Contacts of the helix formed by residues 189 - 200 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49O PRO* 6.3 2.9 - - + -
185P THR 4.8 4.7 - - - -
186P THR 6.4 0.2 - - - -
187P THR 3.0 2.2 + - - +
188P MET* 1.3 99.9 - - + +
190P ALA* 1.3 60.6 + - - +
191P PHE 3.0 2.7 - - - -
192P LYS* 2.8 54.9 + - + +
193P GLU* 3.0 9.3 + - - +
218P PHE* 3.5 25.9 - + - -
221P GLN* 3.9 16.4 + - - -
222P PHE* 4.5 2.9 - + - -
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Residues in contact with ALA 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P HIS* 6.1 0.2 - - - -
131P ALA* 3.5 21.3 - - + -
132P GLU* 3.6 30.3 - - + +
161P VAL 5.7 0.4 - - - +
163P ALA* 5.4 0.2 - - - +
187P THR 3.2 14.8 + - - +
188P MET 3.2 0.2 - - - -
189P TYR* 1.3 76.9 - - - +
191P PHE* 1.3 56.7 + - - +
193P GLU* 3.5 13.6 + - - +
194P VAL* 3.0 34.9 + - + +
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Residues in contact with PHE 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P HIS* 5.0 2.9 - - - -
131P ALA* 4.0 10.3 - - + -
180P GLY* 3.6 29.4 - - - -
181P THR 3.6 12.8 - - - -
182P ALA* 3.5 28.3 - - + -
188P MET 3.1 16.8 + - - +
190P ALA* 1.3 76.5 - - - +
192P LYS* 1.3 55.2 + - - +
194P VAL 3.2 0.9 + - - -
195P ASN* 2.8 36.0 + - - +
207P PHE* 3.4 24.0 - + + -
209P CYS* 3.6 28.7 - - + -
210P GLY 3.6 2.2 - - - -
214P VAL* 3.6 22.2 - - + -
218P PHE* 4.0 13.2 - + - -
219P VAL* 5.3 0.4 - - + -
222P PHE* 4.0 15.0 - + + -
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Residues in contact with LYS 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P TYR* 2.8 35.3 + - + +
191P PHE* 1.3 79.4 - - - +
193P GLU* 1.3 56.8 + - + +
195P ASN* 3.1 1.4 + - - +
196P ASP* 2.9 61.6 + - - +
222P PHE* 3.1 39.5 - - + -
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Residues in contact with GLU 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P GLU* 2.9 31.3 - - - +
163P ALA* 4.6 13.7 - - + +
164P GLU* 5.5 2.6 - - - +
189P TYR 3.0 8.7 + - - +
190P ALA* 3.5 12.2 - - - +
192P LYS* 1.3 81.0 - - + +
194P VAL* 1.3 57.5 + - - +
196P ASP* 4.5 3.3 - - - +
197P MET* 3.1 31.7 + - - +
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Residues in contact with VAL 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P HIS* 4.0 18.8 - - + +
131P ALA* 6.5 0.2 - - - -
161P VAL 5.4 1.6 - - - +
163P ALA* 4.1 27.4 - - + +
166P VAL* 3.8 13.7 - - + -
178P LEU* 3.8 20.9 - - + -
190P ALA* 3.0 23.5 + - + +
191P PHE 3.2 4.2 + - - +
193P GLU* 1.3 74.3 - - - +
195P ASN* 1.3 63.7 + - - +
197P MET* 4.3 5.1 - - + +
198P LEU* 3.2 28.6 + - + +
207P PHE* 3.7 24.2 - - + -
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Residues in contact with ASN 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191P PHE 2.8 16.9 + - - +
192P LYS* 3.1 5.8 + - - +
194P VAL* 1.3 78.5 - - - +
196P ASP* 1.3 76.0 + - - +
198P LEU* 3.1 16.0 + - - +
199P LEU* 3.2 27.7 + - - +
207P PHE* 4.2 11.0 - - + -
222P PHE* 3.5 25.1 - - + +
223P ALA 3.8 5.9 + - - -
224P LEU* 2.9 48.0 - - - +
225P GLY 4.1 1.2 - - - +
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Residues in contact with ASP 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192P LYS* 2.9 47.2 + - - +
193P GLU* 4.5 3.2 - - - +
195P ASN* 1.3 84.2 - - - +
197P MET* 1.3 63.7 + - - +
199P LEU* 3.1 12.6 + - - +
200P GLU* 3.0 39.9 + - - +
222P PHE* 5.5 1.2 - - - -
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Residues in contact with MET 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P ALA* 3.1 45.8 - - + +
164P GLU* 3.3 25.6 - - - +
167P LEU* 3.3 28.6 - - + +
193P GLU 3.1 17.2 + - - +
194P VAL* 4.3 4.9 - - + +
196P ASP* 1.3 78.5 - - - +
198P LEU* 1.3 62.1 + - + +
200P GLU* 3.7 12.5 + - + +
201P ASN* 3.6 23.1 + - - +
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Residues in contact with LEU 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P VAL* 5.6 0.9 - - + -
167P LEU* 4.3 14.8 - - + +
170P VAL* 4.3 18.8 - - + -
178P LEU* 3.8 28.0 - - + -
194P VAL* 3.2 27.8 + - + +
195P ASN* 3.1 6.6 + - - +
196P ASP 3.1 0.4 - - - -
197P MET* 1.3 77.1 - - + +
199P LEU* 1.3 64.8 + - - +
201P ASN* 3.3 8.0 + - - +
202P GLY 3.6 0.2 + - - -
203P ILE* 3.1 60.5 + - + +
205P ILE* 5.3 4.9 - - + -
207P PHE* 5.1 3.8 - - + -
224P LEU* 3.8 24.7 - - + -
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Residues in contact with LEU 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195P ASN* 3.5 30.3 - - - +
196P ASP* 3.1 13.4 + - - +
198P LEU* 1.3 71.8 - - - +
200P GLU* 1.3 60.6 + - + +
201P ASN 2.9 11.4 + - - -
202P GLY* 2.9 14.7 + - - -
203P ILE 3.9 11.9 - - - +
204P LYS* 5.6 2.2 - - + -
223P ALA* 4.2 18.6 - - + -
224P LEU* 3.8 26.9 - - + -
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Residues in contact with GLU 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196P ASP* 3.0 34.4 + - - +
197P MET* 4.1 8.6 + - + +
198P LEU 3.3 0.8 - - - -
199P LEU* 1.3 75.7 - - + +
201P ASN* 1.3 68.1 + - - +
202P GLY 3.7 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