Contacts of the helix formed by residues 152 - 160 (chain A) in PDB entry 4I6J
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 ASP 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TYR* 6.1 1.2 - - - -
146A ASN* 3.8 19.4 + - - +
151A TYR* 1.3 74.4 - - - +
153A LEU* 1.3 64.7 + - - +
154A ASP* 2.6 39.8 + - - +
155A ARG* 2.9 35.2 + - + +
156A ILE* 3.2 12.5 + - - +
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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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118A TYR* 5.7 3.1 - - + -
120A SER* 3.3 37.7 - - - +
146A ASN* 4.9 0.6 - - - +
149A THR* 3.6 30.5 + - + +
151A TYR 3.4 3.3 + - - +
152A ASP* 1.3 73.2 + - - +
154A ASP* 1.3 64.1 + - - +
156A ILE* 3.4 7.3 + - + +
157A ILE* 3.2 27.2 + - - +
312A GLU* 3.4 25.8 - - - +
315A TYR* 3.9 13.2 - - + -
316A THR* 3.8 27.4 - - - +
319A THR* 4.2 14.8 - - + +
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Residues in contact with ASP 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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118A TYR* 4.3 16.5 + - - -
125A LYS* 5.6 1.4 + - - -
152A ASP* 2.6 24.6 + - - +
153A LEU* 1.3 74.0 - - - +
155A ARG* 1.3 63.6 + - - +
157A ILE* 3.2 9.2 + - - +
158A GLU* 2.9 22.5 + - - +
162A GLN* 5.1 1.0 - - - +
319A THR* 5.0 6.9 - - - +
320A ASN* 4.5 16.5 + - - +
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Residues in contact with ARG 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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152A ASP* 2.9 25.4 + - + +
154A ASP* 1.3 77.9 - - - +
156A ILE* 1.3 65.2 + - - +
158A GLU* 2.9 38.7 + - - +
159A LEU* 2.9 46.7 + - + +
178A MET* 4.6 5.4 - - + -
179A GLU* 3.5 33.7 + - - -
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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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151A TYR* 4.1 19.1 - - + -
152A ASP 3.2 8.3 + - - +
153A LEU* 3.7 8.3 - - - +
154A ASP 3.3 0.2 - - - -
155A ARG* 1.3 78.7 - - - +
157A ILE* 1.3 62.0 + - - +
159A LEU* 3.4 1.7 + - - +
160A ASN* 3.1 20.6 + - - +
165A PRO* 4.3 9.4 - - + -
171A PHE* 4.0 14.1 - - + -
174A LEU* 3.7 19.8 - - + +
175A ILE* 3.9 18.8 - - + -
178A MET* 3.9 30.3 - - + -
312A GLU* 4.4 4.3 - - - +
316A THR* 3.8 32.3 - - + +
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Residues in contact with ILE 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 3.2 14.1 + - - +
154A ASP* 3.2 12.3 + - - +
155A ARG 3.1 0.6 - - - -
156A ILE* 1.3 75.0 - - - +
158A GLU* 1.3 57.5 + - - +
160A ASN 3.1 8.3 + - - -
161A GLY 3.4 0.3 + - - -
162A GLN* 2.7 45.0 + - - +
163A LYS 3.3 29.8 + - - +
164A PRO* 4.1 15.7 - - + -
316A THR* 3.6 36.1 - - + +
319A THR* 4.4 7.2 - - - +
320A ASN* 3.7 28.0 - - + +
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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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154A ASP 2.9 12.7 + - - +
155A ARG* 2.9 35.2 + - - +
157A ILE* 1.3 75.8 - - - +
159A LEU* 1.3 65.9 + - + +
161A GLY* 3.0 14.4 + - - -
162A GLN* 3.2 35.3 + - - +
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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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155A ARG* 2.9 57.8 + - + +
156A ILE 3.8 7.4 - - - +
158A GLU* 1.3 79.7 - - + +
160A ASN* 1.3 55.6 + - - +
161A GLY 3.2 3.0 + - - -
170A ARG* 5.3 1.0 + - - -
174A LEU* 4.5 18.3 - - + +
178A MET* 3.8 34.3 - - + -
179A GLU* 5.1 1.3 - - - +
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Residues in contact with ASN 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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156A ILE 3.1 13.5 + - - +
157A ILE 3.1 3.2 + - - -
159A LEU* 1.3 74.2 - - - +
161A GLY* 1.3 62.5 + - - +
162A GLN 3.3 1.3 - - - -
163A LYS* 3.0 35.7 + - - +
164A PRO 3.5 2.2 + - - -
165A PRO* 3.2 34.0 - - + +
170A ARG* 3.2 31.3 + - - +
174A LEU* 3.9 10.3 - - + -
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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