Contacts of the helix formed by residues 158 - 168 (chain A) in PDB entry 2JDQ
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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119A ASP* 5.2 1.4 + - - -
157A GLY* 1.3 73.9 - - - +
159A SER* 1.3 55.4 + - - +
160A LEU* 3.7 17.5 - - + +
161A GLN* 2.7 46.8 + - - +
162A THR* 2.7 36.6 + - - -
199A ASP* 4.1 0.4 - - - -
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Residues in contact with SER 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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158A ASN* 1.3 70.4 - - - +
160A LEU* 1.3 68.4 + - - +
162A THR* 3.3 2.1 + - - -
163A ARG* 2.9 43.8 + - - +
199A ASP* 2.6 41.4 + - - +
200A SER* 5.0 3.1 - - - -
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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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158A ASN* 3.2 17.7 - - + +
159A SER* 1.3 80.1 - - - +
161A GLN* 1.3 61.8 + - + +
163A ARG* 3.3 57.1 - - - +
164A ILE* 3.6 14.5 - - - +
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Residues in contact with GLN 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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118A ILE* 3.5 38.7 - - + +
119A ASP* 2.9 30.1 + - - +
122A ILE* 3.9 16.8 - - + +
154A ILE* 3.8 28.3 - - - +
157A GLY* 3.6 1.6 - - - -
158A ASN* 2.7 53.3 + - + +
159A SER 3.3 0.4 - - - -
160A LEU* 1.3 79.0 - - + +
162A THR* 1.3 59.3 + - - +
163A ARG 3.1 1.4 + - - -
164A ILE* 3.5 11.3 + - - +
165A VAL 3.9 3.3 + - - -
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Residues in contact with THR 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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154A ILE 4.6 3.4 - - - -
155A ALA* 3.0 22.4 + - - +
158A ASN 2.7 23.1 + - - -
159A SER 3.3 4.5 + - - -
161A GLN* 1.3 72.9 - - - +
163A ARG* 1.3 63.0 + - - +
165A VAL* 3.7 6.3 + - + +
166A ILE* 3.5 23.9 + - + +
196A ILE* 4.2 29.4 - - + -
199A ASP* 3.8 26.2 - - + +
203A CYS* 6.0 0.2 - - - -
752E LYS* 2.8 14.7 + - - -
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Residues in contact with ARG 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 SER* 2.9 31.1 + - - +
160A LEU* 3.3 41.6 - - - +
161A GLN 3.1 0.4 - - - -
162A THR* 1.3 75.4 - - - +
164A ILE* 1.3 62.9 + - + +
166A ILE* 3.2 8.6 + - + +
167A GLN* 2.9 44.8 + - - +
199A ASP* 5.6 1.3 - - - +
202A MET* 6.3 0.8 - - - +
203A CYS* 6.4 2.2 - - - -
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Residues in contact with ILE 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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122A ILE* 3.2 43.3 - - + +
128A VAL* 3.9 22.9 - - + -
160A LEU 3.6 19.7 - - - +
161A GLN* 3.5 8.8 + - - +
162A THR 3.5 0.2 - - - -
163A ARG* 1.3 78.4 - - + +
165A VAL* 1.3 53.9 + - + +
167A GLN* 3.7 11.3 - - - +
168A ALA* 2.8 33.7 + - + +
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Residues in contact with VAL 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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128A VAL* 4.6 5.8 - - + -
151A LEU* 4.3 30.3 - - + +
154A ILE* 3.4 37.0 - - + -
155A ALA* 4.5 6.1 - - + +
161A GLN 4.0 4.0 - - - +
162A THR* 3.7 9.6 + - + +
163A ARG 3.2 0.6 - - - -
164A ILE* 1.3 78.7 - - + +
166A ILE* 1.3 62.0 + - - +
168A ALA* 3.6 5.1 + - - +
169A GLY 3.5 3.5 + - - -
170A ALA* 3.4 37.5 + - + +
174A PHE* 4.9 1.8 - - + -
196A ILE* 4.1 21.5 - - + -
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Residues in contact with ILE 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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162A THR 3.5 15.0 + - - +
163A ARG* 3.2 9.5 + - + +
165A VAL* 1.3 75.4 - - - +
167A GLN* 1.3 60.3 + - + +
169A GLY* 2.7 26.9 + - - -
170A ALA 4.1 0.4 + - - +
171A VAL* 4.3 11.1 + - + -
196A ILE* 3.8 26.2 - - + -
203A CYS* 3.6 33.9 - - + -
206A TYR* 3.8 37.6 + - + -
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Residues in contact with GLN 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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163A ARG* 2.9 32.4 + - + +
164A ILE* 4.0 10.6 - - - +
166A ILE* 1.3 82.7 - - + +
168A ALA* 1.3 60.2 + - - +
169A GLY* 3.1 1.6 + - - -
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Residues in contact with ALA 168 (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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128A VAL* 4.1 14.6 - - + +
129A ALA* 4.6 12.2 - - + +
132A VAL* 3.7 35.1 - - + +
164A ILE* 2.8 19.7 + - + +
165A VAL 3.8 4.7 - - - +
166A ILE 3.2 0.2 - - - -
167A GLN* 1.3 75.6 - - - +
169A GLY* 1.3 59.0 + - - +
170A ALA 3.6 0.2 - - - -
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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