Contacts of the helix formed by residues 122 - 132 (chain D) in PDB entry 1PQ3
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 LEU 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ALA* 3.5 35.0 - - + +
33D PHE* 3.5 35.0 - - + -
73D PHE* 4.6 5.6 - - + -
95D ALA* 5.4 2.2 - - + +
96D ASN* 3.1 11.3 - - - +
99D LEU* 3.6 21.9 - - + +
115D THR* 5.3 2.7 - - + -
116D LEU 5.2 0.2 - - - -
117D GLY* 3.6 18.8 - - - -
118D GLY* 3.9 5.4 - - - -
119D ASP 3.2 18.2 - - - +
120D HIS* 4.7 0.4 - - - -
121D SER* 1.3 79.5 + - - +
123D ALA* 1.3 62.3 + - - +
125D GLY* 2.9 13.3 + - - -
126D THR* 3.1 17.1 + - + +
295D VAL* 4.9 5.2 - - + -
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Residues in contact with ALA 123 (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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120D HIS* 3.1 34.2 + - + +
121D SER 3.0 0.6 - - - -
122D LEU* 1.3 77.9 - - - +
124D ILE* 1.3 63.1 - - - +
126D THR* 3.3 12.7 + - - +
127D ILE* 2.9 30.7 + - + +
141D TRP* 3.6 23.3 - - + -
163D PRO* 4.3 3.1 - - + -
167D LEU* 4.2 2.2 - - + +
249D SER* 4.2 4.3 - - - +
293D ASP* 4.4 4.5 - - - +
295D VAL* 5.8 0.8 - - - +
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Residues in contact with ILE 124 (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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92D VAL* 5.0 2.5 - - + -
96D ASN* 3.7 14.8 - - - +
121D SER* 3.3 19.3 - - - +
122D LEU 3.0 0.8 - - - -
123D ALA* 1.3 77.8 - - - +
125D GLY* 1.3 58.3 + - - +
128D SER* 2.9 36.8 + - - +
159D LEU* 5.5 2.5 - - + +
163D PRO* 4.0 24.4 - - + +
166D PHE* 3.7 28.5 - - + -
167D LEU* 4.0 13.5 - - + +
181D PHE* 3.9 17.9 - - + -
183D TRP* 4.3 4.7 - - + -
184D ILE* 3.4 33.4 - - + -
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Residues in contact with GLY 125 (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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96D ASN* 2.8 42.4 + - - -
99D LEU* 4.5 2.0 - - - -
100D ALA* 3.4 18.4 - - - +
122D LEU 2.9 1.6 + - - -
124D ILE* 1.3 74.9 - - - +
126D THR* 1.3 54.5 + - - -
128D SER* 3.2 1.1 + - - -
129D GLY 2.8 31.2 + - - -
183D TRP* 4.4 0.9 - - - -
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Residues in contact with THR 126 (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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99D LEU* 3.6 19.7 - - + +
103D VAL* 3.6 16.8 - - + +
115D THR* 3.5 22.4 - - + +
122D LEU* 3.1 12.3 + - + +
123D ALA* 3.3 10.7 + - - -
125D GLY* 1.3 74.0 - - - +
127D ILE* 1.3 60.0 + - - +
130D HIS* 2.9 31.4 + - - +
247D HIS* 3.5 8.4 + - - -
293D ASP* 3.0 40.8 + - - +
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Residues in contact with ILE 127 (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 ALA* 2.9 19.7 + - + +
126D THR* 1.3 77.0 + - - +
128D SER* 1.3 60.1 + - - +
130D HIS* 3.9 2.2 - - - +
131D ALA* 2.9 28.6 + - - +
137D LEU* 4.6 10.3 - - + -
139D VAL* 4.1 20.4 - - + -
141D TRP* 4.0 23.3 - - + -
167D LEU* 3.5 34.5 - - + -
187D CYS* 4.5 9.2 - - - -
188D ILE* 4.6 9.0 - - + -
247D HIS* 3.3 35.7 - - + +
293D ASP* 4.6 0.4 - - - +
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Residues in contact with SER 128 (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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100D ALA* 4.3 1.3 - - - -
124D ILE* 2.9 26.1 + - - +
125D GLY 3.2 3.6 + - - -
127D ILE* 1.3 78.5 - - - +
129D GLY* 1.3 64.6 + - - +
131D ALA* 3.2 2.4 + - - +
132D ARG* 3.0 28.8 + - - +
167D LEU* 4.2 10.6 - - - +
183D TRP* 3.8 28.3 - - - -
184D ILE* 4.7 6.6 - - - +
185D LYS 5.2 3.1 + - - -
187D CYS* 4.6 11.2 - - - -
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Residues in contact with GLY 129 (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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100D ALA* 3.2 29.7 - - - +
103D VAL* 4.1 1.6 - - - -
104D SER* 3.0 31.3 - - - -
107D VAL* 5.0 0.2 - - - +
125D GLY 2.8 17.6 + - - -
126D THR 4.0 0.4 - - - -
128D SER* 1.3 74.1 - - - +
130D HIS* 1.3 61.0 + - - +
132D ARG* 3.1 11.7 - - - +
133D HIS* 4.1 1.9 + - - +
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Residues in contact with HIS 130 (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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103D VAL* 3.9 6.4 - - + +
107D VAL* 4.0 21.0 - - + +
126D THR 2.9 20.2 + - - +
127D ILE* 3.9 2.9 - - - +
129D GLY* 1.3 73.1 - - - +
131D ALA* 1.3 65.8 + - - +
132D ARG 3.0 1.6 - - - -
133D HIS* 3.0 14.0 + - - +
134D CYS* 3.0 30.1 + - + +
137D LEU* 3.6 19.1 - - + +
245D PRO* 4.2 0.8 - - + +
246D ILE 4.2 2.5 - - - -
247D HIS* 2.9 32.2 + - + +
290D SER* 3.1 36.9 + - - -
291D ALA* 3.5 14.3 - - + +
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Residues in contact with ALA 131 (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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127D ILE* 2.9 21.0 + - + +
128D SER 3.7 3.4 - - - +
130D HIS* 1.3 76.4 - - - +
132D ARG* 1.3 64.3 + - - +
133D HIS 2.9 1.7 + - - -
134D CYS 3.6 5.8 - - - +
135D PRO* 3.1 30.4 - - + +
137D LEU* 3.5 20.3 - - + +
187D CYS* 4.0 27.4 - - + -
188D ILE* 5.5 0.7 - - + -
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Residues in contact with ARG 132 (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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97D GLN* 6.2 1.2 - - - +
100D ALA* 3.5 35.7 + - - +
101D GLU* 3.7 24.0 + - - +
104D SER* 4.0 16.0 + - - +
128D SER* 3.0 16.6 + - - +
129D GLY* 3.1 19.5 - - - +
130D HIS 3.0 0.4 - - - -
131D ALA* 1.3 76.5 - - - +
133D HIS* 1.3 67.2 + - + +
135D PRO* 4.9 4.2 - - - +
183D TRP* 4.5 16.2 - - - -
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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