Contacts of the helix formed by residues 140 - 152 (chain D) in PDB entry 5IRC
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 LYS 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D ARG* 3.7 2.2 - - - +
137D GLU* 2.6 38.8 + - - -
138D PRO 4.3 4.7 - - - +
139D VAL* 1.3 76.5 - - - +
141D PRO* 1.3 77.0 - - + +
142D GLU* 3.2 29.2 - - + +
143D GLU* 2.6 41.6 + - + +
144D GLY* 3.2 8.3 + - - -
158D GLU* 4.6 0.2 - - - +
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Residues in contact with PRO 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 ARG* 3.5 31.6 - - - +
140D LYS* 1.3 88.0 - - + +
142D GLU* 1.3 63.5 + - - +
144D GLY* 3.1 3.5 + - - -
145D ARG* 3.0 25.4 + - - +
156D TYR* 3.7 8.2 - - + -
158D GLU* 3.3 21.1 - - - +
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Residues in contact with GLU 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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140D LYS* 3.3 35.2 - - + +
141D PRO* 1.3 84.0 - - - +
143D GLU* 1.3 66.1 + - + +
145D ARG* 3.8 7.3 - - - +
146D ASP* 2.9 43.5 + - - +
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Residues in contact with GLU 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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92D LEU* 4.2 13.4 - - + +
137D GLU* 5.1 3.5 - - - +
138D PRO 4.3 1.0 - - - +
139D VAL* 3.4 16.4 - - + +
140D LYS* 2.6 53.3 + - + +
142D GLU* 1.3 84.1 - - + +
144D GLY* 1.3 60.2 - - - +
146D ASP* 3.5 8.0 + - - +
147D MET* 3.1 23.9 + - - +
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Residues in contact with GLY 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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84D PHE* 4.4 10.8 - - - -
92D LEU* 4.8 1.3 - - - -
114D LEU* 3.6 7.3 - - - +
139D VAL* 4.3 2.3 - - - +
140D LYS 3.2 4.4 + - - -
141D PRO 3.1 4.2 + - - -
143D GLU* 1.3 77.5 - - - +
145D ARG* 1.3 57.6 + - - +
147D MET* 3.2 7.6 + - - +
148D ALA* 2.9 25.1 + - - +
156D TYR* 3.5 30.5 - - - -
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Residues in contact with ARG 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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141D PRO 3.0 15.0 + - - +
142D GLU* 3.9 8.3 - - - +
144D GLY* 1.3 72.3 - - - +
146D ASP* 1.3 67.6 + - - +
148D ALA* 3.2 21.8 + - - +
149D ASN* 3.0 50.7 + - - +
153D ALA 4.5 11.1 + - - -
154D PHE 5.6 0.4 + - - -
155D GLY* 4.4 4.8 - - - -
156D TYR* 3.8 37.4 + - + +
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Residues in contact with ASP 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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142D GLU* 2.9 30.4 + - - +
143D GLU* 3.8 7.7 - - - +
145D ARG* 1.3 79.0 - - - +
147D MET* 1.3 58.5 + - - +
149D ASN* 3.3 16.2 + - - +
150D ARG* 3.0 27.6 + - - +
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Residues in contact with MET 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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92D LEU* 3.9 31.0 - - + +
93D GLU* 5.3 1.8 - - - -
95D ILE* 3.7 23.1 - - + -
96D PRO* 3.7 37.7 - - + -
114D LEU* 3.9 7.4 - - + -
143D GLU 3.1 13.5 + - - +
144D GLY 3.2 7.8 + - - +
146D ASP* 1.3 74.9 - - - +
148D ALA* 1.3 65.0 + - - +
150D ARG* 3.2 26.1 + - - +
151D ILE* 3.0 25.9 + - - +
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Residues in contact with ALA 148 (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 LEU* 3.5 11.8 - - + +
144D GLY 2.9 13.6 + - - +
145D ARG* 3.5 26.3 + - - +
147D MET* 1.3 75.3 - - - +
149D ASN* 1.3 63.5 + - - +
151D ILE* 3.4 1.2 + - - -
152D GLY 3.0 3.3 + - - -
153D ALA* 2.9 43.2 + - + +
156D TYR* 3.7 20.2 - - + -
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Residues in contact with ASN 149 (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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145D ARG* 3.0 50.7 + - - +
146D ASP* 3.4 19.4 + - - +
148D ALA* 1.3 76.4 - - - +
150D ARG* 1.3 63.9 + - - +
152D GLY* 3.2 13.1 + - - -
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Residues in contact with ARG 150 (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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1242A TRP* 3.8 17.1 - - + -
1243A GLU* 2.7 44.3 + - - +
96D PRO* 3.5 36.6 - - - +
97D GLU* 5.3 5.5 + - - -
146D ASP 3.0 13.5 + - - +
147D MET* 3.2 27.1 + - - +
149D ASN* 1.3 77.7 - - - +
151D ILE* 1.3 59.8 + - + +
152D GLY 3.6 0.2 + - - -
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Residues in contact with ILE 151 (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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1242A TRP* 4.0 22.1 - - + -
82D MET* 4.0 19.7 - - + -
95D ILE* 4.1 16.2 - - + -
96D PRO* 5.0 1.3 - - + -
100D THR* 3.4 32.3 - - + +
104D LYS* 3.8 22.5 - - - -
112D ILE* 4.4 11.9 - - + +
114D LEU* 4.3 12.3 - - + -
147D MET* 3.0 28.0 + - - +
148D ALA* 3.7 5.6 - - - +
150D ARG* 1.3 77.8 - - + +
152D GLY* 1.3 62.6 + - - +
153D ALA* 3.8 16.8 - - + +
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Residues in contact with GLY 152 (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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104D LYS* 4.9 7.3 + - - -
112D ILE* 5.5 2.0 + - - +
148D ALA 3.0 5.4 + - - -
149D ASN 3.2 10.8 + - - -
150D ARG 3.4 0.8 + - - -
151D ILE* 1.3 79.8 - - - +
153D ALA* 1.3 66.4 + - - +
154D PHE* 3.6 1.2 + - - -
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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