Contacts of the helix formed by residues 189 - 201 (chain N) in PDB entry 2I2X
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 TYR 189 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49M PRO* 6.1 6.1 - - + -
50M GLU* 5.8 4.0 - - - -
185N THR 4.9 3.1 - - - +
187N THR* 3.0 3.1 + - - +
188N MET* 1.3 96.1 - - + +
190N ALA* 1.3 57.6 + - - +
191N PHE 3.3 1.1 - - - -
192N LYS* 3.4 36.1 - - + +
193N GLU* 4.4 5.9 + - - +
218N PHE* 3.5 31.2 - + - -
221N GLN* 4.4 10.3 + - - -
222N PHE* 5.1 2.2 - + - -
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Residues in contact with ALA 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N HIS* 5.3 0.2 + - - -
131N ALA* 3.7 4.3 - - + -
132N GLU* 3.5 48.9 - - + +
163N ALA* 4.9 1.4 - - - +
187N THR 3.0 15.1 + - - +
189N TYR* 1.3 76.5 - - - +
191N PHE* 1.3 64.9 + - - +
192N LYS 3.2 1.7 + - - -
193N GLU* 3.7 12.6 + - - +
194N VAL* 3.4 25.0 + - - +
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Residues in contact with PHE 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N HIS* 5.3 2.5 - - - -
131N ALA* 3.9 15.5 - - + -
180N GLY* 3.4 28.7 - - - -
181N THR 3.6 7.9 - - - -
182N ALA* 3.6 31.0 - - + -
188N MET 3.0 18.6 + - - +
190N ALA* 1.3 76.8 - - - +
192N LYS* 1.3 63.2 + - - +
194N VAL* 3.3 8.9 + - - +
195N ASN* 3.1 21.3 + - - +
207N PHE* 3.8 13.8 - + + -
209N CYS* 3.2 43.1 - - + -
210N GLY 4.0 2.7 - - - -
214N VAL* 4.1 17.0 - - + -
218N PHE* 4.9 1.6 - + - -
219N VAL* 5.4 0.9 - - + -
222N PHE* 4.2 24.0 - + + -
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Residues in contact with LYS 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N TYR* 3.4 30.8 + - + +
191N PHE* 1.3 76.8 - - - +
193N GLU* 1.3 56.1 + - + +
195N ASN* 3.0 5.2 + - - +
196N ASP* 2.8 66.9 + - - +
221N GLN* 5.7 8.5 + - - -
222N PHE* 3.5 33.0 - - + -
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Residues in contact with GLU 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N GLU* 2.9 31.5 - - - +
163N ALA* 4.2 13.0 - - + -
164N GLU* 4.9 11.2 - - - +
189N TYR 4.8 3.8 - - - +
190N ALA* 3.7 12.7 + - - +
191N PHE 3.5 0.4 - - - -
192N LYS* 1.3 81.8 - - + +
194N VAL* 1.3 62.4 + - - +
196N ASP* 4.2 8.3 + - - +
197N MET* 3.1 31.7 + - + +
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Residues in contact with VAL 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N HIS* 3.6 23.8 - - + +
161N VAL 6.0 0.2 - - - +
163N ALA* 3.8 23.8 - - + -
166N VAL* 3.9 10.9 - - + +
178N LEU* 3.5 25.1 - - + -
190N ALA 3.4 15.7 + - - +
191N PHE* 3.3 8.7 + - - +
192N LYS 3.2 0.8 - - - -
193N GLU* 1.3 77.2 - - - +
195N ASN* 1.3 57.2 + - - +
197N MET* 4.4 3.1 - - - +
198N LEU* 3.3 26.3 + - - +
207N PHE* 3.4 26.9 - - + -
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Residues in contact with ASN 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191N PHE 3.1 10.1 + - - +
192N LYS 3.0 6.7 + - - +
194N VAL* 1.3 75.3 - - - +
196N ASP* 1.3 66.4 + - - +
197N MET 3.3 0.2 - - - -
198N LEU* 3.5 4.4 + - - +
199N LEU* 3.1 30.4 + - - +
207N PHE* 3.8 15.3 - - + -
222N PHE* 3.4 30.9 - - + +
223N ALA* 4.2 3.8 - - - +
224N LEU* 3.2 51.1 + - - +
225N GLY 3.6 6.5 - - - +
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Residues in contact with ASP 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N LYS* 2.8 56.8 + - - +
193N GLU* 4.0 7.5 + - - +
195N ASN* 1.3 73.9 - - - +
197N MET* 1.3 58.0 + - - +
199N LEU* 3.4 8.4 + - - +
200N GLU* 3.1 40.8 + - - +
222N PHE* 5.7 1.6 - - - -
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Residues in contact with MET 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N ALA* 3.2 44.9 - - + +
164N GLU* 3.5 33.9 - - - +
167N LEU* 3.6 25.2 - - + +
193N GLU* 3.1 16.9 + - - +
194N VAL* 4.5 2.9 - - - +
196N ASP* 1.3 73.6 - - + +
198N LEU* 1.3 61.1 + - - +
199N LEU 3.2 1.3 - - - -
200N GLU* 4.0 5.7 - - + +
201N ASN* 3.1 29.9 + - + +
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Residues in contact with LEU 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166N VAL* 5.5 2.7 - - + -
167N LEU* 4.3 11.9 - - + -
170N VAL* 4.2 18.6 - - + -
178N LEU* 3.8 26.7 - - + -
194N VAL* 3.3 25.7 + - + +
195N ASN* 3.9 5.4 - - - +
196N ASP 3.5 0.2 - - - -
197N MET* 1.3 77.6 - - - +
199N LEU* 1.3 55.7 + - - +
201N ASN* 4.0 1.3 - - - -
202N GLY 3.2 2.8 + - - -
203N ILE* 2.7 76.8 + - + +
205N ILE* 5.2 6.5 - - + -
207N PHE* 5.2 5.4 - - + -
224N LEU* 4.0 21.1 - - + -
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Residues in contact with LEU 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195N ASN* 3.1 34.2 + - - +
196N ASP* 3.6 9.2 - - - +
197N MET 3.2 0.2 - - - -
198N LEU* 1.3 78.3 - - - +
200N GLU* 1.3 59.2 + - + +
201N ASN 3.1 4.3 - - - -
202N GLY* 3.0 19.1 + - - -
203N ILE 4.3 6.3 - - - +
204N LYS* 5.9 1.8 - - + -
223N ALA* 3.7 24.0 - - + -
224N LEU* 4.3 18.4 - - + -
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Residues in contact with GLU 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196N ASP* 3.1 29.4 + - - +
197N MET* 3.8 4.8 + - - +
199N LEU* 1.3 76.2 - - + +
201N ASN* 1.3 57.1 + - - +
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Residues in contact with ASN 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N LEU* 3.8 16.8 - - + +
171N GLN* 3.2 31.4 + - - +
197N MET* 3.1 19.8 + - + +
198N LEU 4.4 2.5 - - - +
199N LEU 3.1 0.4 - - - -
200N GLU* 1.3 77.1 - - - +
202N GLY* 1.3 61.6 + - - +
203N ILE* 3.5 15.9 - - + +
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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