Contacts of the helix formed by residues 178 - 190 (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 ARG 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B ALA* 4.6 4.5 - - - -
177B ALA* 1.3 70.4 - - - +
179B ALA* 1.3 67.4 + - - +
180B GLN* 2.8 20.4 + - + +
181B ASP* 3.0 41.2 + - + +
182B LEU 2.6 20.4 + - - -
135C GLU* 5.8 1.0 + - - -
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Residues in contact with ALA 179 (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* 3.5 30.7 - - + +
148B GLU* 3.4 32.1 - - + +
149B ALA* 4.3 5.4 - - - +
177B ALA 3.2 2.6 + - - -
178B ARG* 1.3 69.3 - - - +
180B GLN* 1.3 54.5 + - - +
182B LEU* 3.8 7.9 - - - -
183B ILE* 2.3 47.8 + - + +
132C ILE* 5.4 4.0 - - + -
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Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ARG* 2.8 20.7 + - + +
179B ALA* 1.3 86.0 - - - +
181B ASP* 1.3 75.3 + - - +
182B LEU 2.5 8.7 + - - -
183B ILE* 2.7 12.1 + - - +
184B LYS* 3.0 29.4 + - + +
132C ILE* 5.9 1.1 - - - +
133C ARG* 4.5 7.3 + - - +
134C LEU* 2.6 47.5 + - - +
135C GLU* 3.1 33.1 + - - +
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Residues in contact with ASP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA* 5.1 4.7 - - + -
178B ARG* 3.0 45.5 + - + +
180B GLN* 1.3 92.0 - - - +
182B LEU* 1.3 59.3 + - - +
184B LYS* 4.5 12.9 - - - +
185B GLU* 3.2 22.8 + - - +
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Residues in contact with LEU 182 (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 4.0 2.2 - - - +
146B ALA* 3.8 15.9 - - - -
149B ALA* 3.7 11.2 - - + -
167B VAL* 3.3 32.5 - - + +
170B LEU* 3.5 44.9 - - + +
171B LEU* 4.2 11.4 - - + -
177B ALA* 3.7 28.7 - - + +
178B ARG 2.6 18.7 + - - +
179B ALA 3.2 3.4 - - - +
180B GLN 2.5 4.9 + - - -
181B ASP* 1.3 70.6 - - - +
183B ILE* 1.3 69.9 + - - +
185B GLU* 3.4 7.1 + - - +
186B ALA* 3.2 13.8 + - + +
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Residues in contact with ILE 183 (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 4.2 1.3 - - - +
149B ALA* 3.3 33.2 - - + +
152B ALA* 3.1 32.1 - - + -
153B LEU* 3.8 16.4 - - + +
156B LEU* 6.4 0.9 - - + -
179B ALA* 2.3 34.0 + - + +
180B GLN* 2.7 3.5 + - - +
182B LEU* 1.3 65.7 - - - +
184B LYS* 1.3 73.9 + - - +
186B ALA* 2.6 22.4 + - - +
187B LEU* 3.3 12.5 + - + +
121C ILE* 5.1 4.5 - - + -
132C ILE* 4.3 19.5 - - + -
134C LEU* 3.9 22.2 - - + -
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Residues in contact with LYS 184 (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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180B GLN* 3.2 34.0 + - + +
181B ASP* 4.7 11.0 - - - +
183B ILE* 1.3 79.9 - - + +
185B GLU* 1.3 55.4 + - - +
186B ALA 2.3 15.9 + - - -
187B LEU* 2.5 37.5 + - - +
188B LYS* 3.4 2.6 + - - -
85C ALA* 4.0 25.8 - - + +
86C ASN* 4.3 25.7 - - + +
134C LEU* 4.5 14.8 - - + -
135C GLU* 4.5 22.5 + - - +
137C PRO* 5.9 1.2 - - - +
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Residues in contact with GLU 185 (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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170B LEU* 3.9 28.0 - - + +
173B GLN* 5.8 0.2 - - - +
174B ASN* 6.3 0.4 - - - +
181B ASP 3.2 20.4 + - - +
182B LEU* 3.4 5.6 + - - +
184B LYS* 1.3 76.0 - - - +
186B ALA* 1.3 57.9 + - - +
188B LYS* 2.9 48.5 + - - +
189B ARG* 3.6 13.5 + - - +
86C ASN* 5.7 1.4 - - - +
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Residues in contact with ALA 186 (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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153B LEU* 3.9 28.0 - - + -
166B VAL* 4.5 13.2 - - + +
167B VAL* 5.5 1.8 - - + -
170B LEU* 4.1 11.9 - - + -
182B LEU 3.2 7.8 + - - +
183B ILE* 2.6 20.7 + - - +
184B LYS 2.3 12.5 + - - -
185B GLU* 1.3 66.5 - - - +
187B LEU* 1.3 53.4 + - + +
188B LYS 2.9 1.3 - - - -
189B ARG* 2.9 6.4 + - - +
190B LEU* 2.6 40.4 + - + +
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Residues in contact with LEU 187 (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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153B LEU* 4.5 12.6 - - + -
156B LEU* 5.6 8.1 - - + -
158B PHE* 3.4 32.7 - - + -
183B ILE* 4.1 12.8 - - + +
184B LYS* 2.5 34.5 + - - +
186B ALA* 1.3 74.3 - - - +
188B LYS* 1.3 55.7 - - - +
190B LEU* 3.3 5.3 - - + -
191B ARG* 2.8 33.5 + - - +
78C GLY 4.3 6.7 - - - +
81C ALA* 4.7 7.6 - - + -
82C ALA* 4.0 32.1 - - + +
85C ALA* 4.4 17.7 - - + +
134C LEU* 5.6 2.7 - - + -
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Residues in contact with LYS 188 (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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184B LYS 3.4 2.2 + - - -
185B GLU* 2.9 43.8 + - - +
187B LEU* 1.3 78.9 - - - +
189B ARG* 1.3 81.2 + - - +
190B LEU 3.2 1.7 + - - -
191B ARG* 3.0 58.8 + - - +
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Residues in contact with ARG 189 (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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166B VAL* 5.2 19.5 + - + +
169B ASP* 3.9 21.6 + - - +
170B LEU* 4.2 15.0 - - + +
173B GLN* 2.9 37.4 + - - +
185B GLU* 3.6 12.7 + - - +
186B ALA* 2.9 11.5 + - - +
188B LYS* 1.3 96.2 - - - +
190B LEU* 1.3 65.3 + - - +
191B ARG* 3.5 0.8 - - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.6 8.3 - - + -
158B PHE* 3.2 64.4 - - + -
162B GLN* 4.0 32.8 - - + +
163B ALA* 4.2 20.6 - - + +
166B VAL* 4.4 14.1 - - + -
186B ALA 2.6 22.3 + - - +
187B LEU 3.3 4.0 - - - +
188B LYS 3.0 0.2 - - - -
189B ARG* 1.3 79.8 - - - +
191B ARG* 1.3 71.2 + - - +
76C LYS* 4.3 2.3 - - - -
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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