Contacts of the helix formed by residues 193 - 207 (chain B) in PDB entry 2NXJ
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 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B LEU* 1.3 84.4 - - + +
194B ALA* 1.3 67.4 + - - +
195B GLU* 3.5 28.9 - - + +
196B LEU* 3.1 57.7 + - + +
197B HIS* 3.2 18.2 + - - -
218B GLY 3.7 13.5 - - - +
219B ILE* 4.7 0.2 - - - -
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B TYR* 1.3 73.7 - - - +
195B GLU* 1.3 71.0 + - - +
197B HIS* 3.5 2.6 + - - -
198B ALA* 3.0 23.0 + - - +
218B GLY 4.5 1.8 + - - -
219B ILE* 4.3 11.6 - - + +
220B LEU 5.6 0.4 - - - +
223B ARG* 3.7 40.6 - - + +
226B LEU* 4.1 9.1 - - + +
227B VAL* 3.7 22.4 - - + +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B TYR* 3.2 26.4 + - + +
194B ALA* 1.3 84.9 + - - +
196B LEU* 1.3 58.7 + - - +
198B ALA* 3.4 5.5 + - - +
199B ALA* 3.1 28.4 + - - +
223B ARG* 3.8 24.9 + - - +
226B LEU* 4.1 19.9 - - + +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 4.2 27.1 - - + -
193B TYR* 3.1 47.5 + - + +
195B GLU* 1.3 77.2 - - - +
197B HIS* 1.3 64.8 + - - +
199B ALA* 3.4 8.1 + - + +
200B LEU* 3.0 51.6 + - + +
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Residues in contact with HIS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ALA* 3.4 24.5 - - + -
192B LEU* 3.5 17.2 - - + +
193B TYR 3.2 23.3 + - - -
194B ALA* 3.9 4.5 - - - +
196B LEU* 1.3 77.4 - - - +
198B ALA* 1.3 56.8 + - - +
201B ALA* 2.7 32.7 + - - +
204B TYR* 2.8 35.3 + - + +
216B LEU* 3.6 23.7 - - + +
217B THR 2.8 24.5 + - - -
219B ILE* 3.5 27.0 - - + +
227B VAL* 4.3 7.9 - - + -
230B ALA* 5.1 0.2 - - - -
231B MET* 5.1 0.7 - - - +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ALA 3.0 14.2 + - - +
195B GLU* 3.6 11.9 - - - +
196B LEU 3.3 0.2 - - - -
197B HIS* 1.3 76.7 - - - +
199B ALA* 1.3 60.3 + - - +
200B LEU 3.3 0.9 + - - -
201B ALA* 3.5 11.8 + - - +
202B PRO* 3.9 5.2 - - - +
226B LEU* 4.2 17.9 - - + +
227B VAL* 5.0 1.2 - - - +
230B ALA* 3.5 26.9 - - + +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLU 3.1 16.5 + - - +
196B LEU* 3.4 10.1 + - + +
198B ALA* 1.3 74.8 - - - +
200B LEU* 1.3 63.4 + - + +
202B PRO* 4.2 7.9 - - - +
203B ARG* 3.4 24.7 + - - +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 4.2 9.9 - - + -
175B SER* 5.9 2.5 - - - +
176B LEU* 3.8 23.8 - - + -
192B LEU* 4.4 3.4 - - + -
196B LEU* 3.0 44.7 + - + +
199B ALA* 1.3 85.6 - - + +
201B ALA* 1.3 65.8 + - - +
202B PRO* 3.3 3.1 - - - -
203B ARG* 2.8 39.1 + - - +
204B TYR* 2.9 42.5 + - + +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B HIS 2.7 21.1 + - - +
198B ALA 3.7 6.3 - - - +
200B LEU* 1.3 70.7 - - - +
202B PRO* 1.4 70.0 - - + +
204B TYR* 3.2 27.6 + - - +
205B ARG 3.5 4.7 + - - -
230B ALA* 3.8 25.8 - - + +
231B MET* 3.8 18.4 - - - -
234B ALA* 3.6 4.7 - - + +
236B PHE* 3.5 8.8 - - - -
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Residues in contact with PRO 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ALA 3.9 9.2 - - - +
199B ALA 4.2 11.2 - - - +
200B LEU 3.5 1.6 - - - -
201B ALA* 1.4 91.8 - - + +
203B ARG* 1.3 68.4 + - - +
205B ARG* 3.3 21.9 - - + +
206B GLU* 3.8 10.1 - - - +
230B ALA 5.4 0.7 - - - +
234B ALA* 3.5 19.9 - - + -
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Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 4.2 18.4 - - + +
177B GLU* 4.0 24.2 + - - +
180B LEU* 4.4 7.2 - - + +
199B ALA* 3.4 22.2 + - - +
200B LEU* 2.8 31.6 + - - +
202B PRO* 1.3 83.2 - - - +
204B TYR* 1.3 64.0 + - - +
205B ARG 3.1 1.9 + - - -
206B GLU* 3.4 32.2 + - - +
207B ALA* 3.4 11.8 + - - +
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.6 22.7 - - + -
176B LEU* 3.6 11.7 - - + -
188B LEU* 4.0 20.1 - - + +
190B ALA* 4.2 1.0 - - - +
192B LEU* 3.5 14.9 - - - +
197B HIS* 2.8 48.1 + - + -
200B LEU* 2.9 25.0 + - + +
201B ALA* 3.2 21.7 + - - +
203B ARG* 1.3 76.6 - - - +
205B ARG* 1.3 59.5 + - - +
207B ALA* 3.2 8.5 + - - +
208B LEU* 3.2 28.0 + - + +
214B ALA* 5.2 1.6 - - + -
216B LEU* 3.9 23.8 - - + -
231B MET* 4.0 14.8 - - + -
236B PHE* 3.6 12.1 - - + -
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ALA 3.5 2.2 + - - +
202B PRO* 3.3 22.0 - - + +
203B ARG 3.1 1.4 - - - -
204B TYR* 1.3 74.2 - - - +
206B GLU* 1.3 65.0 + - + +
207B ALA 3.1 4.9 - - - -
208B LEU* 3.2 8.1 + - - +
234B ALA 3.3 20.4 + - - +
235B GLY* 3.6 24.4 + - - -
236B PHE* 3.5 25.1 - - + -
254B ARG* 3.1 68.0 + - + +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.3 22.0 - - + +
184B PRO* 4.9 6.6 - - - +
202B PRO 3.8 14.6 - - - +
203B ARG* 3.4 24.8 + - - +
205B ARG* 1.3 80.5 - - + +
207B ALA* 1.3 57.3 + - - +
208B LEU 4.4 2.6 - - - +
254B ARG* 5.0 4.3 + - - +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 4.0 13.2 - - + -
180B LEU* 3.6 26.9 - - + +
184B PRO* 3.4 7.2 - - - +
185B PHE* 2.7 44.2 + - + -
188B LEU* 4.4 10.5 - - + -
203B ARG 3.4 6.2 + - - +
204B TYR* 3.2 11.8 + - - +
205B ARG 3.1 0.6 - - - -
206B GLU* 1.3 78.6 - - - +
208B LEU* 1.3 53.9 + - - +
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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