Contacts of the helix formed by residues 208 - 222 (chain B) in PDB entry 1NW9
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 THR 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ASP 5.4 1.6 - - - +
207B LEU* 1.3 77.8 - - - +
209B ALA* 1.3 66.2 + - - +
210B LYS* 3.6 6.3 + - - +
211B LYS* 3.1 40.4 + - + +
212B MET* 2.9 18.2 + - - +
252B GLY* 3.8 0.9 - - - -
253B THR* 3.7 13.7 - - - +
254B ASP* 3.4 23.6 - - + +
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Residues in contact with ALA 209 (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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208B THR* 1.3 73.1 - - - +
210B LYS* 1.3 64.6 + - + +
212B MET* 3.1 14.2 + - - +
213B VAL* 3.1 18.3 + - - +
252B GLY* 3.6 5.7 - - - -
254B ASP* 3.3 9.7 + - - +
256B CYS* 3.5 41.1 - - + +
257B PRO 4.4 2.5 - - - +
258B VAL* 3.5 20.3 - - + +
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Residues in contact with LYS 210 (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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208B THR* 3.3 7.2 + - - +
209B ALA* 1.3 81.5 - - + +
211B LYS* 1.3 57.8 + - + +
213B VAL* 3.3 9.7 + - - +
214B LEU* 2.9 36.2 + - + +
254B ASP* 4.7 1.0 + - - -
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Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP 5.8 0.7 - - - +
207B LEU* 3.7 20.4 - - + +
208B THR* 3.1 37.4 + - + +
210B LYS* 1.3 76.6 - - + +
212B MET* 1.3 60.8 + - - +
214B LEU* 3.7 16.6 - - + +
215B ALA* 2.9 29.8 + - - +
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Residues in contact with MET 212 (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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166B ILE* 4.0 15.6 - - + +
168B ASN* 3.8 9.2 - - - +
207B LEU* 3.5 23.6 - - + -
208B THR 2.9 15.4 + - - +
209B ALA* 3.1 10.1 + - - +
211B LYS* 1.3 75.8 - - - +
213B VAL* 1.3 58.8 + - + +
215B ALA* 3.3 2.8 + - - +
216B LEU* 2.9 39.7 + - + +
234B ILE* 3.7 28.5 - - + -
250B VAL* 3.6 27.6 - - + -
251B TYR 3.8 3.1 - - - +
252B GLY* 3.6 29.6 - - - -
258B VAL* 4.4 10.8 - - + -
263B ILE* 5.2 1.1 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ALA 3.1 14.8 + - - +
210B LYS* 3.5 10.1 - - - +
211B LYS 3.3 0.2 - - - -
212B MET* 1.3 77.5 - - - +
214B LEU* 1.3 53.0 + - + +
216B LEU* 3.0 10.4 + - + +
217B LEU* 2.7 58.6 + - + +
258B VAL* 4.2 24.0 - - + -
262B LYS* 4.1 36.1 - - + +
266B ILE* 4.7 7.0 - - + -
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Residues in contact with LEU 214 (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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210B LYS* 2.9 25.2 + - + +
211B LYS* 3.7 19.3 - - + +
212B MET 3.3 0.2 - - - -
213B VAL* 1.3 77.6 - - + +
215B ALA* 1.3 57.4 + - - +
217B LEU* 3.1 18.0 + - + +
218B GLU* 2.8 36.6 + - - +
221B ARG* 4.7 2.9 + - - +
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Residues in contact with ALA 215 (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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164B LEU* 3.8 7.9 - - + +
166B ILE* 4.3 7.9 - - + -
204B LYS* 4.0 27.2 + - + +
207B LEU* 3.9 17.9 - - + -
211B LYS 2.9 19.0 + - - +
212B MET 3.6 4.7 - - - +
214B LEU* 1.3 76.9 - - - +
216B LEU* 1.3 57.8 + - - +
218B GLU* 3.5 9.2 - - - +
219B LEU* 3.1 25.1 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.0 15.0 - - + -
166B ILE* 5.1 5.4 - - + -
212B MET* 2.9 29.4 + - + +
213B VAL* 3.5 9.0 - - + +
215B ALA* 1.3 74.8 - - - +
217B LEU* 1.3 66.5 + - - +
218B GLU 3.2 0.2 - - - -
219B LEU* 3.3 1.6 + - - +
220B ALA* 2.9 24.6 + - - +
232B VAL* 3.8 29.2 - - + -
234B ILE* 4.8 4.7 - - + -
258B VAL* 5.4 1.1 - - + -
263B ILE* 3.7 41.7 - - + -
266B ILE* 3.5 10.8 - - + +
267B PHE* 3.7 25.5 - - + -
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Residues in contact with LEU 217 (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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213B VAL* 2.7 41.8 + - + +
214B LEU* 3.6 18.2 - - + +
216B LEU* 1.3 71.7 - - - +
218B GLU* 1.3 58.5 + - - +
220B ALA* 3.2 2.9 + - + +
221B ARG* 2.8 52.1 + - - +
266B ILE* 3.7 33.2 - - + +
271B SER* 5.5 5.6 - - - +
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Residues in contact with GLU 218 (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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204B LYS* 3.7 22.9 + - - +
214B LEU* 2.8 20.6 + - - +
215B ALA* 3.5 8.1 - - - +
217B LEU* 1.3 76.8 - - - +
219B LEU* 1.3 62.4 + - - +
221B ARG* 3.1 29.0 + - - +
222B GLN* 3.3 25.8 + - + +
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Residues in contact with LEU 219 (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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162B HIS* 3.6 32.3 - - + -
164B LEU* 3.7 33.4 - - + +
215B ALA 3.1 14.2 + - - +
216B LEU* 3.3 5.6 + - - +
218B GLU* 1.3 79.4 - - - +
220B ALA* 1.3 59.8 + - - +
222B GLN* 3.4 16.9 + - - +
224B HIS* 2.8 36.9 + - + -
230B CYS* 3.8 19.1 - - - -
231B VAL 4.4 2.5 - - - +
232B VAL* 3.9 15.9 - - + -
267B PHE* 3.8 10.3 - - + -
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Residues in contact with ALA 220 (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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216B LEU 2.9 16.8 + - - +
217B LEU* 3.2 5.1 + - + +
219B LEU* 1.3 78.0 - - - +
221B ARG* 1.3 59.5 + - - +
222B GLN 3.2 2.1 + - - +
224B HIS* 4.5 0.2 - - - -
266B ILE* 3.5 31.4 - - + +
267B PHE* 4.0 15.9 - - + -
271B SER* 3.6 15.7 - - - +
272B CYS* 3.2 30.9 - - + -
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Residues in contact with ARG 221 (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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214B LEU* 4.7 3.0 + - - +
217B LEU* 2.8 46.1 + - - +
218B GLU* 3.1 19.0 + - - +
220B ALA* 1.3 75.5 - - - +
222B GLN* 1.3 63.4 + - + +
271B SER 4.9 4.0 - - - -
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Residues in contact with GLN 222 (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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162B HIS* 4.3 26.6 + - - +
202B GLU* 5.7 3.4 + - - -
218B GLU* 3.3 23.9 + - + +
219B LEU* 3.6 19.7 - - - +
220B ALA 3.2 5.2 - - - +
221B ARG* 1.3 84.0 - - - +
223B ASP* 1.3 62.6 + - - +
224B HIS* 3.1 23.1 + - + +
272B CYS* 4.6 0.2 - - - -
274B SER* 4.4 5.4 + - - -
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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