Contacts of the helix formed by residues 134 - 145 (chain D) in PDB entry 4PIW
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 GLU 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D ARG* 4.6 10.7 + - - +
107D ILE 5.9 0.2 + - - -
109D GLU* 4.0 32.1 + - + +
133D CYS* 1.3 69.0 - - - +
135D MSE 1.3 63.0 + - - +
136D ASP* 3.3 2.2 - - + -
137D THR* 3.3 25.0 + - - +
138D ILE* 3.2 25.1 + - - +
161D TYR* 2.8 28.4 + - - +
162D LYS* 4.2 10.3 + - - -
283D PRO* 6.2 0.3 - - - +
284D ASP 5.7 0.5 - - - +
286D CYS* 5.7 0.9 - - - -
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Residues in contact with MSE 135 (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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125D PRO* 4.0 7.4 - - + -
127D HIS* 3.8 27.6 - - + -
133D CYS* 2.7 18.3 + - - +
134D GLU* 1.3 70.6 - - - +
136D ASP* 1.3 59.1 + - - +
138D ILE* 4.0 21.3 - - + -
139D MSE 2.7 61.5 + - + +
149D VAL* 4.0 14.4 - - + -
151D GLU* 4.2 3.8 - - + -
161D TYR* 3.4 23.2 + - + -
164D ARG* 5.3 0.2 - - - -
169D ILE* 3.3 48.9 - - + +
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Residues in contact with ASP 136 (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 GLU* 5.1 2.2 - - + -
135D MSE 1.3 75.9 - - - +
137D THR* 1.3 62.3 + - - +
139D MSE 4.4 4.0 - - - +
140D ALA* 3.3 22.0 + - - +
161D TYR* 3.1 13.6 + - - +
162D LYS* 2.7 37.0 + - - +
164D ARG* 3.6 20.4 + - - -
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Residues in contact with THR 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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109D GLU* 4.0 32.3 - - + +
110D THR* 5.8 1.6 - - + -
134D GLU* 3.3 28.7 + - - +
135D MSE 3.2 0.4 - - - -
136D ASP* 1.3 76.6 - - - +
138D ILE* 1.3 66.1 + - - +
140D ALA* 3.3 7.9 + - + +
141D LEU* 3.1 27.3 + - + +
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Residues in contact with ILE 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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107D ILE* 4.7 4.7 - - + +
109D GLU* 4.3 9.4 - - + -
112D ILE* 4.0 24.5 - - + -
123D ILE* 3.7 23.5 - - + +
125D PRO* 3.9 27.8 - - + -
133D CYS* 3.9 17.7 - - + -
134D GLU 3.2 15.5 - - - +
135D MSE 3.1 19.0 + - + +
137D THR* 1.3 74.3 - - - +
139D MSE 1.3 60.1 + - - +
141D LEU* 3.0 11.9 + - - +
142D ALA* 3.0 25.3 + - - +
149D VAL* 4.5 11.7 - - + -
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Residues in contact with MSE 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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135D MSE 2.7 45.9 + - + +
136D ASP* 4.4 3.8 - - - +
138D ILE* 1.3 72.7 - - - +
140D ALA* 1.3 56.2 + - - +
142D ALA* 3.4 5.3 + - + +
143D LYS* 3.0 28.4 + - - +
149D VAL* 3.7 25.8 - - + -
164D ARG* 5.2 4.0 - - - +
169D ILE* 4.0 18.4 - - + +
170D GLY* 4.0 22.2 - - - +
171D HIS* 4.3 14.4 - - + -
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Residues in contact with ALA 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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136D ASP 3.3 15.3 + - - +
137D THR* 3.3 13.6 + - + +
139D MSE 1.3 79.8 - - - +
141D LEU* 1.3 62.3 + - + +
143D LYS* 3.6 6.1 + - - +
144D LYS* 3.2 23.7 + - - +
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Residues in contact with LEU 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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109D GLU 3.9 14.1 - - - +
112D ILE* 3.7 37.9 - - + -
113D GLU* 3.5 43.3 - - + +
116D ILE* 4.9 3.8 - - + -
123D ILE* 5.0 6.1 - - + -
137D THR* 3.1 21.4 + - + +
138D ILE* 3.0 9.9 + - - +
140D ALA* 1.3 77.6 - - + +
142D ALA* 1.3 58.2 + - - +
144D LYS* 3.4 3.8 + - + -
145D HIS* 3.0 46.5 + - + +
147D LEU* 4.7 2.5 - - - +
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Residues in contact with ALA 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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123D ILE* 4.5 2.6 - - + +
138D ILE 3.0 8.7 + - - +
139D MSE 3.7 14.1 - - + +
140D ALA 3.3 0.2 - - - -
141D LEU* 1.3 77.9 - - - +
143D LYS* 1.3 56.1 + - - +
146D ASN* 2.9 11.1 + - - -
147D LEU* 2.8 49.3 + - + +
149D VAL* 3.6 31.2 - - + -
171D HIS* 4.9 2.5 - - + -
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Residues in contact with LYS 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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139D MSE 3.0 17.5 + - - +
140D ALA* 3.8 7.4 - - - +
141D LEU 3.3 0.2 - - - -
142D ALA* 1.3 78.5 - - - +
144D LYS* 1.3 64.1 + - - +
146D ASN* 3.3 19.2 - - - +
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Residues in contact with LYS 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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118B ASP* 5.1 5.0 - - - +
119B LYS* 5.7 11.2 - - - +
113D GLU* 2.9 24.8 + - - +
140D ALA 3.2 15.3 + - - +
141D LEU* 4.6 3.8 - - + -
142D ALA 3.4 0.2 - - - -
143D LYS* 1.3 84.1 - - - +
145D HIS* 1.3 83.8 + - + +
146D ASN* 3.3 6.3 + - - +
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Residues in contact with HIS 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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113D GLU* 3.3 31.1 + - + +
116D ILE* 3.4 39.9 - - + +
141D LEU* 3.0 30.9 + - - +
144D LYS* 1.3 100.8 - - + +
146D ASN* 1.3 73.1 + - - +
147D LEU* 3.4 25.6 - - + +
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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