Contacts of the helix formed by residues 169 - 185 (chain B) in PDB entry 4IF8
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 ASN 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ASN* 2.9 27.5 + - - +
167B PHE 3.1 0.4 - - - -
168B GLN* 1.3 88.5 + - - +
170B LEU* 1.3 58.3 + - - +
171B GLU* 3.4 12.6 + - - +
172B MET* 3.2 34.4 + - + +
173B ALA 2.8 23.2 + - - -
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Residues in contact with LEU 170 (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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167B PHE* 3.6 37.0 - - + +
168B GLN 4.1 0.4 - - - -
169B ASN* 1.3 68.6 + - - +
171B GLU* 1.3 59.4 + - - +
173B ALA* 3.6 3.1 - - + +
174B GLN* 2.9 32.1 + - - +
196B ILE* 3.6 47.4 - - + +
197B ASP 3.9 11.7 - - - +
198B PRO* 4.3 11.7 - - + -
199B GLY 4.8 2.2 - - - +
200B THR 4.3 5.8 - - - +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASN* 3.3 9.5 + - - +
170B LEU* 1.3 77.3 - - - +
172B MET* 1.3 61.9 + - - +
174B GLN* 3.5 6.0 + - - +
175B LYS* 3.3 43.6 + - - +
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Residues in contact with MET 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LYS* 6.1 4.7 - - - -
166B ASN* 2.9 35.7 - - + +
169B ASN* 3.2 31.7 + - + +
171B GLU* 1.3 76.6 - - - +
173B ALA* 1.4 59.2 + - - +
175B LYS* 3.5 10.3 + - - +
176B GLN* 3.0 45.8 + - + +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR* 3.8 13.5 - - + -
166B ASN 3.4 20.2 + - - +
167B PHE* 3.8 29.4 - - + -
169B ASN 2.8 8.5 + - - +
170B LEU* 3.2 11.4 + - - +
172B MET* 1.4 75.5 - - - +
174B GLN* 1.3 57.3 + - - +
176B GLN* 3.3 4.4 + - - +
177B ILE* 2.8 36.6 + - - +
196B ILE* 4.2 2.9 - - + -
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Residues in contact with GLN 174 (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 2.9 17.2 + - - +
171B GLU* 3.7 7.1 - - - +
173B ALA* 1.3 75.9 - - - +
175B LYS* 1.3 59.2 + - + +
177B ILE* 3.4 4.3 + - - +
178B ASN* 2.8 39.9 + - - +
193B ILE* 3.4 34.7 + - + +
194B GLU* 3.2 28.7 + - - +
195B ASN* 3.4 10.6 + - - -
196B ILE* 3.7 14.6 + - + +
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Residues in contact with LYS 175 (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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174A GLN* 5.3 3.4 + - - -
191A ASN* 3.0 38.5 + - + +
193A ILE 5.3 1.0 + - - -
194A GLU* 3.8 41.0 + - + +
171B GLU* 3.3 32.9 + - - +
172B MET* 3.7 10.8 - - - +
174B GLN* 1.3 77.3 - - + +
176B GLN* 1.4 53.9 + - + +
178B ASN* 3.3 1.4 + - - +
179B ASP* 2.8 33.2 + - - +
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Residues in contact with GLN 176 (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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414A LYS* 3.8 36.4 - - + +
139B PHE* 5.0 2.0 - - + -
142B GLN* 5.2 0.4 + - - -
163B ILE* 6.5 0.7 - - + -
164B LEU 5.1 1.6 - - - -
165B THR* 3.4 15.1 - - + +
166B ASN* 2.9 38.8 + - - +
172B MET* 3.0 35.1 + - + +
173B ALA* 3.6 3.3 - - - +
175B LYS* 1.4 74.7 - - + +
177B ILE* 1.3 58.6 + - - +
179B ASP* 3.7 6.0 - - - +
180B PHE* 2.9 31.2 + - - +
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Residues in contact with ILE 177 (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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139B PHE* 3.7 44.4 - - + -
165B THR* 4.3 4.9 - - + -
167B PHE* 4.0 22.0 - - + -
173B ALA 2.8 19.8 + - - +
174B GLN* 3.7 4.0 - - - +
176B GLN* 1.3 77.3 - - - +
178B ASN* 1.3 63.5 + - - +
180B PHE* 3.3 2.9 + - - +
181B ILE* 3.1 28.9 + - + +
192B LEU* 5.1 1.8 - - + -
193B ILE* 3.6 25.1 - - + -
196B ILE* 4.0 14.1 - - + -
