Contacts of the helix formed by residues 158 - 167 (chain A) in PDB entry 4I06
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 ASN 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLY 3.3 12.3 - - - +
37A GLN* 3.9 11.0 - - - +
38A LYS* 2.8 44.5 + - - +
87A VAL* 3.7 8.9 - - - +
154A THR* 4.6 0.7 + - - -
156A SER* 3.1 25.4 + - - +
157A GLY* 1.3 78.0 - - - +
159A LEU* 1.3 65.4 + - - +
160A HIS* 3.5 19.4 + - + +
161A GLY* 3.1 13.9 + - - -
162A GLN* 3.2 10.2 + - - +
406A X8A 4.5 1.6 + - - +
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Residues in contact with LEU 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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36A GLY* 3.0 10.1 + - - -
86A ILE* 3.8 18.4 - - + -
87A VAL* 3.6 21.2 - - - +
89A PRO* 3.9 14.8 - - + -
92A VAL* 3.7 28.9 - - + -
121A SER* 3.9 18.8 - - - -
124A ILE* 5.2 2.0 - - + +
157A GLY 3.5 1.2 + - - -
158A ASN* 1.3 71.8 - - - +
160A HIS* 1.3 57.4 + - - +
161A GLY 3.0 0.7 - - - -
162A GLN* 3.0 40.9 + - - +
163A PRO* 3.3 11.1 - - - +
166A PHE* 3.9 26.7 - - + -
178A LEU* 4.0 4.5 - - + -
181A PHE* 4.0 7.9 - - + -
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Residues in contact with HIS 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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36A GLY* 2.8 22.8 + - - +
37A GLN* 3.6 23.7 - - + +
119A ASP* 3.5 19.1 - - - +
120A HIS* 3.8 2.3 - - - +
121A SER 3.7 13.7 - - - +
147A ASP* 3.5 4.0 - - - +
158A ASN* 3.1 20.2 + - + +
159A LEU* 1.3 76.2 - - - +
161A GLY* 1.3 60.7 + - - +
162A GLN 3.3 1.3 - - - -
163A PRO* 3.3 12.6 - - - +
264A GLY* 6.2 1.8 - - - -
265A THR* 4.2 10.5 + - - -
296A GLU* 2.8 29.2 + - - +
406A X8A 3.2 47.7 + - + +
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Residues in contact with GLY 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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147A ASP* 3.3 21.1 - - - -
149A ASN* 3.3 21.6 + - - +
158A ASN 3.1 9.2 + - - -
159A LEU 3.0 1.2 - - - -
160A HIS* 1.3 79.8 - - - +
162A GLN* 1.3 61.8 + - - +
163A PRO* 3.6 4.0 - - - -
205A GLU* 4.0 0.5 - - - +
406A X8A 3.8 30.5 - - - -
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Residues in contact with GLN 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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86A ILE* 3.9 3.9 - - - +
147A ASP 3.3 3.4 - - - -
149A ASN* 3.2 28.0 - - + +
150A THR 3.9 0.4 - - - -
151A PRO* 3.1 35.3 - - - +
154A THR* 3.7 24.9 + - - +
157A GLY 3.8 5.7 - - - -
158A ASN 3.2 26.8 + - - +
159A LEU* 3.0 22.4 + - - +
161A GLY* 1.3 84.0 - - - +
163A PRO* 1.4 67.2 - - - +
164A VAL 3.2 2.7 - - - -
165A SER* 2.9 20.1 + - - -
166A PHE* 3.4 13.0 - - + -
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Residues in contact with PRO 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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120A HIS 3.7 23.8 - - - +
121A SER* 4.4 1.8 - - - -
123A ALA* 4.7 0.7 - - + -
124A ILE* 3.6 32.4 - - + +
141A TRP* 3.7 26.5 - - + -
147A ASP* 3.4 8.3 - - + +
159A LEU 3.3 6.2 - - - +
160A HIS 3.3 15.7 - - - +
161A GLY 3.6 0.7 - - - -
162A GLN* 1.4 88.1 - - - +
164A VAL* 1.3 63.1 + - - +
166A PHE* 3.2 16.7 + - + +
167A LEU* 3.5 16.9 - - + +
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Residues in contact with VAL 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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141A TRP* 3.6 38.4 - - + -
146A ALA 3.8 4.3 - - - +
147A ASP 3.0 15.0 + - - +
148A ILE* 3.7 7.4 - - + -
163A PRO* 1.3 77.4 - - - +
165A SER* 1.3 62.9 + - - +
167A LEU* 3.1 17.3 + - + -
168A LEU* 3.3 40.4 + - + +
193A ILE* 4.0 11.7 - - + -
195A TYR* 3.4 26.7 - - - +
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Residues in contact with SER 165 (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 ILE* 3.9 8.0 - - - +
149A ASN 3.1 21.5 + - - -
150A THR* 3.7 27.5 - - - -
151A PRO* 4.2 1.2 - - - +
162A GLN 2.9 16.8 + - - -
164A VAL* 1.3 79.9 - - - +
166A PHE* 1.3 71.6 + - - +
167A LEU 3.5 0.3 + - - -
168A LEU 4.2 5.7 + - - +
171A LEU* 4.0 19.8 - - - +
172A GLN* 5.3 1.9 + - - +
175A VAL* 3.5 19.9 - - - +
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Residues in contact with PHE 166 (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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124A ILE* 3.8 21.5 - - + -
151A PRO* 3.8 17.0 - - + -
159A LEU* 3.9 9.4 - - + -
162A GLN* 3.4 38.1 - - + -
163A PRO 3.2 5.3 + - - +
164A VAL 3.1 1.0 - - - -
165A SER* 1.3 79.8 - - - +
167A LEU* 1.3 59.5 + - + +
168A LEU 3.7 0.2 - - - -
172A GLN* 6.2 0.4 - - - -
175A VAL* 3.8 25.8 - - + -
176A PRO 4.8 3.6 - - - -
178A LEU* 3.7 21.8 - - + -
181A PHE* 3.7 35.9 - + + -
184A ILE* 3.6 24.4 - - + +
186A PRO* 3.2 25.9 - - - +
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Residues in contact with LEU 167 (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 ALA 3.9 10.1 - - - +
124A ILE* 4.0 17.7 - - + +
127A ILE* 3.7 44.4 - - + -
128A SER* 3.8 23.3 - - - +
141A TRP* 5.0 4.0 - - + -
163A PRO* 3.5 21.5 - - + +
164A VAL* 3.1 10.7 + - + +
166A PHE* 1.3 85.1 - - + +
168A LEU* 1.3 67.6 + - + +
169A ARG 3.6 1.2 + - - -
184A ILE* 4.8 4.0 - - + -
186A PRO* 3.5 18.6 - - + +
187A CYS 4.0 0.2 + - - -
188A ILE* 3.6 20.3 + - + +
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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