Contacts of the helix formed by residues 153 - 164 (chain A) in PDB entry 3IO6
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 GLU 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ASN* 3.3 26.7 + - - +
151A LEU 3.3 0.9 - - - -
152A GLN* 1.3 86.5 - - + +
154A PRO* 1.3 71.2 - - - +
155A TYR* 4.2 8.9 - - + +
156A PHE* 3.4 18.6 + - + +
157A THR* 3.1 23.8 + - - +
344A ARG* 3.3 36.1 + - - -
347A VAL* 6.0 0.9 - - - -
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Residues in contact with PRO 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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153A GLU* 1.3 89.8 - - + +
155A TYR* 1.3 61.3 + - - +
156A PHE 3.0 2.9 - - - -
157A THR* 3.3 9.9 - - - +
158A TRP* 2.8 36.9 + - + +
339A PHE* 5.6 0.2 - - + -
340A TRP* 3.7 31.0 - - + +
343A VAL* 3.8 20.4 - - + -
344A ARG* 3.6 49.1 - - + +
347A VAL* 5.3 2.4 - - + -
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Residues in contact with TYR 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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111A GLU* 4.8 5.4 + - - +
113A LEU* 3.2 36.2 + - + +
153A GLU* 3.2 9.6 - - + +
154A PRO* 1.3 80.2 - - - +
156A PHE* 1.3 78.8 + + + +
158A TRP* 4.6 1.2 - - - +
159A PRO* 3.7 8.0 - - - +
230A TRP* 3.7 36.4 - + - -
258A PHE* 3.7 49.3 + + + -
260A GLY 5.5 1.2 + - - -
330A MET* 4.0 15.9 - - + -
340A TRP* 3.7 17.0 - + + -
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Residues in contact with PHE 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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113A LEU* 3.8 22.6 - - + +
149A PHE* 3.9 13.5 - + + -
150A ASN* 3.2 52.7 - - + +
153A GLU* 3.4 11.8 + - + +
154A PRO 3.0 0.8 - - - -
155A TYR* 1.3 98.5 - + + +
157A THR* 1.3 59.7 + - - +
158A TRP 3.4 0.7 - - - -
159A PRO* 3.3 15.7 - - - +
210A TYR* 3.8 26.7 - + - -
226A ILE* 3.6 35.5 - - + +
227A ASN* 3.9 11.7 - - - -
230A TRP* 4.2 12.1 - + - -
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Residues in contact with THR 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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149A PHE* 4.0 9.0 - - + -
150A ASN 4.0 0.4 - - - +
151A LEU* 3.8 44.0 - - + +
153A GLU 3.1 17.8 + - - +
154A PRO* 3.3 12.1 - - - +
156A PHE* 1.3 75.5 - - - +
158A TRP* 1.3 64.2 + - - +
159A PRO* 3.3 1.3 - - - -
160A LEU* 3.1 18.6 + - - +
161A ILE* 3.5 17.2 + - - +
195A LEU* 3.9 20.0 - - + +
347A VAL* 4.0 16.4 - - + +
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Residues in contact with TRP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PRO* 2.8 18.8 + - + +
155A TYR 4.6 0.2 - - - +
157A THR* 1.3 78.5 + - - +
159A PRO* 1.3 62.2 - - + +
160A LEU 3.0 0.3 + - - -
161A ILE* 3.1 28.2 + - + -
162A ALA* 2.8 50.1 + - + +
166A GLY* 4.7 2.7 - - - -
167A TYR* 3.7 35.8 - - - +
168A ALA 4.8 1.8 - - - +
182A GLY 4.4 2.2 - - - -
183A VAL* 4.1 18.4 - - + -
188A ALA* 5.3 0.7 - - + -
256A LYS 3.9 10.1 + - - -
257A PRO 5.4 0.2 - - - -
258A PHE* 3.2 41.3 - + + -
328A GLU* 5.9 4.0 - - + +
339A PHE* 3.8 31.2 - + - -
340A TRP* 5.5 0.2 - - + -
343A VAL* 4.2 24.9 - - + -
361A LEU* 6.0 1.1 - - + -
