Contacts of the helix formed by residues 192 - 211 (chain B) in PDB entry 6UPR
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 SER 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A ARG* 3.4 13.3 - - - +
257A LEU 3.4 25.1 - - - -
258A TYR* 3.7 9.4 - - - -
191B ILE* 1.3 75.4 - - - +
193B LYS* 1.3 61.6 + - - +
194B SER* 4.1 4.6 + - - -
195B GLU* 3.0 37.9 + - - +
196B LEU* 2.8 26.5 + - - +
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Residues in contact with LYS 193 (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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257A LEU 4.9 1.2 + - - -
259A PRO* 5.3 18.0 - - + +
191B ILE 3.9 0.6 + - - -
192B SER* 1.3 75.1 - - - +
194B SER* 1.3 58.3 + - - +
196B LEU* 3.9 10.2 - - - +
197B HIS* 3.1 27.9 + - - +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B SER* 3.2 5.2 + - - -
193B LYS* 1.3 76.3 - - - +
195B GLU* 1.3 65.6 + - - +
197B HIS* 3.4 6.0 + - - +
198B LYS* 3.2 30.9 + - - +
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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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256A ARG* 2.9 35.4 + - - -
1401A GDP 2.3 46.9 + - - +
161B GLY* 5.7 2.4 - - - +
191B ILE* 3.5 15.6 - - + +
192B SER* 3.0 23.7 + - - +
194B SER* 1.3 76.7 - - - +
196B LEU* 1.3 51.9 + - - +
198B LYS* 3.3 6.8 + - - +
199B PHE* 2.7 36.2 + - - +
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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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185B ILE* 3.9 22.4 - - + -
188B ALA* 5.3 4.0 - - + +
191B ILE* 3.4 32.7 - - + +
192B SER 2.8 16.4 + - - +
193B LYS* 3.9 9.4 - - + +
194B SER 3.3 0.2 - - - -
195B GLU* 1.3 77.6 - - - +
197B HIS* 1.3 63.0 + - - +
199B PHE* 4.0 2.0 - - + -
200B LYS* 2.9 42.9 + - + +
238B ALA* 3.7 33.7 - - + -
270B HIS 5.8 3.6 - - - +
271B CYS* 6.4 0.4 - - - -
272B ASP* 5.5 0.2 - - - +
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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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193B LYS 3.1 18.7 + - - +
194B SER* 3.6 7.4 - - - +
195B GLU 3.3 0.2 - - - -
196B LEU* 1.3 79.2 - - - +
198B LYS* 1.3 71.0 + - + +
200B LYS* 3.5 6.9 + - - +
201B ILE* 3.3 51.2 + - + +
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Residues in contact with LYS 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 SER* 3.2 17.7 - - - +
195B GLU* 3.3 6.2 + - - +
197B HIS* 1.3 83.7 - - - +
199B PHE* 1.3 66.1 + - - +
201B ILE* 3.4 10.5 + - + +
202B LYS* 3.1 37.9 + - - +
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Residues in contact with PHE 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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157B ILE* 4.4 3.1 - - + -
158B THR 4.0 13.9 - - - -
159B PRO* 4.1 9.9 - - + -
160B THR* 4.2 1.3 - - - -
161B GLY* 3.5 26.9 - - - +
162B HIS 3.0 37.9 - - - -
163B SER 3.6 14.6 - - - -
185B ILE* 3.9 29.4 - - + -
191B ILE* 4.0 15.7 - - + -
195B GLU 2.7 22.8 + - - +
196B LEU* 3.2 6.7 + - + +
198B LYS* 1.3 70.4 - - - +
200B LYS* 1.3 65.7 + - - +
202B LYS* 3.2 7.5 + - - +
203B ILE* 3.0 54.5 + - + +
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Residues in contact with LYS 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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185B ILE* 3.9 14.4 - - + -
196B LEU* 2.9 43.1 + - + +
197B HIS* 3.8 7.4 - - - +
199B PHE* 1.3 74.6 - - - +
201B ILE* 1.3 64.4 + - + +
203B ILE* 3.3 5.3 + - - +
204B MET* 2.9 29.9 + - + +
233B ALA 6.0 0.9 - - - +
234B HIS* 3.2 28.5 + - - +
235B LEU 4.8 3.1 - - - +
236B PRO* 3.2 28.5 + - + +
238B ALA* 4.1 2.9 - - - -
272B ASP* 2.9 29.1 + - - -
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Residues in contact with ILE 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* 3.3 46.3 + - + +
198B LYS* 3.7 11.2 - - + +
199B PHE 3.2 0.8 - - - -
200B LYS* 1.3 76.1 - - + +
202B LYS* 1.3 62.3 + - + +
204B MET* 3.8 3.4 - - - +
205B GLY* 2.8 29.4 + - - -
