Contacts of the helix formed by residues 136 - 147 (chain D) in PDB entry 2HJ9
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 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D HIS* 4.0 12.8 - - + +
134D GLY 2.9 12.4 + - - +
135D VAL* 1.3 74.6 - - - +
137D ASP* 1.3 55.4 + - - +
138D LEU* 3.0 12.8 + - - +
139D ILE* 2.8 39.8 + - - +
140D LEU* 2.8 33.2 + - - +
161D SER* 6.3 1.0 - - - -
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Residues in contact with ASP 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ILE* 5.4 0.3 - - - +
126D ASP* 4.8 3.5 - - - +
131D HIS* 2.7 36.9 + - - -
136D ASN* 1.3 75.2 - - - +
138D LEU* 1.3 61.8 + - - +
140D LEU* 3.7 13.3 - - - +
141D ASP* 3.1 27.2 + - - +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ASN* 3.0 12.6 + - - +
137D ASP* 1.3 76.9 - - - +
139D ILE* 1.3 62.2 + - + +
141D ASP* 3.1 13.2 - - + +
142D SER* 3.0 26.5 + - - -
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLY 3.6 20.9 - - - +
135D VAL* 4.0 14.8 - - + -
136D ASN* 2.8 35.1 + - - +
138D LEU* 1.3 74.6 - - + +
140D LEU* 1.3 57.2 + - - +
142D SER* 3.1 11.7 + - - +
143D LEU* 3.0 32.7 + - + +
158D VAL* 3.9 33.2 - - + -
159D MET 3.7 22.2 - - - +
160D THR* 4.2 8.5 - - + -
161D SER 5.4 0.7 - - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D PHE* 4.0 15.0 - - + -
116D PHE* 3.3 43.2 - - + -
123D ILE* 3.7 22.8 - - + +
126D ASP* 3.8 30.3 - - + +
130D ALA* 4.2 10.3 - - + -
131D HIS* 4.4 1.6 - - - +
135D VAL* 4.0 16.9 - - + +
136D ASN 2.8 18.1 + - - +
137D ASP* 3.7 21.5 - - - +
139D ILE* 1.3 72.1 - - - +
141D ASP* 1.3 57.1 - - - +
143D LEU* 3.4 6.2 - - + +
144D ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLY* 5.8 1.0 - - - -
123D ILE* 4.4 20.6 + - - +
137D ASP 3.1 11.5 + - - +
138D LEU* 3.1 20.2 - - + +
140D LEU* 1.3 80.2 - - - +
142D SER* 1.3 60.3 + - - +
144D ALA* 3.3 6.9 + - - +
145D ASN* 2.9 36.5 + - - -
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 3.0 12.2 + - - -
139D ILE* 3.1 22.5 + - - +
141D ASP* 1.3 74.6 - - - +
143D LEU* 1.3 52.9 + - - +
145D ASN* 3.2 9.3 + - - +
146D ARG* 2.8 46.0 + - - +
158D VAL* 5.4 4.0 - - - +
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D PHE* 4.0 22.4 - - + -
116D PHE* 4.7 7.9 - - + -
135D VAL* 3.9 26.2 - - + -
139D ILE* 3.0 20.3 + - + +
140D LEU* 3.4 10.5 - - + +
142D SER* 1.3 76.9 + - - +
144D ALA* 1.3 62.1 + - - +
146D ARG* 3.3 6.4 + - - +
147D VAL* 3.1 30.7 + - - +
156D ILE* 3.7 40.4 - - + -
158D VAL* 5.5 2.0 - - + -
167D MET* 3.9 16.4 - - + -
169D VAL* 4.6 12.6 - - + -
187D PHE* 4.8 1.3 - - - -
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 4.1 16.5 - - + -
118D THR* 4.4 9.6 - - + -
123D ILE* 4.6 4.9 - - + -
140D LEU 3.1 13.7 + - - +
141D ASP* 3.5 12.8 - - - +
143D LEU* 1.3 74.6 - - - +
145D ASN* 1.3 65.7 + - - +
147D VAL 3.3 17.2 - - - +
148D SER* 5.1 0.2 - - - -
171D ARG* 4.6 4.0 + - - -
187D PHE* 3.7 23.2 - - + -
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A HIS* 3.5 28.9 + - + -
224A ASN* 6.0 1.4 - - - +
141D ASP* 2.9 31.4 + - - -
142D SER* 3.2 10.1 + - - +
144D ALA* 1.3 79.9 - - - +
146D ARG* 1.3 65.2 + - - +
147D VAL 3.5 0.2 + - - -
148D SER* 3.7 7.4 - - - -
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Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A HIS* 5.5 1.2 - - - -
142D SER* 2.8 25.1 + - - +
143D LEU* 3.6 9.9 - - - +
145D ASN* 1.3 79.2 - - - +
147D VAL* 1.3 56.7 + - - +
148D SER* 3.1 10.9 + - - -
154D TYR* 3.4 19.1 - - + -
156D ILE* 4.1 42.0 - - + +
157D ASN 4.0 19.0 + - - +
158D VAL* 4.6 13.1 - - - +
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU 3.1 17.9 + - - +
144D ALA 3.3 9.3 - - - +
145D ASN 3.3 0.4 - - - -
146D ARG* 1.3 73.0 - - - +
148D SER* 1.3 58.4 + - - +
149D PHE 3.6 5.6 - - - +
154D TYR* 3.9 27.6 - - + -
156D ILE* 3.8 24.0 - - + -
169D VAL* 3.9 20.9 - - + -
170D ARG 4.3 2.5 - - - -
171D ARG* 3.2 42.4 + - + +
187D PHE* 3.8 18.2 - - + -
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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