Contacts of the helix formed by residues 191 - 200 (chain F) 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 PHE 191 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129F HIS* 4.6 4.7 - - - -
131F ALA* 4.0 12.6 - - + -
180F GLY* 3.4 31.2 - - - -
181F THR 3.6 12.3 - - - -
182F ALA* 3.7 22.4 - - + -
188F MET 3.3 17.0 - - - +
189F TYR 3.1 0.2 - - - -
190F ALA* 1.3 82.3 - - - +
192F LYS* 1.3 63.5 + - - +
194F VAL* 3.6 3.1 + - - +
195F ASN* 3.1 23.9 + - - +
207F PHE* 3.9 15.2 - + + -
209F CYS* 3.4 37.5 - - + -
210F GLY 3.8 1.6 - - - -
214F VAL* 3.9 17.3 - - + -
218F PHE* 4.4 12.3 - + - -
219F VAL* 5.5 0.2 - - + -
222F PHE* 4.0 19.5 - + + -
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Residues in contact with LYS 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F TYR* 3.8 28.8 + - + +
191F PHE* 1.3 73.6 - - - +
193F GLU* 1.3 55.6 + - + +
194F VAL 2.9 5.4 + - - -
195F ASN* 3.0 2.6 + - - -
196F ASP* 2.7 62.6 + - - +
221F GLN* 4.6 19.6 + - - +
222F PHE* 3.3 36.5 - - + -
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Residues in contact with GLU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLU* 3.9 17.8 - - - +
163F ALA* 3.9 13.6 - - + +
164F GLU* 5.5 2.4 - - - +
189F TYR 4.4 10.3 + - - +
190F ALA* 4.3 9.6 + - - +
191F PHE 3.6 0.4 - - - -
192F LYS* 1.3 78.7 - - + +
194F VAL* 1.3 58.6 + - - +
196F ASP* 4.5 6.5 - - + -
197F MET* 3.0 36.0 - - - +
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Residues in contact with VAL 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F HIS* 3.9 18.6 - - + +
161F VAL 5.9 0.2 - - - +
163F ALA* 4.1 22.9 - - + +
166F VAL* 4.4 10.1 - - + -
178F LEU* 3.9 11.2 - - + -
190F ALA 3.4 17.7 - - - +
191F PHE 3.6 7.5 + - - +
192F LYS 2.9 0.8 + - - -
193F GLU* 1.3 78.8 - - - +
195F ASN* 1.3 64.2 + - - +
197F MET* 3.4 6.0 + - + +
198F LEU* 3.2 47.2 + - + +
207F PHE* 3.8 22.9 - - + -
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Residues in contact with ASN 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F PHE 3.1 17.3 + - - +
192F LYS 3.0 3.4 + - - +
194F VAL* 1.3 77.5 - - - +
196F ASP* 1.3 68.4 + - - +
198F LEU 3.3 1.4 + - - -
199F LEU* 3.2 42.8 + - - +
207F PHE* 4.5 8.1 - - + -
222F PHE* 3.3 31.1 - - + +
223F ALA 4.0 4.9 + - - -
224F LEU* 3.1 51.0 - - - +
225F GLY 3.9 1.0 - - - +
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Residues in contact with ASP 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LYS* 2.7 53.1 + - - +
193F GLU* 4.5 4.7 - - + -
195F ASN* 1.3 83.1 - - - +
197F MET* 1.3 55.6 + - - +
198F LEU 3.3 0.9 - - - -
199F LEU* 4.2 7.2 - - - +
200F GLU* 2.9 43.1 + - - +
222F PHE* 5.0 2.3 - - - -
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Residues in contact with MET 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F ALA* 3.1 37.2 - - + +
164F GLU* 4.1 26.5 - - - +
167F LEU* 3.4 34.9 - - + +
193F GLU* 3.0 26.4 + - - +
194F VAL* 3.4 7.5 + - + +
195F ASN 3.2 0.6 - - - -
196F ASP* 1.3 78.3 - - - +
198F LEU* 1.3 59.4 + - + +
199F LEU 3.7 0.2 - - - -
200F GLU* 4.3 6.1 - - - +
201F ASN* 3.3 20.7 - - - +
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F VAL* 5.9 0.2 - - + -
167F LEU* 3.8 18.4 - - + -
170F VAL* 4.4 15.0 - - + -
178F LEU* 3.9 16.6 - - + -
194F VAL* 3.2 39.8 + - + +
195F ASN 3.3 0.2 + - - -
197F MET* 1.3 80.8 - - + +
199F LEU* 1.3 57.1 + - - +
201F ASN* 3.8 4.0 - - - -
202F GLY 3.2 3.6 + - - -
203F ILE* 2.6 76.0 + - + +
205F ILE* 5.8 5.4 - - + +
207F PHE* 5.6 3.1 - - + -
224F LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ASN* 3.2 32.3 + - - +
196F ASP* 4.5 6.7 - - - +
198F LEU* 1.3 75.4 - - - +
200F GLU* 1.3 57.3 + - + +
201F ASN 3.1 8.3 + - - -
202F GLY* 3.2 11.7 + - - -
203F ILE 4.3 8.1 - - - +
204F LYS* 5.4 5.8 - - + -
223F ALA* 4.3 19.5 - - + -
224F LEU* 4.1 22.0 - - + -
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Residues in contact with GLU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F ASP* 2.9 29.6 + - - +
197F MET* 4.4 7.3 - - - +
199F LEU* 1.3 78.2 - - + +
201F ASN* 1.3 60.8 + - - +
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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