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Residues in contact with LYS 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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161B GLY 3.3 16.0 + - - -
162B HIS* 2.6 36.7 + - - +
163B SER* 4.6 9.2 - - - +
198B LYS* 3.1 22.3 + - - +
199B PHE* 3.2 19.7 + - - +
201B ILE* 1.3 77.9 - - + +
203B ILE* 1.3 62.8 + - - +
205B GLY* 3.6 1.4 + - - -
206B GLU* 3.1 29.5 + - - +
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Residues in contact with ILE 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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157B ILE* 3.8 24.9 - - + -
163B SER 4.6 4.5 - - - +
164B LEU* 3.9 20.8 - - + +
185B ILE* 3.8 23.1 - - + -
199B PHE* 3.0 60.3 + - + +
200B LYS 3.7 3.8 - - - +
202B LYS* 1.3 75.2 - - - +
204B MET* 1.3 65.9 + - - +
206B GLU* 3.1 5.2 + - - +
207B LEU* 3.0 32.5 + - + +
236B PRO* 3.7 19.1 - - + -
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Residues in contact with MET 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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183B PRO* 5.2 0.4 - - - -
200B LYS 2.9 18.1 + - - +
201B ILE* 4.0 3.8 - - - +
203B ILE* 1.3 75.3 - - - +
205B GLY* 1.3 63.8 + - - +
207B LEU* 3.1 23.5 + - + +
208B VAL* 3.0 39.0 + - + +
214B ILE* 4.2 23.6 - - + -
216B GLN* 6.2 1.1 - - - +
232B ASN 5.8 2.0 - - - +
235B LEU* 3.4 33.7 - - + +
236B PRO* 3.9 7.0 - - + -
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Residues in contact with GLY 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 ILE 2.8 22.0 + - - -
202B LYS* 4.0 2.7 - - - -
204B MET* 1.3 73.4 - - - +
206B GLU* 1.3 56.5 + - - +
208B VAL* 3.5 7.2 + - - +
209B SER* 3.0 28.6 + - - -
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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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70A GLY* 3.6 7.7 - - - -
71A ALA* 3.0 37.8 + - - +
72A ALA* 4.6 0.7 + - - +
163B SER* 3.2 28.7 - - - -
164B LEU* 3.2 22.1 + - + +
169B LEU* 5.0 0.6 - - - +
202B LYS* 3.1 19.9 + - + +
203B ILE 3.1 6.0 + - - +
205B GLY* 1.3 76.4 - - - +
207B LEU* 1.3 64.7 + - - +
209B SER* 3.5 6.4 + - - +
210B ASN* 2.8 41.8 + - - +
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Residues in contact with LEU 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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157B ILE* 6.0 0.2 - - + -
164B LEU* 3.7 22.0 - - + -
169B LEU* 5.7 0.2 - - + -
172B MET* 3.9 18.8 - - + -
183B PRO* 4.5 11.4 - - + -
203B ILE* 3.0 25.6 + - + +
204B MET* 3.6 28.7 - - + +
206B GLU* 1.3 76.0 - - - +
208B VAL* 1.3 58.0 + - + +
211B GLY* 2.8 9.4 + - - -
212B VAL* 2.8 63.8 + - + +
214B ILE* 4.0 19.1 - - + -
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Residues in contact with VAL 208 (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 MET* 3.0 30.4 + - + +
205B GLY* 3.7 7.0 - - - +
207B LEU* 1.3 76.8 - - + +
209B SER* 1.3 60.2 + - - +
211B GLY* 2.9 20.2 + - - -
212B VAL 5.6 0.7 - - - -
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Residues in contact with SER 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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205B GLY 3.0 16.0 + - - -
206B GLU* 3.3 12.3 + - - +
208B VAL* 1.3 80.3 - - - +
210B ASN* 1.3 66.9 + - - +
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Residues in contact with ASN 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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72A ALA* 3.8 14.8 - - - +
169B LEU* 3.4 46.0 - - + +
173B LYS* 6.0 1.7 - - - +
206B GLU* 2.8 43.4 + - - +
207B LEU 4.3 1.3 - - - +
209B SER* 1.3 85.6 + - - +
211B GLY* 1.3 63.4 + - - +
212B VAL* 3.5 5.7 - - + +
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Residues in contact with GLY 211 (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 ASP* 3.6 5.0 - - - +
207B LEU 2.8 8.8 + - - -
208B VAL* 2.9 12.0 + - - -
209B SER 3.3 0.6 - - - -
210B ASN* 1.3 80.0 - - - +
212B VAL* 1.3 58.3 + - - -
213B GLN* 3.2 26.7 + - - +
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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