Contacts of the helix formed by residues 144 - 156 (chain B) in PDB entry 1IXR
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 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B SER* 1.3 69.1 - - - +
145B ALA* 1.3 65.8 + - - +
146B ALA* 2.6 19.5 + - + +
147B GLU* 2.8 43.9 + - + +
148B GLU* 2.6 23.1 + - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER 2.6 13.5 + - - +
144B GLU* 1.3 68.4 - - - +
146B ALA* 1.3 65.9 + - - +
148B GLU* 3.4 13.4 - - - +
149B ALA* 2.6 20.4 + - - +
177B ALA 4.1 8.3 - - - +
178B ARG* 4.6 2.7 - - - -
179B ALA* 3.5 33.9 - - + +
182B LEU* 4.0 1.3 - - - +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 2.6 20.1 + - + +
145B ALA* 1.3 73.8 - - - +
147B GLU* 1.3 57.3 + - - +
149B ALA* 2.5 34.8 + - - +
150B VAL* 3.2 4.1 + - - +
167B VAL* 4.2 6.7 - - + -
168B LEU* 5.7 7.4 - - + -
171B LEU* 3.4 27.8 - - + +
182B LEU* 3.8 13.9 - - - +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 2.8 36.7 + - + +
146B ALA* 1.3 76.1 - - - +
148B GLU* 1.3 65.0 + - - +
150B VAL* 2.7 31.5 + - + +
151B MET* 2.7 36.8 + - + +
164B ARG* 4.8 17.7 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLU* 5.7 1.2 - - - +
143B SER* 3.5 14.4 + - - +
144B GLU 2.6 22.0 + - - +
145B ALA* 3.4 11.8 - - - +
147B GLU* 1.3 72.5 - - - +
149B ALA* 1.3 65.3 + - - +
151B MET* 3.6 13.7 + - - +
152B ALA* 3.1 18.0 + - - +
179B ALA* 3.4 22.5 - - + +
123C ILE* 5.7 1.1 - - + -
130C ARG* 2.8 31.9 + - - +
132C ILE* 3.7 23.7 - - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ALA 2.6 12.7 + - - +
146B ALA 2.5 21.7 + - - +
148B GLU* 1.3 68.1 - - - +
150B VAL* 1.3 66.0 + - - +
152B ALA* 2.7 22.2 + - - +
153B LEU* 3.0 6.3 + - + -
167B VAL* 3.7 9.9 - - + -
179B ALA* 4.5 2.0 - - - +
182B LEU* 3.7 23.8 - - + -
183B ILE* 3.3 28.5 - - + +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ALA 3.7 7.2 - - - +
147B GLU* 2.7 26.7 + - + +
149B ALA* 1.3 74.3 - - - +
151B MET* 1.3 58.8 + - + +
153B LEU* 2.5 36.8 + - - +
154B ALA* 2.8 12.2 + - + +
160B GLU* 4.1 22.4 - - + +
163B ALA* 4.1 2.5 - - + -
164B ARG* 3.5 38.4 - - + +
167B VAL* 3.3 26.2 - - + +
168B LEU* 5.2 2.7 - - + -
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Residues in contact with MET 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLU* 2.7 40.2 + - + +
148B GLU* 3.6 12.1 - - - +
150B VAL* 1.3 74.0 - - + +
152B ALA* 1.3 62.7 + - - +
154B ALA* 3.7 7.9 + - - +
155B ALA* 3.4 17.8 + - - +
123C ILE* 3.1 34.3 - - + +
124C GLY* 6.2 0.7 - - - -
125C GLN* 4.2 27.4 - - + +
130C ARG* 6.4 0.4 - - - -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLU 3.1 4.2 + - - -
149B ALA 2.7 13.4 + - - +
150B VAL 2.6 3.4 + - - -
151B MET* 1.3 70.7 - - - +
153B LEU* 1.3 65.4 + - + +
155B ALA* 2.8 18.6 + - - -
156B LEU* 3.0 17.3 + - + +
183B ILE* 3.1 26.5 - - + -
121C ILE* 4.5 17.3 - - + -
123C ILE* 4.1 2.2 - - - +
132C ILE* 3.3 21.3 - - + -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ALA* 3.0 2.7 + - + +
150B VAL* 2.5 15.8 + - - +
152B ALA* 1.3 73.9 - - - +
154B ALA* 1.3 62.5 + - - +
156B LEU* 2.9 21.1 + - + +
157B GLY 3.3 6.4 + - - -
158B PHE* 3.8 21.4 + - + -
163B ALA* 3.0 43.7 - - + +
167B VAL* 3.9 15.0 - - + -
183B ILE* 3.8 43.1 - - + +
186B ALA* 3.9 17.7 - - + -
187B LEU* 4.5 9.4 - - + -
190B LEU* 4.6 3.4 - - + -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B VAL 2.8 13.4 + - - +
151B MET* 3.9 12.3 - - - +
153B LEU* 1.3 71.2 - - - +
155B ALA* 1.3 58.5 + - - +
157B GLY* 2.9 27.2 + - - +
158B PHE 3.2 15.7 + - - +
160B GLU* 4.4 22.2 - - + +
163B ALA* 4.6 1.0 - - - +
125C GLN* 6.2 0.2 - - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B MET 3.4 8.7 + - - +
152B ALA* 2.8 14.3 + - - +
154B ALA* 1.3 74.6 - - - +
156B LEU* 1.3 67.1 + - + +
157B GLY 3.3 1.8 - - - -
77C PRO* 4.7 7.1 - - - +
109C HIS* 6.0 0.7 + - - -
121C ILE* 5.0 0.4 - - + -
122C VAL 4.5 15.3 - - - +
123C ILE* 5.2 6.5 - - + -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA* 3.0 11.6 + - + +
153B LEU* 2.9 16.5 + - + +
155B ALA* 1.3 85.4 - - - +
157B GLY* 1.3 56.9 + - - +
158B PHE* 3.9 9.7 + - + -
183B ILE* 6.4 0.7 - - + -
187B LEU* 5.6 7.9 - - + -
76C LYS* 3.7 4.3 - - - +
77C PRO* 3.1 17.5 - - + +
78C GLY* 3.0 45.0 + - - +
81C ALA* 4.2 4.9 - - + -
109C HIS* 5.8 6.5 - - + +
119C MET* 3.9 15.0 - - + -
121C ILE* 3.2 53.4 - - + -
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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