Contacts of the helix formed by residues 150 - 164 (chain A) in PDB entry 2JPD
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 PRO 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A HIS* 3.1 35.9 - - + +
147A ASN 5.1 2.7 - - - +
148A LEU 3.9 6.3 - - - +
149A HIS* 1.3 86.5 - - + +
151A ASP* 1.3 66.5 + - + +
153A ILE* 3.2 12.6 - - - +
154A HIS* 2.8 25.8 + - + +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A HIS* 3.3 18.3 + - + +
150A PRO* 1.3 80.3 - - + +
152A TYR* 1.3 64.6 + - - +
154A HIS* 3.2 12.4 + - - +
155A GLY* 3.1 22.7 + - - -
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Residues in contact with TYR 152 (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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107A GLN* 5.1 3.1 - - - +
129A ASP* 3.2 9.9 + - - -
140A PHE 3.7 17.1 + - - -
141A LEU* 3.8 20.0 - - + -
142A SER 5.8 0.2 - - - -
145A TYR* 3.4 40.6 - + + -
149A HIS* 3.7 24.8 + + + +
150A PRO 3.2 0.6 - - - -
151A ASP* 1.3 77.6 - - - +
153A ILE* 1.3 67.3 + - + +
155A GLY* 4.1 0.7 - - - -
156A ARG* 3.1 66.3 + - + +
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Residues in contact with ILE 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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139A LEU* 4.6 2.9 - - + -
140A PHE 5.4 0.4 - - - +
141A LEU* 3.8 26.7 - - + -
146A HIS* 3.3 21.8 - - + +
149A HIS 4.8 0.2 + - - -
150A PRO 3.2 17.4 + - - +
152A TYR* 1.3 80.2 - - + +
154A HIS* 1.3 67.3 + - - +
156A ARG* 3.2 18.5 - - + +
157A LEU* 2.9 42.0 + - + +
169A LEU* 3.5 28.3 - - + -
188A MET* 3.5 30.1 - - + -
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Residues in contact with HIS 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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146A HIS* 4.1 11.4 - + - -
150A PRO* 2.8 30.1 + - + -
151A ASP* 3.2 15.2 + - - +
153A ILE* 1.3 79.7 - - + +
155A GLY* 1.3 57.0 + - - +
157A LEU* 3.2 10.7 + - + +
158A GLN* 2.9 34.8 + - + +
184A GLU* 6.4 1.6 - - + -
188A MET* 3.7 35.2 - - + +
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Residues in contact with GLY 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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151A ASP* 3.1 16.1 + - - -
152A TYR 4.2 1.1 - - - -
154A HIS* 1.3 74.1 - - - +
156A ARG* 1.3 60.0 + - - +
158A GLN* 3.3 10.1 + - - +
159A SER* 2.7 35.1 + - - -
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Residues in contact with ARG 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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104A SER* 5.5 1.0 - - - -
106A ARG* 6.3 0.4 - - - +
107A GLN* 3.7 17.8 + - - +
126A VAL 5.4 1.4 + - - -
127A ILE* 3.8 25.1 + - - +
128A PRO 4.2 2.7 + - - -
129A ASP* 2.6 41.8 + - - +
139A LEU* 3.8 23.3 - - + -
152A TYR* 3.1 43.6 + - + +
153A ILE* 3.2 22.0 - - + +
155A GLY* 1.3 77.8 - - - +
157A LEU* 1.3 62.4 + - - +
159A SER* 3.3 7.3 + - - -
160A LEU* 3.1 26.7 + - + +
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Residues in contact with LEU 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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139A LEU* 4.7 7.6 - - + -
153A ILE* 2.9 30.0 + - + +
154A HIS* 3.6 9.4 - - + +
156A ARG* 1.3 74.3 - - - +
158A GLN* 1.3 60.6 + - + +
160A LEU* 3.2 21.2 + - + +
161A GLY* 3.0 26.5 + - - -
167A ARG* 5.3 4.6 + - - -
169A LEU* 4.8 4.0 - - + -
188A MET* 3.8 38.1 - - + -
192A ALA* 3.9 29.0 - - + +
194A CYS* 4.0 24.7 - - + -
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Residues in contact with GLN 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 HIS* 2.9 23.6 + - + +
155A GLY* 3.5 11.0 - - - +
157A LEU* 1.3 77.5 - - - +
159A SER* 1.3 61.4 + - - +
161A GLY* 3.3 10.4 + - - +
162A LYS* 2.9 28.2 + - - +
192A ALA* 6.3 1.0 - - - +
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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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127A ILE* 3.7 23.8 - - - -
155A GLY 2.7 19.8 + - - -
156A ARG* 3.4 11.0 - - - -
157A LEU 3.2 0.2 - - - -
158A GLN* 1.3 78.2 - - - +
160A LEU* 1.3 61.6 + - - +
161A GLY 3.3 0.5 + - - -
162A LYS* 3.4 12.9 - - - +
163A ASN* 3.0 25.6 + - - +
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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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127A ILE* 4.0 14.1 - - + +
128A PRO* 4.0 24.0 - - + -
137A CYS* 4.0 3.1 - - - -
139A LEU* 3.4 39.3 - - + -
156A ARG* 3.1 16.4 - - + +
157A LEU* 3.2 18.3 + - + +
159A SER* 1.3 71.0 - - - +
161A GLY* 1.3 64.0 - - - +
162A LYS 3.1 3.4 - - - -
163A ASN 3.7 2.2 - - - +
164A PHE* 3.0 54.4 + - + +
167A ARG* 3.3 21.6 + - + +
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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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157A LEU 3.0 14.5 + - - -
158A GLN* 3.3 7.4 + - - -
159A SER 3.1 2.0 - - - -
160A LEU* 1.3 78.5 - - - +
162A LYS* 1.3 59.7 + - - +
167A ARG* 3.3 26.1 + - - -
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Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A GLN* 2.9 25.3 + - - +
159A SER* 3.4 17.4 - - - +
161A GLY* 1.3 78.0 - - - +
163A ASN* 1.3 76.4 + - - +
164A PHE 3.5 3.9 + - - +
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Residues in contact with ASN 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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127A ILE* 4.5 19.6 - - + +
134A GLN 4.9 2.8 - - - +
159A SER* 3.0 22.8 + - - +
160A LEU* 3.3 1.2 + - - -
162A LYS* 1.3 90.2 - - - +
164A PHE* 1.3 87.2 + - + +
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Residues in contact with PHE 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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126A VAL* 5.7 1.6 - - + -
127A ILE* 4.1 10.8 - - + -
128A PRO* 3.5 31.6 - - + -
131A VAL* 3.9 20.4 - - + -
134A GLN* 3.6 28.7 - - - -
135A SER* 4.2 7.6 - - - +
137A CYS* 3.5 28.9 - - + -
160A LEU* 3.0 24.3 + - + +
162A LYS 4.6 3.1 - - - +
163A ASN* 1.3 101.0 - - + +
165A ALA* 1.3 55.4 + - - +
166A LEU 4.5 0.4 - - - +
167A ARG* 2.8 32.8 + - - +
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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