Contacts of the helix formed by residues 144 - 154 (chain A) in PDB entry 1P9B
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 GLY 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.4 11.0 - - - +
120A HIS* 3.4 34.5 - - - +
121A GLN* 3.6 1.7 - - - +
124A ASP* 2.9 14.2 + - - +
142A LYS 3.3 2.6 + - - -
143A ARG* 1.3 78.1 - - - +
145A ILE* 1.3 62.2 + - - +
146A GLY 3.5 2.2 - - - -
147A PRO* 3.6 2.8 - - - +
148A CYS* 3.2 18.0 + - - +
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Residues in contact with ILE 145 (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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48A GLY* 4.8 2.9 - - - -
49A GLY* 4.0 8.7 - - - -
50A ALA 4.0 6.5 - - - +
51A ASN* 3.4 49.8 - - + +
86A VAL* 3.8 11.7 - - + -
116A LEU* 3.7 20.4 - - + -
124A ASP* 3.9 2.2 + - - -
143A ARG* 4.1 11.2 - - + +
144A GLY* 1.3 73.9 - - - +
146A GLY* 1.3 67.2 + - - +
148A CYS* 3.2 3.5 + - - +
149A TYR* 3.1 47.6 + - + -
247A THR* 4.2 7.4 - - - +
248A SER* 4.0 4.5 - - - +
1601A IMO 4.3 11.0 - - - +
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Residues in contact with GLY 146 (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 ASP* 4.9 1.2 + - - -
127A GLN* 5.4 0.4 - - - -
145A ILE* 1.3 77.7 - - - +
147A PRO* 1.3 64.6 - - - +
149A TYR* 3.2 4.9 + - - +
150A SER* 2.9 32.1 + - - -
248A SER* 3.2 20.7 + - - -
1601A IMO 4.4 8.5 + - - -
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Residues in contact with PRO 147 (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* 3.5 33.5 + - - +
123A ILE* 3.6 22.9 - - + -
124A ASP* 3.6 13.7 - - + +
127A GLN* 3.6 25.8 - - - +
144A GLY* 3.6 13.0 - - - +
146A GLY* 1.3 90.6 - - - +
148A CYS* 1.3 55.9 + - - +
150A SER* 3.2 10.4 + - - +
151A THR* 3.0 30.4 + - + +
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Residues in contact with CYS 148 (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 VAL* 3.4 33.4 - - + -
114A HIS* 4.2 9.7 + - - -
115A ILE 3.6 25.8 - - - -
116A LEU* 3.8 13.9 - - + -
120A HIS* 3.4 17.6 + - - +
144A GLY 3.2 19.0 + - - +
145A ILE 3.7 2.5 - - - +
146A GLY 3.2 0.2 - - - -
147A PRO* 1.3 74.0 - - - +
149A TYR* 1.3 64.8 + - - +
151A THR* 3.0 15.3 + - - -
152A LYS* 3.1 12.5 + - - +
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Residues in contact with TYR 149 (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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48A GLY* 2.9 25.6 + - - -
84A GLY 2.7 28.5 + - - -
85A MET 5.2 0.2 - - - -
86A VAL* 3.5 30.3 - - + +
145A ILE* 3.1 26.8 + - + -
146A GLY 3.8 2.2 - - - +
148A CYS* 1.3 76.7 - - - +
150A SER* 1.3 58.3 + - - +
152A LYS* 3.3 27.8 + - + +
153A ALA* 3.0 27.2 + - - +
248A SER* 3.2 42.4 - - - +
249A SER* 3.4 23.4 - - - -
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Residues in contact with SER 150 (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 GLN* 5.6 3.6 + - - -
146A GLY 2.9 21.7 + - - -
147A PRO* 3.3 14.1 - - - +
148A CYS 3.1 0.2 - - - -
149A TYR* 1.3 78.3 - - - +
151A THR* 1.3 58.3 + - - +
153A ALA* 3.2 8.2 + - - +
154A SER* 3.0 27.2 + - - -
184A TYR* 5.9 2.9 - - - -
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Residues in contact with THR 151 (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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114A HIS* 5.2 0.2 + - - -
120A HIS* 3.0 32.6 + - + +
147A PRO* 3.0 13.9 + - + +
148A CYS* 3.0 11.3 + - - -
150A SER* 1.3 74.0 - - - +
152A LYS* 1.3 60.6 + - - +
154A SER* 3.1 7.4 + - - +
155A ARG 3.0 20.3 + - - -
156A ILE* 3.0 29.8 + - + -
157A GLY* 3.1 15.0 + - - -
176A LEU* 4.9 1.1 - - + -
180A LEU* 4.1 27.8 - - + -
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Residues in contact with LYS 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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83A ASN* 4.2 18.2 + - - +
84A GLY* 4.2 13.1 + - - -
85A MET 5.5 1.0 + - - +
86A VAL* 5.5 0.2 - - + -
114A HIS* 3.3 46.5 - - + +
148A CYS 3.1 13.8 + - - +
149A TYR* 3.3 35.6 - - + +
151A THR* 1.3 77.3 + - - +
153A ALA* 1.3 59.6 + - - +
155A ARG* 2.8 26.9 + - - +
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Residues in contact with ALA 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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149A TYR 3.0 13.4 + - - +
150A SER* 3.5 10.1 - - - +
152A LYS* 1.3 77.7 - - - +
154A SER* 1.3 60.9 + - - +
155A ARG* 3.0 22.8 + - - +
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Residues in contact with SER 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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150A SER 3.0 9.4 + - - -
151A THR* 3.1 19.4 + - - +
153A ALA* 1.3 74.0 - - - +
155A ARG* 1.3 76.9 + - - +
156A ILE* 3.2 31.0 + - - +
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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