203B LEU* 3.9 28.5 - - + -
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Residues in contact with ASN 178 (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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190A ASN* 5.4 0.4 - - - -
191A ASN* 4.1 16.1 + - - +
174B GLN* 2.8 31.2 + - - +
175B LYS* 3.9 2.4 - - - +
177B ILE* 1.3 71.9 - - - +
179B ASP* 1.3 57.4 + - - +
181B ILE* 3.5 4.7 + - - +
182B SER* 3.0 33.5 + - - -
189B ILE 4.6 0.9 - - - +
191B ASN* 3.8 21.3 + - - +
192B LEU* 3.3 13.3 + - - +
193B ILE* 2.8 53.4 + - - +
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Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LYS 5.3 1.4 - - - +
190A ASN* 3.0 33.9 + - - +
191A ASN* 3.6 13.4 - - - +
355A LYS* 4.9 5.9 + - - -
175B LYS 2.8 23.5 + - - +
176B GLN* 3.7 6.6 - - - +
178B ASN* 1.3 69.7 - - - +
180B PHE* 1.3 65.5 + - - +
182B SER* 3.3 2.1 + - - -
183B GLN* 2.6 52.9 + - - +
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 3.6 24.2 - - + -
139B PHE* 3.8 24.7 - + + -
161B GLU* 4.0 17.3 - - + -
163B ILE* 3.5 38.6 - - + -
176B GLN 2.9 18.8 + - - +
177B ILE 3.3 4.2 + - - +
179B ASP* 1.3 81.4 + - - +
181B ILE* 1.3 61.7 + - + +
183B GLN* 3.6 11.5 - - + +
184B LYS* 2.9 42.7 + - + +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 3.9 21.5 - - - +
139B PHE* 4.0 17.3 - - + -
177B ILE* 3.1 19.0 + - + +
178B ASN 4.1 3.1 - - - +
180B PHE* 1.3 77.0 - - + +
182B SER* 1.3 59.9 + - - +
184B LYS* 3.3 6.4 + - + +
185B THR* 2.8 39.3 + - + +
189B ILE* 3.7 34.5 - - + +
192B LEU* 3.9 24.7 - - + -
205B ALA* 4.0 14.8 - - + -
207B TYR* 4.7 15.3 - - + -
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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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182A SER* 4.1 1.0 + - - -
187A GLY* 3.5 3.5 - - - -
190A ASN* 3.4 32.0 + - - +
178B ASN 3.0 22.4 + - - -
179B ASP 3.6 0.2 - - - -
181B ILE* 1.3 77.5 - - - +
183B GLN* 1.4 61.4 + - - +
185B THR* 3.9 1.6 - - - -
186B HIS* 3.1 3.5 + - - -
187B GLY 2.7 27.2 + - - -
189B ILE 3.4 12.0 + - - -
190B ASN* 2.7 30.1 + - - +
191B ASN 4.5 0.7 + - - -
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Residues in contact with GLN 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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186A HIS 4.9 0.3 - - - +
187A GLY 3.5 20.9 - - - +
188A LYS* 5.5 2.2 - - - +
190A ASN* 3.8 4.5 - - - +
211A ARG* 5.7 0.3 + - - -
312A HIS* 3.1 36.0 + - + -
357A GLU* 5.9 0.4 - - - +
359A LYS* 4.7 6.8 + - - -
179B ASP* 2.6 43.4 + - - +
180B PHE* 3.6 13.5 - - + +
182B SER* 1.4 73.5 - - - +
184B LYS* 1.3 65.1 + - - +
186B HIS* 3.2 23.7 + - - -
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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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134B ILE 5.4 1.4 + - - -
135B GLY* 4.0 14.6 - - - -
136B ASN 5.4 0.2 - - - +
137B THR* 4.2 4.7 - - - +
159B SER* 4.9 6.3 + - - -
161B GLU* 2.7 36.0 + - - +
180B PHE* 2.9 36.4 + - + +
181B ILE* 3.7 7.9 - - + +
183B GLN* 1.3 80.7 - - - +
185B THR* 1.4 58.9 + - + +
186B HIS* 3.6 13.7 + - - -
207B TYR* 3.6 35.8 + - + +
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Residues in contact with THR 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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181B ILE* 2.8 24.6 + - + +
182B SER 3.6 2.1 + - - -
184B LYS* 1.4 75.9 - - + +
186B HIS* 1.3 65.8 + - - +
188B LYS* 2.8 38.8 + - - +
189B ILE* 2.9 47.9 + - + -
207B TYR* 3.4 40.2 - - + -
209B PHE* 6.5 0.2 - - - -
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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