Contacts of the helix formed by residues 169 - 185 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASN* 3.4 26.8 + - - +
167A PHE 3.2 0.9 - - - -
168A GLN* 1.4 77.0 - - - +
170A LEU* 1.3 57.4 + - - +
171A GLU* 3.6 14.0 + - - +
172A MET* 3.1 42.5 + - + +
173A ALA* 2.9 24.3 + - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE* 3.3 27.8 - - + +
168A GLN 3.8 2.2 + - - +
169A ASN* 1.3 72.0 - - - +
171A GLU* 1.3 70.6 + - - +
173A ALA* 3.7 4.3 - - - +
174A GLN* 3.0 29.3 + - - +
196A ILE* 3.7 47.6 - - + +
197A ASP 4.2 5.8 - - - +
198A PRO* 3.8 34.3 - - + -
199A GLY 5.4 1.3 - - - +
200A THR* 5.5 0.9 - - - +
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 3.4 12.1 - - - +
170A LEU* 1.3 86.9 + - - +
172A MET* 1.3 59.9 + - - +
174A GLN* 3.5 6.4 + - - +
175A LYS* 3.3 41.9 + - - +
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Residues in contact with MET 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 4.3 28.5 - - + +
169A ASN* 3.1 33.7 + - + +
171A GLU* 1.3 73.4 - - - +
173A ALA* 1.4 60.4 + - - +
175A LYS* 3.4 13.8 + - + +
176A GLN* 2.9 33.5 + - + +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A THR* 3.7 26.9 - - + -
166A ASN 3.7 9.3 + - - +
167A PHE* 4.1 9.9 - - + -
169A ASN 2.9 18.3 + - - +
170A LEU* 3.7 7.0 - - - +
171A GLU 3.4 0.2 - - - -
172A MET* 1.4 74.9 - - - +
174A GLN* 1.3 57.4 + - - +
176A GLN* 3.3 4.6 + - - +
177A ILE* 2.9 34.5 + - - +
196A ILE* 3.9 14.4 - - + -
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU 3.0 17.6 + - - +
171A GLU* 3.7 7.2 - - - +
173A ALA* 1.3 76.3 - - - +
175A LYS* 1.4 58.0 + - + +
177A ILE* 3.4 3.7 + - - +
178A ASN* 2.9 36.4 + - - +
193A ILE* 3.5 31.7 - - + +
194A GLU* 3.1 34.4 + - - +
195A ASN* 3.2 11.9 - - - +
196A ILE* 3.6 13.6 - - + +
175B LYS* 5.3 3.1 + - - -
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 3.3 30.0 + - - +
172A MET* 3.9 11.7 - - + +
174A GLN* 1.4 75.1 - - + +
176A GLN* 1.3 57.1 + - - +
178A ASN* 3.5 2.0 + - - +
179A ASP* 2.8 37.9 + - - +
191B ASN* 3.4 26.4 + - + +
194B GLU* 5.3 18.4 + - + +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 4.5 3.0 - - - -
163A ILE* 3.6 16.0 - - - +
164A LEU 3.2 23.0 + - - -
165A THR* 3.2 34.6 + - - +
166A ASN 4.2 2.4 + - - -
172A MET* 2.9 20.5 + - + +
173A ALA* 3.6 4.1 - - - +
175A LYS* 1.3 76.6 - - - +
177A ILE* 1.3 56.7 + - - +
179A ASP* 3.9 4.0 - - - +
180A PHE* 2.8 34.2 + - + +
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 3.6 48.7 - - + -
165A THR* 4.7 5.2 - - + -
167A PHE* 4.2 7.9 - - + -
173A ALA 2.9 22.4 + - - +
174A GLN 3.8 2.9 - - - +
176A GLN* 1.3 75.1 - - + +
178A ASN* 1.3 63.8 + - - +
180A PHE* 3.3 1.7 + - - +
181A ILE* 3.0 43.9 + - + +
193A ILE* 3.5 26.2 - - + -
196A ILE* 3.9 22.7 - - + -
203A LEU* 4.0 18.4 - - + -
