Contacts of the helix formed by residues 181 - 195 (chain B) in PDB entry 1IAX
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 THR 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B HIS 5.7 0.2 + - - -
176B ASN* 3.4 29.4 - - - +
179B LYS* 3.5 4.4 + - + +
180B ILE* 1.3 75.0 - - - +
182B SER* 1.3 65.8 + - - +
183B LYS* 4.0 9.1 + - - +
184B ALA* 2.9 34.1 + - - +
185B VAL* 2.9 14.8 + - - +
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Residues in contact with SER 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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180B ILE 4.1 1.4 + - - -
181B THR* 1.3 70.0 - - - +
183B LYS* 1.3 64.2 + - - +
185B VAL* 3.1 9.1 + - - +
186B LYS* 2.9 51.7 + - - +
222B SER* 5.3 18.7 - - - -
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Residues in contact with LYS 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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181B THR* 3.2 8.8 + - - +
182B SER* 1.3 77.7 + - - +
184B ALA* 1.3 59.1 + - + +
186B LYS* 3.5 7.2 + - - +
187B GLU* 2.7 75.8 + - + +
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Residues in contact with ALA 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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170B ILE* 4.0 9.5 - - + +
171B HIS* 3.9 32.4 + - + +
181B THR* 2.9 24.3 + - - +
183B LYS* 1.3 76.9 - - + +
185B VAL* 1.3 65.7 + - - +
187B GLU* 3.6 11.9 - - - +
188B ALA* 3.1 25.1 + - - +
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Residues in contact with VAL 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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146B LEU* 4.8 2.8 - - + +
170B ILE* 4.2 17.9 - - + +
180B ILE* 3.4 32.5 - - + -
181B THR 2.9 14.2 + - - +
182B SER* 3.6 9.6 - - - +
184B ALA* 1.3 75.5 - - - +
186B LYS* 1.3 63.9 + - + +
188B ALA* 4.0 2.3 - - - +
189B TYR* 3.2 21.7 + - - +
202B LEU* 4.3 18.6 - - + -
222B SER 6.1 0.9 - - - +
223B VAL* 5.0 11.2 - - + -
226B PHE* 3.6 34.8 - - + -
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Residues in contact with LYS 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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182B SER* 2.9 34.6 + - - +
183B LYS* 3.7 6.3 - - - +
185B VAL* 1.3 75.4 - - + +
187B GLU* 1.3 69.1 + - + +
189B TYR* 2.9 2.9 + - - +
190B GLU* 2.8 44.9 + - - +
226B PHE* 3.6 40.2 - - + -
229B GLN* 5.5 7.9 + - - +
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Residues in contact with GLU 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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183B LYS* 2.7 76.0 + - + +
184B ALA* 3.6 10.1 - - - +
185B VAL 3.5 0.2 - - - -
186B LYS* 1.3 73.6 - - + +
188B ALA* 1.3 60.4 + - - +
190B GLU* 4.1 11.6 + - - +
191B ASN* 3.2 29.3 + - - +
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Residues in contact with ALA 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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146B LEU* 4.1 8.1 - - + -
168B ILE* 4.4 8.8 - - + +
169B PRO 3.6 23.6 - - - +
170B ILE* 4.0 18.2 - - + -
171B HIS 5.4 0.2 - - - +
184B ALA 3.1 15.1 + - - +
185B VAL 4.0 0.7 - - - +
187B GLU* 1.3 77.5 - - - +
189B TYR* 1.3 65.2 + - - +
191B ASN* 3.4 8.2 + - - +
192B ALA* 3.3 16.5 + - - +
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Residues in contact with TYR 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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146B LEU* 3.9 16.3 - - + +
185B VAL 3.2 15.3 + - - +
186B LYS 2.9 4.1 + - - +
188B ALA* 1.3 75.9 - - - +
190B GLU* 1.3 68.3 + - + +
192B ALA* 2.8 29.4 + - - +
193B GLN* 3.1 43.7 + - + +
199B VAL* 3.8 37.9 + - + -
226B PHE* 3.3 25.1 - + + -
230B HIS* 3.0 40.7 + + - +
232B ILE* 4.2 14.4 - - + +
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Residues in contact with GLU 190 (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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186B LYS* 2.8 42.2 + - + +
187B GLU* 4.1 10.7 + - - +
189B TYR* 1.3 79.9 - - + +
191B ASN* 1.3 61.9 + - - +
193B GLN* 3.4 20.1 + - - +
194B LYS* 3.1 29.0 + - + +
226B PHE* 5.8 0.7 - - + -
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Residues in contact with ASN 191 (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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187B GLU* 3.2 22.3 + - - +
188B ALA* 3.4 8.5 - - - +
189B TYR 3.0 0.6 + - - -
190B GLU* 1.3 74.2 - - - +
192B ALA* 1.3 60.7 + - - +
194B LYS* 3.1 13.6 + - - +
195B SER* 2.9 36.3 + - - -
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Residues in contact with ALA 192 (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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168B ILE* 3.9 20.0 - - + -
188B ALA 3.3 6.5 + - - +
189B TYR* 2.8 11.9 + - - +
191B ASN* 1.3 77.0 - - - +
193B GLN* 1.3 58.2 + - - +
195B SER* 2.7 24.7 + - - +
196B ASN 2.9 10.4 + - - -
197B ILE* 3.0 18.7 + - + +
199B VAL* 3.4 28.7 - - + -
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Residues in contact with GLN 193 (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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189B TYR* 3.1 54.3 + - + +
190B GLU* 3.6 19.6 - - - +
192B ALA* 1.3 76.1 - - + +
194B LYS* 1.3 66.3 + - - +
196B ASN* 3.0 23.0 + - - +
197B ILE 4.8 4.7 - - - +
199B VAL* 5.7 1.8 - - + -
230B HIS* 5.2 0.4 + - - -
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Residues in contact with LYS 194 (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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190B GLU* 3.1 21.1 + - + +
191B ASN* 3.2 17.0 - - - +
193B GLN* 1.3 84.6 - - - +
195B SER* 1.3 58.3 + - - +
196B ASN* 3.4 8.1 + - - +
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Residues in contact with SER 195 (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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191B ASN* 2.9 18.0 + - - -
192B ALA* 2.7 10.2 + - - -
194B LYS* 1.3 79.1 + - - +
196B ASN* 1.3 73.4 + - - +
197B ILE* 3.1 26.3 - - - +
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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