Contacts of the helix formed by residues 189 - 200 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49G PRO* 6.2 3.4 - - + -
185H THR 4.8 5.2 - - - -
186H THR 6.1 0.4 - - - -
187H THR* 2.8 5.1 + - - +
188H MET* 1.3 103.7 - - + +
190H ALA* 1.3 54.8 + - - +
191H PHE 3.1 5.4 - - - +
192H LYS* 3.3 46.2 - - + +
193H GLU* 3.6 10.5 - - - +
218H PHE* 3.7 26.7 - + - -
221H GLN* 5.2 7.7 + - - -
222H PHE* 4.9 3.1 - + - -
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Residues in contact with ALA 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H HIS* 5.0 1.1 + - - +
131H ALA* 3.7 6.5 - - + -
132H GLU* 3.5 46.7 - - + +
161H VAL 5.6 0.7 - - - +
163H ALA* 5.7 0.2 - - - +
187H THR* 3.0 13.6 + - - +
189H TYR* 1.3 76.8 - - - +
191H PHE* 1.3 63.2 + - - +
192H LYS 3.3 0.7 - - - -
193H GLU* 3.9 12.2 + - - +
194H VAL* 3.2 30.1 + - + +
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Residues in contact with PHE 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H HIS* 4.8 2.5 - + - -
131H ALA* 4.0 11.9 - - + -
180H GLY* 3.4 39.9 - - - -
181H THR 3.8 2.5 - - - -
182H ALA* 3.9 18.4 - - + -
188H MET 3.1 17.9 + - - +
189H TYR 3.1 0.4 - - - -
190H ALA* 1.3 81.9 - - - +
192H LYS* 1.3 65.3 + - - +
195H ASN* 3.2 23.0 + - - +
207H PHE* 4.1 16.5 - + + -
209H CYS* 3.4 33.7 - - + -
210H GLY 3.7 9.0 - - - -
214H VAL* 3.6 23.1 - - + -
218H PHE* 4.4 6.5 - + - -
219H VAL* 4.5 5.4 - - + -
222H PHE* 4.1 16.8 - + + -
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Residues in contact with LYS 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H TYR* 3.3 35.5 + - + +
191H PHE* 1.3 76.9 - - - +
193H GLU* 1.3 58.8 + - + +
195H ASN* 3.0 5.9 + - - +
196H ASP* 2.8 61.5 + - - +
221H GLN* 5.6 5.1 + - - -
222H PHE* 3.5 30.1 - - + -
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Residues in contact with GLU 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H GLU* 4.2 16.9 - - - +
163H ALA* 4.2 16.1 - - + +
189H TYR 3.6 17.1 + - - +
190H ALA* 3.9 13.9 + - - +
191H PHE 3.6 0.2 - - - -
192H LYS* 1.3 81.5 - - + +
194H VAL* 1.3 57.0 + - - +
196H ASP* 4.4 7.4 - - - +
197H MET* 2.8 40.2 + - + +
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Residues in contact with VAL 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H HIS* 4.1 16.8 - - + +
161H VAL 5.7 0.9 - - - +
163H ALA* 4.1 24.7 - - + +
166H VAL* 3.8 16.2 - - + -
178H LEU* 3.7 29.8 - - + -
190H ALA* 3.2 21.4 + - + +
192H LYS 3.2 0.8 - - - -
193H GLU* 1.3 75.1 - - - +
195H ASN* 1.3 62.6 + - - +
197H MET* 4.0 7.5 - - + +
198H LEU* 3.2 31.0 + - + +
207H PHE* 3.9 16.4 - - + -
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Residues in contact with ASN 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H PHE 3.2 19.0 + - - +
192H LYS 3.0 3.6 + - - +
194H VAL* 1.3 79.2 - - - +
196H ASP* 1.3 69.4 + - - +
198H LEU* 3.4 10.0 + - - +
199H LEU* 3.6 15.6 + - - +
207H PHE* 4.5 12.7 - - + -
222H PHE* 3.7 20.9 - - + +
223H ALA* 3.3 23.6 + - - +
224H LEU* 3.0 48.2 - - - +
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Residues in contact with ASP 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LYS* 2.8 54.7 + - - +
193H GLU* 4.1 5.8 + - - +
195H ASN* 1.3 77.6 - - - +
197H MET* 1.3 57.3 + - - +
198H LEU 3.1 5.9 + - - -
199H LEU* 3.3 4.4 + - - +
200H GLU* 3.1 43.7 + - - +
222H PHE* 5.3 2.3 - - - -
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Residues in contact with MET 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H ALA* 3.3 40.8 - - + +
164H GLU* 4.0 27.4 - - - +
167H LEU* 3.6 35.8 - - + +
193H GLU* 2.8 27.5 + - + +
194H VAL* 4.0 11.4 - - + +
196H ASP* 1.3 71.4 - - - +
198H LEU* 1.3 57.7 + - + +
200H GLU* 3.6 16.5 - - + +
201H ASN* 3.6 17.9 - - - +
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Residues in contact with LEU 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H VAL* 5.2 0.9 - - + -
167H LEU* 3.8 31.9 - - + +
170H VAL* 4.5 14.4 - - + -
178H LEU* 3.7 30.5 - - + -
194H VAL* 3.2 25.6 + - + +
195H ASN* 3.8 6.1 - - - +
196H ASP 3.1 1.4 - - - -
197H MET* 1.3 81.0 - - + +
199H LEU* 1.3 60.1 + - - +
200H GLU 3.6 0.2 - - - -
201H ASN* 3.6 4.9 - - - +
202H GLY 3.2 4.9 + - - -
203H ILE* 2.9 54.5 + - + +
205H ILE* 5.4 3.8 - - + +
207H PHE* 5.8 2.2 - - + -
224H LEU* 4.7 15.0 - - + -
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Residues in contact with LEU 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H ASN* 3.6 12.9 + - - +
196H ASP* 3.3 6.5 + - - +
198H LEU* 1.3 76.1 - - - +
200H GLU* 1.3 58.5 + - + +
201H ASN 2.8 9.5 + - - -
202H GLY* 3.1 13.7 + - - +
203H ILE 3.5 26.0 - - - +
204H LYS* 4.6 14.8 - - + -
223H ALA* 4.0 26.0 - - + -
224H LEU* 4.4 14.8 - - + -
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Residues in contact with GLU 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H ASP* 3.1 36.2 + - - +
197H MET* 3.6 12.8 + - + +
199H LEU* 1.3 72.8 - - - +
201H ASN* 1.3 67.3 + - - +
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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