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Residues in contact with ASN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLN* 2.9 29.6 + - - +
175A LYS* 4.0 3.5 - - - +
177A ILE* 1.3 73.9 - - - +
179A ASP* 1.3 56.7 + - - +
181A ILE* 3.5 4.1 + - - +
182A SER* 3.0 34.2 + - - +
189A ILE 4.8 0.3 - - - +
191A ASN* 3.8 18.5 + - - +
192A LEU* 3.2 15.6 + - - +
193A ILE* 2.9 50.8 + - - +
190B ASN* 5.6 0.4 - - - -
191B ASN* 4.3 17.4 + - - +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LYS 2.8 23.4 + - - +
176A GLN* 3.9 4.0 - - - +
178A ASN* 1.3 69.7 - - - +
180A PHE* 1.3 61.1 + - - +
182A SER* 3.9 0.6 - - - -
183A GLN* 2.7 64.5 + - - +
190B ASN* 3.0 33.8 + - - +
191B ASN* 4.0 9.7 + - - +
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A THR* 4.0 20.4 - - + -
139A PHE* 3.7 23.8 - + + -
161A GLU* 4.1 13.2 - - - -
163A ILE* 3.9 33.7 - - + -
176A GLN* 2.8 20.7 + - + +
177A ILE 3.5 4.5 - - - +
179A ASP* 1.3 78.3 + - - +
181A ILE* 1.3 62.3 + - + +
183A GLN* 3.5 5.3 + - - +
184A LYS* 3.0 52.9 + - + +
207A TYR* 4.4 0.7 - - - -
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 4.1 3.6 - - + -
177A ILE* 3.0 35.8 + - + +
178A ASN* 4.1 3.4 - - - +
180A PHE* 1.3 86.0 - - + +
182A SER* 1.3 60.9 + - - +
184A LYS* 3.4 3.7 + - - +
185A THR* 2.8 29.8 + - - +
189A ILE* 3.5 36.3 - - + +
192A LEU* 3.9 17.0 - - + -
205A ALA* 3.7 30.3 - - + -
207A TYR* 4.1 26.5 - - + -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASN 3.0 20.0 + - - -
179A ASP 3.9 0.2 - - - -
181A ILE* 1.3 74.9 - - - +
183A GLN* 1.3 61.4 + - - +
185A THR* 3.9 0.9 - - - -
186A HIS* 3.1 3.1 + - - -
187A GLY 2.7 27.6 + - - -
189A ILE 3.3 12.7 + - - -
190A ASN* 2.7 30.5 + - - +
191A ASN 4.4 1.0 + - - -
182B SER* 4.1 1.2 + - - -
187B GLY* 3.7 3.9 - - - -
190B ASN* 3.3 31.9 + - - +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 2.7 43.2 + - - +
180A PHE* 3.8 5.5 - - - +
182A SER* 1.3 77.8 - - - +
184A LYS* 1.3 62.1 + - - +
186A HIS* 3.2 22.9 + - - -
186B HIS 5.0 0.3 - - - +
187B GLY 3.5 21.4 - - - +
188B LYS* 5.9 2.0 - - - -
190B ASN* 3.6 6.5 - - - +
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE 5.4 0.2 + - - -
135A GLY* 4.3 11.9 - - - -
136A ASN 4.8 0.2 - - - +
159A SER 4.9 4.6 + - - -
161A GLU* 2.8 39.8 + - - +
180A PHE* 3.0 33.4 + - + +
181A ILE* 3.4 5.6 + - - +
183A GLN* 1.3 76.2 - - - +
185A THR* 1.3 60.4 + - + +
186A HIS* 3.3 17.1 + - - -
207A TYR* 3.1 27.4 + - + +
209A PHE* 5.4 1.0 - - - -
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE 2.8 21.3 + - - +
182A SER 3.6 2.9 + - - -
184A LYS* 1.3 77.7 - - + +
186A HIS* 1.3 70.5 + - - +
188A LYS* 3.1 22.7 + - - +
189A ILE* 3.0 44.8 + - + +
207A TYR* 3.7 25.6 - - + -
209A PHE* 3.9 27.2 - - + -
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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