Contacts of the helix formed by residues 185 - 201 (chain N) in PDB entry 3O3U
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 ASN 185 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165N GLY 3.0 25.7 + - - +
167N TYR* 3.6 19.4 + - - -
182N GLY* 3.5 17.9 + - - -
183N VAL 3.6 0.6 - - - -
184N ASP* 1.3 83.4 + - - +
186N ALA* 1.3 65.2 + - - +
187N GLY 3.2 4.2 + - - -
188N ALA* 2.9 23.6 + - - +
189N LYS* 3.0 22.0 + - - +
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Residues in contact with ALA 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164N ASP* 4.7 1.8 - - - -
185N ASN* 1.3 76.3 - - - +
187N GLY* 1.3 58.5 + - - +
189N LYS* 3.4 10.2 + - - +
190N ALA* 2.9 29.6 + - - +
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Residues in contact with GLY 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N ILE 3.5 9.9 - - - +
164N ASP* 3.2 41.3 + - - +
165N GLY* 3.8 2.6 - - - -
166N GLY 3.9 1.3 - - - -
185N ASN* 3.2 6.8 + - - -
186N ALA* 1.3 76.7 - - - +
188N ALA* 1.3 63.9 + - - +
190N ALA* 3.2 3.5 + - - +
191N GLY 3.1 18.2 + - - -
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Residues in contact with ALA 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N ILE* 3.5 30.8 - - + +
166N GLY* 3.7 3.6 - - - +
182N GLY 3.9 6.1 - - - +
183N VAL* 3.1 31.2 - - - +
185N ASN* 2.9 18.9 + - - +
187N GLY* 1.3 73.4 - - - +
189N LYS* 1.3 63.1 + - - +
191N GLY* 3.3 2.1 + - - -
192N LEU* 3.0 26.2 + - - +
361N LEU* 3.9 3.5 - - + +
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Residues in contact with LYS 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N ASP* 3.2 32.9 + - - +
185N ASN 3.0 17.6 + - - +
186N ALA* 3.7 7.6 - - - +
188N ALA* 1.3 77.6 - - - +
190N ALA* 1.3 56.8 + - - +
193N THR* 2.8 37.3 + - - +
357N VAL* 3.9 2.5 - - + +
358N ASP* 3.4 47.6 + - - +
361N LEU* 3.7 21.1 - - + -
362N ALA* 6.2 1.2 - - - +
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Residues in contact with ALA 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N ASP* 3.6 20.4 - - - +
186N ALA 2.9 18.2 + - - +
187N GLY 3.2 1.8 + - - +
189N LYS* 1.3 76.7 - - - +
191N GLY* 1.3 62.8 + - - +
193N THR* 3.4 5.2 + - - -
194N PHE* 3.0 18.0 + - - +
250N PHE* 3.5 19.5 - - + -
251N LYS* 4.0 12.8 - - + +
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Residues in contact with GLY 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N LEU* 3.7 31.5 - - - +
161N ILE* 4.3 4.7 - - - -
187N GLY 3.1 12.2 + - - -
188N ALA 3.3 2.7 + - - -
190N ALA* 1.3 78.0 - - - +
192N LEU* 1.3 60.6 + - - +
194N PHE* 3.2 5.2 + - - +
195N LEU* 3.1 17.7 + - - +
250N PHE* 3.7 17.0 - - - -
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Residues in contact with LEU 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N ILE* 4.3 15.2 - - + +
188N ALA 3.0 15.9 + - - +
191N GLY* 1.3 76.3 - - - +
193N THR* 1.3 58.0 + - - +
195N LEU* 3.2 26.7 + - + -
196N VAL* 2.9 35.1 + - + +
346N ALA* 4.4 8.5 - - + +
347N VAL* 4.3 24.9 - - + +
350N ALA* 4.0 17.3 - - + -
351N ALA* 6.2 0.2 - - + -
357N VAL* 4.1 18.4 - - + +
360N ALA* 5.2 0.4 - - + -
361N LEU* 3.8 33.7 - - + -
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Residues in contact with THR 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N LYS* 2.8 25.2 + - - +
190N ALA* 3.7 6.7 - - - -
192N LEU* 1.3 77.2 - - - +
