 + - - +
156B ILE* 3.2 6.5 + - + +
157B LYS* 2.9 47.5 + - + +
163B ILE* 3.8 26.5 - - + -
181B MET* 4.1 3.8 - - + +
184B LEU* 4.1 34.3 - - + +
185B LEU* 4.7 11.2 - - + -
188B ASN* 3.7 24.2 - - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.6 34.6 - - + +
19B ARG* 4.9 5.4 + - - -
150B LYS 3.1 13.6 + - - +
151B GLY* 3.6 8.3 - - - +
153B LEU* 1.3 74.3 - - - +
155B LEU* 1.3 58.7 + - - +
157B LYS* 3.2 13.5 + - - +
158B GLU* 2.9 49.3 + - + +
278B MET* 3.7 10.3 - - + -
282B MET* 4.6 7.0 - - + -
285B GLN* 5.1 9.8 + - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.9 19.1 - - + +
9B GLY* 4.5 7.2 - - - +
12B ILE* 3.6 30.3 - - + -
151B GLY 3.0 19.8 + - - +
152B CYS* 3.6 7.2 - - - +
153B LEU 3.2 0.2 - - - -
154B GLU* 1.3 76.0 - - - +
156B ILE* 1.3 63.2 + - - +
158B GLU* 3.1 17.8 + - - +
159B THR* 3.6 9.5 + - - +
234B ILE* 4.3 10.1 - - + -
269B THR* 3.8 21.1 - - + -
274B GLY 4.0 12.3 - - - +
275B VAL* 3.9 23.1 - - + -
278B MET* 3.9 22.2 - - + -
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B CYS 3.0 20.7 + - - +
153B LEU* 3.2 8.9 + - + +
155B LEU* 1.3 72.9 - - - +
157B LYS* 1.3 59.3 + - - +
159B THR* 2.6 35.1 + - - -
161B VAL 4.7 1.4 - - - +
163B ILE* 3.8 30.5 - - + -
166B ARG* 4.3 11.2 - - - +
181B MET* 4.3 7.0 - - + -
185B LEU* 4.0 17.0 - - + -
211B ILE* 3.7 26.5 - - + -
213B VAL* 4.2 9.2 - - + -
232B ILE* 4.2 10.5 - - + -
234B ILE* 3.7 23.6 - - + -
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 2.9 45.6 + - + +
154B GLU* 3.2 13.9 + - - +
156B ILE* 1.3 75.7 - - - +
158B GLU* 1.3 61.4 + - + +
160B GLY* 3.1 16.2 + - - +
161B VAL 5.5 3.1 - - - -
163B ILE* 4.0 15.7 - - + -
188B ASN* 3.1 28.4 + - - +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.5 6.5 - - + +
12B ILE* 4.1 43.7 - - + +
15B GLN* 4.8 6.0 - - - +
16B ILE* 6.1 0.2 - - - +
19B ARG* 4.8 10.5 + - - -
154B GLU* 2.9 35.5 + - + +
155B LEU* 3.1 11.5 + - - +
157B LYS* 1.3 76.4 - - - +
159B THR* 1.3 60.4 + - - +
160B GLY* 3.4 0.7 + - - -
267B PHE* 5.5 0.3 - - - -
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.0 9.2 - - + -
155B LEU 3.7 9.4 - - - +
156B ILE* 2.6 24.0 + - - +
158B GLU* 1.3 77.3 - - - +
160B GLY* 1.3 58.2 + - - +
161B VAL* 3.1 25.8 + - - +
232B ILE* 3.8 12.9 - - + +
267B PHE* 3.5 65.2 - - + -
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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