Contacts of the helix formed by residues 166 - 181 (chain A) in PDB entry 1I4A
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 ASP 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A TYR* 3.9 27.8 + - + -
165A LEU* 1.3 72.8 - - - +
167A ASP* 1.3 53.9 + - - +
168A ALA* 3.2 11.1 + - - +
169A LEU* 2.8 42.0 + - + +
170A MET* 2.7 36.4 + - - +
203A HIS* 3.7 10.9 + - + -
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Residues in contact with ASP 167 (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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165A LEU* 3.4 19.8 + - + +
166A ASP* 1.3 70.8 + - - +
168A ALA* 1.3 65.8 + - - +
170A MET* 3.2 3.4 + - - +
171A ARG* 2.6 67.5 + - - +
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Residues in contact with ALA 168 (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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166A ASP* 3.2 7.2 + - - +
167A ASP* 1.3 83.1 + - - +
169A LEU* 1.3 63.3 + - - +
171A ARG* 3.2 7.1 + - - +
172A GLN* 3.0 22.7 + - - +
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Residues in contact with LEU 169 (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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166A ASP* 2.8 33.9 + - + +
168A ALA* 1.3 74.1 - - - +
170A MET* 1.3 58.3 + - - +
172A GLN* 3.2 10.2 + - + -
173A ASP* 2.8 53.3 + - - +
199A ARG* 3.7 29.8 - - - +
203A HIS* 3.9 8.7 - - + -
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Residues in contact with MET 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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165A LEU* 4.5 9.0 - - + -
166A ASP 2.7 23.3 + - - +
167A ASP* 3.4 5.6 - - - +
168A ALA 3.2 0.2 - - - -
169A LEU* 1.3 73.3 - - - +
171A ARG* 1.3 94.7 + - + +
173A ASP 3.4 0.2 + - - -
174A ALA* 3.2 18.9 + - - +
203A HIS* 3.4 19.2 - - + +
206A HIS* 3.7 27.6 - - + +
207A VAL* 3.4 27.4 - - + +
210A GLU* 3.6 28.5 - - + +
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Residues in contact with ARG 171 (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 ASP* 2.6 58.9 + - - +
168A ALA* 3.7 6.3 - - - +
170A MET* 1.3 100.8 - - + +
172A GLN* 1.3 61.1 + - - +
174A ALA* 3.5 4.2 + - - +
175A GLN* 3.2 25.6 + - - +
210A GLU* 3.9 28.2 + - - +
213A ARG* 5.5 2.2 - - - +
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Residues in contact with GLN 172 (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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168A ALA 3.0 13.6 + - - +
169A LEU* 3.2 16.1 + - + +
171A ARG* 1.3 75.4 - - - +
173A ASP* 1.3 59.4 + - - +
175A GLN* 3.2 14.7 + - - +
176A ASP* 2.8 62.0 + - - +
179A GLU* 5.0 4.6 + - - -
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Residues in contact with ASP 173 (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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169A LEU* 2.8 22.8 + - - +
170A MET 3.7 5.2 - - - +
172A GLN* 1.3 76.8 - - - +
174A ALA* 1.3 63.2 + - - +
176A ASP* 3.2 8.4 + - - +
177A LEU* 2.9 31.5 + - - +
195A VAL* 3.6 20.0 - - + +
199A ARG* 2.7 38.4 + - - +
203A HIS* 2.7 29.8 + - - -
207A VAL* 3.8 13.7 - - + -
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Residues in contact with ALA 174 (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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170A MET 3.2 6.3 + - - +
171A ARG 3.7 3.6 - - - +
172A GLN 3.3 0.2 - - - -
173A ASP* 1.3 79.4 - - - +
175A GLN* 1.3 58.2 + - - +
177A LEU* 3.3 5.9 + - - +
178A TYR* 2.9 23.9 + - - +
207A VAL* 3.8 13.1 - - - +
210A GLU* 3.3 39.3 - - + -
211A TYR* 3.7 16.8 - - - +
214A ILE* 3.5 13.8 - - + +
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Residues in contact with GLN 175 (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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171A ARG 3.2 13.2 + - - +
172A GLN* 3.5 21.3 - - - +
174A ALA* 1.3 76.6 - - - +
176A ASP* 1.3 55.6 + - - +
178A TYR* 3.0 13.0 + - - -
179A GLU* 2.7 65.2 + - - +
214A ILE* 3.9 25.3 - - + +
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Residues in contact with ASP 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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172A GLN* 2.8 52.3 + - - +
173A ASP* 3.6 12.0 - - - +
175A GLN* 1.3 72.9 - - - +
177A LEU* 1.3 63.0 + - + +
179A GLU* 3.5 9.0 + - - +
180A ALA* 2.9 30.5 + - - +
191A LYS* 4.3 33.6 + - + +
195A VAL* 5.3 3.0 - - + +
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Residues in contact with LEU 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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173A ASP 2.9 24.6 + - - +
174A ALA 3.5 7.6 - - - +
176A ASP* 1.3 79.8 - - + +
178A TYR* 1.3 65.0 + - - +
180A ALA* 3.3 18.2 + - - +
181A GLY 3.6 3.1 + - - -
191A LYS* 4.1 10.8 - - - +
192A PHE* 4.1 25.7 - - + -
195A VAL* 3.3 29.6 - - + -
196A LEU* 4.2 15.7 - - + -
207A VAL* 4.2 20.4 - - + -
208A PHE* 5.3 3.1 - - + -
211A TYR* 3.8 19.0 + - + -
219A ILE* 3.9 20.9 - - + -
226A GLU* 4.6 1.2 - - - +
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Residues in contact with TYR 178 (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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174A ALA 2.9 14.0 + - - +
175A GLN* 3.5 22.4 - - - +
177A LEU* 1.3 76.2 - - - +
179A GLU* 1.3 63.2 + - + +
181A GLY* 2.9 21.0 + - - -
182A GLU* 3.5 43.6 + - + +
211A TYR* 3.5 14.3 + - + -
214A ILE* 3.8 27.1 + - + -
215A ALA* 3.7 33.2 - - + -
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Residues in contact with GLU 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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172A GLN* 5.0 4.7 + - - -
175A GLN* 2.7 49.6 + - - +
176A ASP* 3.9 8.5 + - - +
178A TYR* 1.3 79.4 - - + +
180A ALA* 1.3 61.5 + - - +
182A GLU* 3.0 22.3 + - + +
183A LYS* 3.4 23.0 + - + +
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Residues in contact with ALA 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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176A ASP 2.9 19.3 + - - +
177A LEU 3.3 9.2 - - - +
178A TYR 3.1 0.4 + - - -
179A GLU* 1.3 76.8 - - - +
181A GLY* 1.3 58.1 + - - +
182A GLU 3.3 0.6 + - - -
183A LYS* 4.0 3.4 - - - +
186A GLY 4.0 3.6 - - - +
187A THR* 3.3 9.6 - - - -
188A ASP* 3.1 53.1 + - + +
191A LYS* 4.1 8.3 - - + -
192A PHE* 4.1 13.9 - - + -
226A GLU* 4.4 1.6 - - - -
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Residues in contact with GLY 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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177A LEU 3.6 2.6 + - - -
178A TYR 2.9 9.1 + - - -
180A ALA* 1.3 80.9 - - - +
182A GLU* 1.3 69.9 + - - +
183A LYS 3.6 2.0 - - - +
187A THR* 5.0 2.7 - - - -
226A GLU* 3.2 34.3 + - - +
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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