194N PHE* 1.3 63.2 + - - +
196N VAL* 3.3 1.7 + - + +
197N ASP* 2.9 40.3 + - - +
357N VAL* 3.6 25.0 - - + +
358N ASP* 5.4 1.0 + - - -
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Residues in contact with PHE 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N TRP* 3.3 44.4 - + + -
130N GLU* 3.8 19.7 - - + -
133N PRO* 4.3 15.9 - - + -
160N LEU* 4.3 11.7 - - + -
190N ALA 3.0 15.0 + - - +
191N GLY* 3.2 8.9 + - - +
193N THR* 1.3 77.6 - - - +
195N LEU* 1.3 62.5 + - - +
197N ASP* 3.3 11.3 + - + +
198N LEU* 3.1 44.7 + - + +
250N PHE* 3.7 23.6 - + + -
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Residues in contact with LEU 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N TRP* 5.4 0.2 - - + -
149N PHE* 4.0 18.4 - - + -
151N LEU* 4.1 5.6 - - + -
157N THR* 3.8 26.5 - - + -
160N LEU* 4.1 18.8 - - + +
161N ILE* 5.8 1.3 - - + -
191N GLY 3.1 11.9 + - - +
192N LEU* 3.2 29.6 + - + +
194N PHE* 1.3 76.9 - - - +
196N VAL* 1.3 63.1 + - + +
198N LEU* 3.1 19.8 + - + +
199N ILE* 3.3 22.0 + - + +
204N MET* 3.5 28.9 - - + -
347N VAL* 4.0 10.5 - - + -
351N ALA* 5.4 1.1 - - + -
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Residues in contact with VAL 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N LEU* 2.9 27.0 + - + +
193N THR* 3.9 3.8 - - - +
195N LEU* 1.3 76.1 - - + +
197N ASP* 1.3 57.8 + - - +
199N ILE* 3.1 10.3 + - + +
200N LYS* 2.8 53.5 + - + +
350N ALA* 3.8 37.2 - - + +
351N ALA* 4.1 8.7 - - + +
353N GLY* 6.3 0.4 - - - -
357N VAL* 3.8 22.7 - - + -
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Residues in contact with ASP 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N THR* 2.9 35.9 + - - +
194N PHE* 3.6 10.5 - - + +
195N LEU 3.2 0.2 - - - -
196N VAL* 1.3 74.6 - - - +
198N LEU* 1.3 66.4 + - - +
200N LYS* 3.7 25.2 + - - +
201N ASN* 2.9 38.1 + - - +
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Residues in contact with LEU 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N TRP* 4.1 19.5 - - + -
132N ILE* 4.8 7.4 - - + -
133N PRO* 3.8 32.8 - - + -
147N LEU* 5.1 2.9 - - + -
194N PHE* 3.1 41.4 + - + +
195N LEU* 3.1 11.6 + - + +
197N ASP* 1.3 76.0 - - - +
199N ILE* 1.3 58.9 + - - +
201N ASN 3.6 0.7 + - - -
202N LYS 3.2 2.4 + - - -
203N HIS* 2.9 49.2 + - + +
204N MET* 3.3 33.2 + - + -
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Residues in contact with ILE 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N LEU* 4.1 19.1 - - + -
195N LEU* 3.3 21.5 + - + +
196N VAL* 3.1 11.1 + - + +
198N LEU* 1.3 76.7 - - - +
200N LYS* 1.3 68.4 + - + +
202N LYS* 2.9 17.5 + - - +
204N MET* 3.4 33.4 - - + +
205N ASN* 4.7 0.2 - - - -
206N ALA* 3.9 15.5 - - + +
351N ALA* 3.5 47.1 - - + +
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Residues in contact with LYS 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196N VAL* 2.8 38.7 + - + +
197N ASP* 3.7 25.9 + - - +
199N ILE* 1.3 73.1 - - + +
201N ASN* 1.3 61.6 + - - +
202N LYS* 3.3 14.7 + - - +
353N GLY* 6.4 1.6 - - - -
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Residues in contact with ASN 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197N ASP* 2.9 28.7 + - - +
200N LYS* 1.3 79.6 + - - +
202N LYS* 1.3 70.1 + - - +
203N HIS* 3.2 35.5 + - + +
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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