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Residues in contact with PRO 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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113A LEU* 4.0 11.9 - - + -
129A TRP* 6.0 2.2 - - + -
155A TYR 3.7 5.2 - - - +
156A PHE 3.3 21.8 - - - +
157A THR 3.4 0.4 - - - -
158A TRP* 1.3 93.7 - - + +
160A LEU* 1.3 55.5 + - - +
163A ALA* 3.3 15.4 + - - +
226A ILE* 5.6 5.6 - - + -
247A LEU* 4.2 18.6 - - + -
255A SER* 3.4 8.1 - - - -
256A LYS 3.2 36.7 + - - +
257A PRO* 3.7 24.2 - - + -
258A PHE 5.5 0.2 - - - +
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Residues in contact with LEU 160 (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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129A TRP* 3.6 55.2 - - + -
149A PHE* 6.2 1.1 - - + -
157A THR* 3.1 10.1 + - - +
158A TRP 3.0 1.0 - - - -
159A PRO* 1.3 78.5 - - - +
161A ILE* 1.3 67.5 + - + +
162A ALA 3.4 0.4 - - - -
163A ALA* 3.4 11.4 + - + +
164A ASP 4.4 1.0 + - - -
191A GLY* 3.9 20.8 - - - +
194A PHE* 4.0 15.7 - - + -
195A LEU* 3.8 37.7 - - + -
250A PHE* 3.9 24.8 - - + -
255A SER* 4.7 1.1 - - - -
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Residues in contact with ILE 161 (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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157A THR* 3.6 24.5 - - - +
158A TRP* 3.1 28.6 + - + +
160A LEU* 1.3 79.8 - - + +
162A ALA* 1.3 61.8 + - - +
163A ALA 3.5 0.2 + - - -
164A ASP 4.1 1.0 + - - -
187A GLY 3.8 5.0 - - - +
188A ALA* 3.2 55.3 + - + +
191A GLY* 4.2 6.9 - - - -
192A LEU* 3.9 26.9 - - + +
195A LEU* 4.7 5.2 - - + -
343A VAL* 5.2 1.1 - - + -
347A VAL* 3.7 30.3 - - + -
361A LEU* 5.0 8.1 - - + -
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Residues in contact with ALA 162 (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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158A TRP* 2.8 43.6 + - + +
161A ILE* 1.3 77.3 - - - +
163A ALA* 1.3 56.4 + - - +
164A ASP 3.2 0.2 - - - -
165A GLY* 2.8 25.2 + - - -
166A GLY* 3.1 28.4 + - - +
256A LYS* 3.5 24.4 - - + +
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Residues in contact with ALA 163 (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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159A PRO 3.3 20.4 + - - +
160A LEU* 3.4 13.0 - - - +
161A ILE 3.3 1.0 - - - -
162A ALA* 1.3 78.1 - - - +
164A ASP* 1.3 58.8 + - - +
165A GLY* 3.5 0.5 + - - -
250A PHE* 4.4 20.0 - - + -
253A GLN* 3.1 25.6 - - - +
254A PRO 3.8 20.9 - - - +
255A SER* 4.0 5.6 - - - +
256A LYS* 4.3 7.4 - - - +
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Residues in contact with ASP 164 (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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160A LEU 4.4 1.0 + - - -
161A ILE 4.1 2.8 + - - +
162A ALA 3.2 0.8 - - - -
163A ALA* 1.3 78.3 - - - +
165A GLY* 1.3 56.4 + - - +
186A ALA 3.8 6.2 - - - +
187A GLY* 3.2 36.1 + - - +
190A ALA* 4.2 5.7 - - - +
250A PHE* 3.9 17.0 - - + -
251A LYS* 3.3 38.0 - - - +
253A GLN* 4.4 12.0 - - - +
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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